@article {pmid41354528,
year = {2025},
author = {Ebmer, D and Czerny, J and Unterköfler, MS and Karbe, M and Gruber, R and Stimac, I and Fuehrer, HP and Joachim, A and Pikalo, J},
title = {Reports of Microthoracius mazzai (Phthiraptera: Anoplura) infestations in alpaca (Vicugna pacos) herds from Austria and Germany.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {66},
number = {},
pages = {101371},
doi = {10.1016/j.vprsr.2025.101371},
pmid = {41354528},
issn = {2405-9390},
mesh = {Animals ; Austria/epidemiology ; Germany/epidemiology ; *Lice Infestations/veterinary/parasitology/epidemiology ; *Anoplura/genetics/classification/anatomy & histology ; Male ; Female ; *Camelids, New World/parasitology ; *Camelidae/parasitology ; Electron Transport Complex IV/genetics ; Phylogeny ; },
abstract = {Sucking lice (Phthiraptera: Anoplura) constitute obligate and permanent insect ectoparasites of mammals and exhibit a hematophagous lifestyle. In South American camelids, three species of the genus Microthoracius have been described, however, reports outside South America are scarce. Here we describe infestations with Microthoracius mazzai in three alpaca (Vicugna pacos) herds from Austria (Styria and Salzburg), and Germany (Bavaria). Overall, lice infestations were detected in eight animals. Four of them exhibited a massive generalized infestation. Lice specimens were identified as M. mazzai using morphological keys. First molecular characterization of M. mazzai, including DNA barcodes based on mitochondrial cytochrome oxidase subunit 1 gene, is provided. Although rarely reported outside South America, lice of the genus Microthoracius should be considered as the cause for pruritus and dermatitis in South American camelids worldwide.},
}

Animals
Austria/epidemiology
Germany/epidemiology
*Lice Infestations/veterinary/parasitology/epidemiology
*Anoplura/genetics/classification/anatomy & histology
Male
Female
*Camelids, New World/parasitology
*Camelidae/parasitology
Electron Transport Complex IV/genetics
Phylogeny

@article {pmid41354072,
year = {2025},
author = {Shneyer, VS and Rodionov, AV},
title = {20 Years of DNA Barcoding - Achievements and Problems.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {11},
pages = {1602-1619},
doi = {10.1134/S0006297925602977},
pmid = {41354072},
issn = {1608-3040},
mesh = {*DNA Barcoding, Taxonomic/methods/history ; Animals ; High-Throughput Nucleotide Sequencing ; *DNA/genetics ; },
abstract = {Over 20 years of extensive studies on DNA barcoding of various types of multicellular organisms have resulted in the selection of specific markers for multiple taxonomic groups, development of primers for many selected markers, establishment of DNA barcodes for more than 400 thousand species, and creation of the BOLD database. Next-generation sequencing methods allow DNA barcodes to be obtained immediately for many samples, including those stored in museum collections. DNA barcode analysis has revealed many previously unknown and undescribed species in various animal groups. DNA barcoding has been successfully used in many practical applications. However, certain problems and controversial issues remain, primarily, regarding description of new species based on DNA barcodes and the accuracy of sample identification using reference libraries.},
}

*DNA Barcoding, Taxonomic/methods/history
Animals
High-Throughput Nucleotide Sequencing
*DNA/genetics

@article {pmid41351823,
year = {2025},
author = {Howard-Stone, R and Măndoiu, II},
title = {MHASS: Microbiome HiFi Amplicon Sequencing Simulator.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf656},
pmid = {41351823},
issn = {1367-4811},
abstract = {SUMMARY: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies, and empirically derived pass-number distributions from actual sequencing runs. MHASS generates datasets tailored for rigorous benchmarking and validation of long-read microbiome analysis workflows, including ASV clustering and taxonomic assignment.

Implemented in Python with automated dependency management, the source code for MHASS is freely available at https://github.com/rhowardstone/MHASS along with installation instructions. Our code is also published on Zenodo at https://doi.org/10.5281/zenodo.17486364.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41351680,
year = {2025},
author = {Fang, XY and Lin, S and Zhong, XP and Zhang, XL and Zhang, YT and Chen, JM and Zhou, KL},
title = {Morphological and Molecular Analyses of Cladonema cf. Californicum (Hydrozoa: Anthoathecata) from China.},
journal = {Zoological science},
volume = {42},
number = {6},
pages = {596-604},
doi = {10.2108/zs240009},
pmid = {41351680},
issn = {0289-0003},
mesh = {Animals ; China ; Phylogeny ; *Hydrozoa/genetics/anatomy & histology/classification ; Electron Transport Complex IV/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, hydrozoan medusae collected from a home aquarium in Sanming, China, were tentatively identified as Cladonema cf. californicum Hyman, 1947, based on DNA barcoding. Morphologically, these specimens differed from known Cladonema medusae, including C. californicum, by possessing a manubrium with protuberances and tentacles with one to three (typically two) adhesive branches, along with three to six (usually four) stinging branches emerging laterally from the main tentacle shaft. These morphological distinctions were supported by molecular phylogenetic analyses using the mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) gene sequences. Nonetheless, COI sequences revealed that C. cf. californicum clustered with juvenile Cladonema californicum medusae from California, USA, with a minimal genetic distance of 0.008, indicating potential conspecificity. Given the morphological similarities among juvenile Cladonema medusae, the Californian specimens may have been misidentified. Further investigations focusing on the polyp stage and geographic distribution are necessary to fully resolve the taxonomic status of these medusae and clarify their relationship with C. californicum.},
}

Animals
China
Phylogeny
*Hydrozoa/genetics/anatomy & histology/classification
Electron Transport Complex IV/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid41351674,
year = {2025},
author = {Hikosaka, A and Nishimoto, A and Takeda, N and Hikosaka-Katayama, T},
title = {Occurrence of 12 Acoela Species in the Seto Inland Sea.},
journal = {Zoological science},
volume = {42},
number = {6},
pages = {540-555},
doi = {10.2108/zs240106},
pmid = {41351674},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; Japan ; RNA, Ribosomal, 18S/genetics ; Oceans and Seas ; Electron Transport Complex IV/genetics ; *Animal Distribution ; Species Specificity ; },
abstract = {The Acoela is a notable taxon in terms of the early evolution of bilaterians and the photosynthetic symbiosis between animals and microalgae. There are approximately 416 described species of Acoela worldwide, which are classified into 16 families. In total, 21 species have been reported in Japan, of which five have been reported in the Seto Inland Sea. We surveyed acoels in the intertidal zone of beaches along the Seto Inland Sea coast of Hiroshima Prefecture and collected specimens. A comparison of mitochondrial cytochrome oxidase subunit I (COI) sequences and molecular phylogenetic analysis suggested that they could be divided into 12 species. Molecular phylogenetic analysis using 18S rRNA sequences suggested that these species belonged to five families: Convolutidae, Otocelididae, Dakuidae, Actinoposthiidae, and Isodiametridae. There have been no previous reports of Dakuidae or Actinoposthiidae in Japan and no reports of Isodiametridae in the Seto Inland Sea. These results suggested that the diversity of Acoela in Japan and the Seto Inland Sea is far richer than is currently known.},
}

Animals
Phylogeny
Japan
RNA, Ribosomal, 18S/genetics
Oceans and Seas
Electron Transport Complex IV/genetics
*Animal Distribution
Species Specificity

@article {pmid41351070,
year = {2025},
author = {Allsopp, RC and Page, K and Wren, E and Nteliopoulos, G and Gleason, KLT and Lall, GM and Bhagani, S and Acheampong, E and Wadsley, MK and Coombes, RC and Shaw, JA},
title = {Concurrent genomic assessment of circulating tumour cells and ctDNA to guide therapy in metastatic breast cancer.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {1858},
pmid = {41351070},
issn = {1471-2407},
mesh = {Humans ; *Neoplastic Cells, Circulating/pathology/metabolism ; *Breast Neoplasms/genetics/pathology/blood/therapy/drug therapy ; Female ; *Circulating Tumor DNA/genetics/blood ; Middle Aged ; *Biomarkers, Tumor/genetics/blood ; Genomics/methods ; Mutation ; DNA Copy Number Variations ; Neoplasm Metastasis ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; Precision Medicine ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Molecular analysis of actionable driver mutations and somatic copy number alterations (sCNAs) in circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) is increasingly being used to guide personalised medicine in patients with cancer. In previous CTC studies, high numbers of CTCs were needed for successful recovery of individual CTCs for molecular analysis at a time when patients typically have very short survival, limiting clinical applicability. Here, by performing longitudinal analyses of ctDNA and CTCs across a broad range of CTC counts, we hypothesized that CTCs could reveal synergistic and additional genomic information to ctDNA at points when therapeutic interventions could be considered in the follow up of patients with metastatic breast cancer (MBC).

METHODS: Eight patients underwent serial blood sampling. CTCs were captured via CellSearch-DEPArray from 7.5 mL (CellSave tubes), while 15 mL (EDTA tubes) was used for cfDNA extraction. A total of 58 cfDNA samples and 192 CTCs from the 8 patients were compared by shallow whole genome sequencing sWGS and targeted next generation sequencing using custom designed mutation panels (cfDNA; dual barcoding Ion AmpliSeq HD technology (556 hotspots across 24 genes) and CTCs; SingleSeq-compatible AmpliSeq technology across 539 of the 556 (97%) hotspots).

RESULTS: The majority of patient samples showed complementary genomic information in CTCs and ctDNA from the same blood sample. However, genome changes were detected in CTCs from some blood samples that were ctDNA negative despite progression providing actionable information at times when ctDNA analysis was not informative. Across the CTCs and ctDNA, common regions of loss included chromosome 13q14 containing the RB1 gene, detected in 3 of 4 patients receiving CDK4/6 inhibitors and amplification of 17q12 containing the ERBB2 gene in 2 of the 7 patients with HER2 negative metastatic disease, suggesting evolution to HER2 positive disease.

CONCLUSIONS: Our study shows that CTCs provide key information that would have been missed by ctDNA monitoring alone and extends CTC and cfDNA genomic profiling to patients with a broad range of CTC counts for blood-based monitoring of HER2 status and other clinically actionable targets for informing treatment decisions in metastatic disease.},
}

Humans
*Neoplastic Cells, Circulating/pathology/metabolism
*Breast Neoplasms/genetics/pathology/blood/therapy/drug therapy
Female
*Circulating Tumor DNA/genetics/blood
Middle Aged
*Biomarkers, Tumor/genetics/blood
Genomics/methods
Mutation
DNA Copy Number Variations
Neoplasm Metastasis
High-Throughput Nucleotide Sequencing
Adult
Aged
Precision Medicine
Whole Genome Sequencing

@article {pmid41347007,
year = {2025},
author = {Réblová, M and Nekvindová, J and Bauchová, L and Hernández-Restrepo, M},
title = {Pleurophragmium parvisporum (Ascomycota): One name, seven stories - a case highlighting the need for verification of strains from public culture collections.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e173033},
pmid = {41347007},
issn = {2210-6340},
abstract = {Public repositories of living fungal strains provide essential reference points and support diverse scientific outcomes. Current best practices for preserving fungal strains emphasise the generation of DNA barcodes and the management of comprehensive metadata. However, challenges arise when type material or authentic reference strains are lacking, as this prevents direct comparison of DNA barcodes and forces identifications to rely solely on morphology. This problem is particularly pronounced for strains deposited during the pre-molecular era, especially those belonging to species with simple or convergent morphologies. In this study, we re-examined seven strains deposited in a public culture collection under the name Pleurophragmium parvisporum, including synonymous designations. Our approach combined cultivation experiments, comparative morphological analyses, multi-locus phylogenetic reconstruction of six nuclear markers, and biogeographic assessments. Our analyses revealed that these strains are scattered across four distinct families or orders in three classes. Two strains belong to Thysanorea (Chaetothyriales, Eurotiomycetes): T. acropleurogena sp. nov. and a sterile strain identified as the already known T. melanica. Two other strains were resolved within Wongia (Papulosaceae incertae sedis, Sordariomycetes) and introduced as W. pallidopolaris sp. nov. and W. rhachidophora sp. nov. Finally, two strains represent novel taxa within the Tubeufiales (Dothideomycetes), described here as Zaanenomyces hilifer sp. nov. and Skoliomycella flava gen. et sp. nov. Of the seven examined strains, only one conformed to the species concept of P. parvisporum and is here regarded as its reference strain. The phylogenetic analyses resolved P. parvisporum within Neomyrmecridium (Myrmecridiales, Sordariomycetes). Consequently, Neomyrmecridium was reduced to synonymy of Pleurophragmium, leading to the proposal of 11 new combinations (P. asiaticum comb. nov., P. asymmetricum comb. nov., P. fusiforme comb. nov., P. gaoligongense comb. nov., P. guizhouense comb. nov., P. luguense comb. nov., P. naviculare comb. nov., P. pteridophytophilum comb. nov., P. septatum comb. nov., P. sichuanense comb. nov., and P. sorbicola comb. nov.), and two new names (P. fluviale nom. nov. and P. jiulongheense nom. nov.). In addition, three species formerly placed in Uncispora are transferred to Thysanorea, with new combinations proposed based on congruent morphology and multi-locus phylogenetic evidence: T. hainanensis comb. nov., T. sinensis comb. nov., and T. wuzhishanensis comb. nov. This study refines the generic limits of Pleurophragmium and morphologically similar genera and reveals several previously unrecognised lineages. It highlights how misinterpretation of subtle morphological features may lead to strains being misidentified and deposited under incorrect names in public collections, where they risk perpetuating taxonomic errors.},
}

@article {pmid41345699,
year = {2025},
author = {Yilmaz, A and Kasap, OE},
title = {Prevalence of Wolbachia in natural sand fly (diptera: psychodidae) populations from Türkiye and its potential role in mitochondrial divergence.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07157-4},
pmid = {41345699},
issn = {1756-3305},
support = {2211-A National PhD Scholarship Program//TÜBİTAK/ ; 101057690//European Commission/ ; 10038150 and 10038150//UK Research and Innovation/ ; TBAG 105T205 and SBAG 114S999//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; 09D01601002 and 01001601001//Hacettepe University Scientific Research Unit/ ; W911QY-16-C-0160//AFHSB-GEIS/ ; },
abstract = {BACKGROUND: Phlebotomine sand flies are vectors of various pathogens, most notably Leishmania spp. Symbiotic bacteria have recently gained considerable attention owing to their effects on hosts and on other organisms co-infecting the same host. In this study, we investigated the natural Wolbachia infection status of sand fly taxa distributed in Türkiye and examined its potential role in driving the deep mitochondrial divergence observed within certain taxa.

METHODS: We analysed 858 sand fly specimens, mostly collected between 2005 and 2016, with additional samples obtained in 2023. Specimens were morphologically identified, and the mitochondrial cox1 gene was sequenced for DNA barcoding. For selected taxa showing marked mitochondrial divergence, species delimitation methods were applied, and genetic diversity indices and neutrality tests were calculated. Wolbachia infection was detected via PCR amplification of the wsp gene, and strain diversity was characterised using multilocus sequence typing (MLST) of five housekeeping genes. Logistic regression was used to evaluate associations between infection status and mitochondrial lineage, sex or collection period.

RESULTS: Wolbachia infection was detected in 16.67% of specimens, occurring exclusively in Phlebotomus papatasi, Ph. major s.l., Ph. tobbi, Ph. economidesi and Sergentomyia minuta. Analyses of wsp and MLST data identified all sequences as belonging to Supergroup A, with multiple strains present within and across host taxa. Infection among the five Ph. major s.l. lineages delineated by species delimitation was significantly associated with lineage, with lineages 3-5 showing a higher probability of infection. The reduced haplotype and nucleotide diversity, along with a significant negative deviation from neutrality observed in lineage 5, suggest a selective sweep likely driven by Wolbachia infection.

CONCLUSIONS: This study represents the first comprehensive screening of Wolbachia infection in sand fly taxa distributed across Türkiye, during which several novel Wolbachia strains were identified. Our findings suggest a potential role of Wolbachia infection in driving lineage differentiation within certain sand fly taxa. However, further detailed investigations are required to elucidate the mechanisms by which Wolbachia influences sand fly diversification and to assess the broader epidemiological implications related to sand fly-borne diseases (SFBDs).},
}

@article {pmid41341958,
year = {2025},
author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M},
title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1701570},
pmid = {41341958},
issn = {2235-2988},
mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; },
abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.},
}

*Nanopore Sequencing/methods/veterinary
Animals
*Veterinary Medicine/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Nanopores
Genomics/methods

@article {pmid41340599,
year = {2025},
author = {Hébert, C and Favret, C},
title = {Large-Scale Integrative Taxonomy of the Smallest Insects Reveals Astonishing Temperate Diversity (Hymenoptera: Chalcidoidea: Mymaridae).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70197},
doi = {10.1111/mec.70197},
pmid = {41340599},
issn = {1365-294X},
support = {RGPIN-2024-05502//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche du Québec-Nature et technologies/ ; },
abstract = {Fairyflies (Hymenoptera: Chalcidoidea: Mymaridae) are a diverse but taxonomically understudied group of parasitoid wasps that attack the eggs of other insects. Being among the very smallest of all insects, they are often ignored in biodiversity surveys despite being one of the most abundant microhymenoptera in many habitats. The traditional approach of morphological species delimitation can be challenging due to their minute size and meticulous slide-mounting technique. Ways to accelerate their discovery are needed. We conducted the first large-scale study of Mymaridae in temperate forests, combining DNA megabarcoding and the large-scale integrative taxonomy (LIT) workflow to describe their diversity. We obtained COI barcodes from 2098 specimens and used ASAP and RESL for species delimitation. Between 42 and 114 molecular clusters were delimited. Reducing morphological validation to only 9% of the sample enabled accurate delimitation while limiting time and effort. We confirmed the presence of 55 species, including many potentially new to science. The LIT workflow was effective for Mymaridae, although cryptic diversity remains unresolved in some large clusters, especially in the genera Alaptus and Anagrus, where high haplotype diversity and morphological ambiguity suggest additional hidden species. DNA reference databases proved unreliable, with less than 1% correct species matches, highlighting the taxonomic gap for this group. Nonetheless, we contributed 16 new identified reference barcodes to public databases and added new provincial and national species records for Canada. Our results demonstrate the value of combining molecular and morphological data in a standardised workflow and underscore the importance of improving reference databases for effective biodiversity assessments of dark taxa like microhymenoptera.},
}

@article {pmid41339720,
year = {2025},
author = {Alsulami, F and Jhanjhi, NZ},
title = {Deep learning framework for barcode localization and decoding using simulated UAV imagery.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29720-w},
pmid = {41339720},
issn = {2045-2322},
abstract = {Automated warehouse stock tracking is becoming increasingly important for improving logistics and reducing manual errors. Unmanned Aerial Vehicles (UAVs) offer a promising solution by enabling automated barcode scanning from above. However, challenges such as poor lighting, shadows, and partial occlusions still limit the reliability of real-time barcode detection and decoding. This research presents a deep learning framework evaluated on simulated UAV imagery for barcode inventory management. The proposed system uses the YOLOv8 object detection model to accurately localize both 1D and 2D barcodes in images captured from a UAV perspective. With a mean Average Precision (mAP) of 92.4%, the model demonstrates strong performance even in complex warehouse conditions. Once localized, the barcode regions are decoded using OpenCV's barcode module. The extracted data, including product ID and quantity, is then automatically updated into a MySQL database to simulate real-time stock updates. Although tested using simulated aerial imagery, the system is designed to be drone-ready with minimal adjustments. This modular approach shows potential for real-world UAV deployment and contributes to reducing human effort and errors in inventory tracking.},
}

@article {pmid41339471,
year = {2025},
author = {Priyadarshini, A and Mahalakshmi, K and Venkatesan, NK and Dhanalakshmi, M},
title = {Whole genome sequencing of a hypermucoviscous, multidrug-resistant Klebsiella pneumoniae subsp. pneumoniae K219 isolated from human sputum.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30811-x},
pmid = {41339471},
issn = {2045-2322},
abstract = {Multidrug-resistant (MDR) strains of Klebsiella pneumoniae pose a significant public health threat due to their ability to evade commonly used antibiotics, restricting therapeutic options and increasing mortality rates especially among immunocompromised individuals. This study aimed to sequence the genome of MDR K. pneumoniae subsp. pneumoniae K219 isolate procured from a tertiary care hospital, Chennai which was isolated from a human sputum sample. Sequencing was performed using third-generation Oxford Nanopore Technologies (MinION platform, FLO-MIN106 flow cell, R9.4.1 pore type) with the EXP-NBD114 barcoding kit and SQK-LSK109 sequencing kit. The genome was analysed using a suite of bioinformatics tools to identify virulence factors, resistance genes, mobile elements, and clustered regularly interspaced short palindromic repeats (CRISPR). The assembled genome of K. pneumoniae K219 comprises a single circular chromosome and four plasmids, with a total genome size of 5,038,803 base pairs. The plasmids measured 229,745; 134,193; 33,455; and 183,631 base pairs, respectively. One CRISPR array was identified. Genomic characterization of K. pneumoniae K219, including its four plasmids and a CRISPR array, offers valuable insights into the genetic architecture of this MDR strain. The data enhance our understanding of its resistance mechanisms, virulence determinants, and interaction with mobile genetic elements. These findings can guide targeted treatment strategies and infection control measures in clinical settings.},
}

@article {pmid41338874,
year = {2025},
author = {Villegas, NK and Tran, MH and Keller, A and Plesa, C},
title = {BAR-CAT: Targeted Recovery of Synthetic Genes via Barcode-Directed CRISPR-dCas9 Enrichment.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1177/25731599251401526},
pmid = {41338874},
issn = {2573-1602},
abstract = {Modern gene synthesis platforms enable investigations of protein function and genome biology at an unprecedented scale. Yet, the proportion of error-free constructs in diverse gene libraries decreases with length due to the propagation of oligo synthesis errors. To rescue these error-free constructs, we developed Barcode-Assisted Retrieval CRISPR-Activated Targeting (BAR-CAT), an in vitro method that uses multiplexed dCas9-single-guide RNA (sgRNA) complexes to extract barcodes corresponding to error-free constructs. After a 15-min incubation and wash regimen, three low-bundance targets in a 300,000-member test library were enriched 600-fold, greatly reducing downstream requirements. When applied to a 384-gene DropSynth gene library, BAR-CAT enriched 12 targets up to 122-fold and revealed practical limits imposed by sgRNA competition and library complexity, which now guide ongoing protocol scaling. By eliminating laborious clone-by-clone validation and working directly on plasmid libraries, BAR-CAT provides a platform for recovering perfect synthetic genes, subsetting large libraries, and ultimately lowering the cost of functional genomics at scale.},
}

@article {pmid41337486,
year = {2025},
author = {Jang, J and Ko, KP and Zhang, J and Jun, S and Park, JI},
title = {Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {49},
pages = {e2509534122},
doi = {10.1073/pnas.2509534122},
pmid = {41337486},
issn = {1091-6490},
support = {CA286761//HHS | NIH | National Cancer Institute (NCI)/ ; CA193297//HHS | NIH | National Cancer Institute (NCI)/ ; CA278971//HHS | NIH | National Cancer Institute (NCI)/ ; CA279867//HHS | NIH | National Cancer Institute (NCI)/ ; CA256207//HHS | NIH | National Cancer Institute (NCI)/ ; CA278967//HHS | NIH | National Cancer Institute (NCI)/ ; P30 CA016672/CA/NCI NIH HHS/United States ; RP180672//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200504//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; CA125123//HHS | National Institutes of Health (NIH)/ ; RR024574//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Esophageal Neoplasms/genetics/pathology/metabolism ; Mice ; Single-Cell Analysis/methods ; *Precancerous Conditions/genetics/pathology/metabolism ; *Transcriptome ; Humans ; Esophagus/pathology/metabolism ; Tumor Suppressor Protein p53/genetics/metabolism ; Cell Lineage ; Receptor, Notch1/genetics ; },
abstract = {Although histologically normal, esophageal preneoplastic cells harbor early genetic alterations and likely exhibit lineage plasticity. However, their origins and trajectories remain unclear. To address this, we combined genetic barcoding with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells. We identified a distinct progenitor-like cell population with high plasticity. Through a scoring system, these high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. This approach uncovers molecular markers, including Nfib and Qk, that define these precursor cells, validated by spatial transcriptomics and a Trp53 Cdkn2a Notch1 mouse model. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early detection and therapeutic targets of esophageal squamous cell cancer. By elucidating the cellular dynamics underlying esophageal preneoplasia, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches.},
}

Animals
*Esophageal Neoplasms/genetics/pathology/metabolism
Mice
Single-Cell Analysis/methods
*Precancerous Conditions/genetics/pathology/metabolism
*Transcriptome
Humans
Esophagus/pathology/metabolism
Tumor Suppressor Protein p53/genetics/metabolism
Cell Lineage
Receptor, Notch1/genetics

@article {pmid41335224,
year = {2026},
author = {Bronnec, P and Dalmon, S and Briand, C and Allatif, O and Broly, M and Marcotte, M and Lombardi, G and Barthes, K and Martel, N and Hughes, S and Gillet, B and Milhavet, F and Atilgan, A and Bachelez, H and Palmeri, S and Prigione, I and Madrange, M and Savey, L and Moutschen, M and Jeru, I and El Moussaoui, M and Belot, A and Sbidian, E and Carbone, A and Jamilloux, Y and Gattorno, M and Smahi, A and Georgin-Lavialle, S and Boursier, G and Magnotti, F and Henry, T},
title = {SpeckSeq enables high-throughput functional stratification of MEFV variants in autoinflammatory diseases.},
journal = {The Journal of experimental medicine},
volume = {223},
number = {2},
pages = {},
doi = {10.1084/jem.20251065},
pmid = {41335224},
issn = {1540-9538},
support = {779295//Agence Nationale pour la Recherche/ ; ANR-21-CE17-0046//Agence Nationale pour la Recherche/ ; EQU202103012640//Fondation pour la Recherche Médicale/ ; },
mesh = {*Pyrin/genetics/chemistry ; Humans ; *Familial Mediterranean Fever/genetics ; High-Throughput Nucleotide Sequencing/methods ; Mutation/genetics ; *Hereditary Autoinflammatory Diseases/genetics ; Inflammasomes/metabolism ; },
abstract = {Variants of uncertain significance (VUS) are a major obstacle in genetic diagnosis, particularly when involving gain-of-function (GoF) mutations that are poorly predicted in silico. MEFV, which encodes the inflammasome sensor pyrin, is mutated in two autoinflammatory diseases, familial Mediterranean fever (FMF) and pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Here, we developed SpeckSeq, a method that combines DNA bar-coding, ASC speck-based single-cell sorting and next-generation sequencing to systematically identify hypermorphic MEFV variants in response to different stimuli. SpeckSeq identified 49 GoF mutations separated into two distinct groups containing either PAAND variants or FMF variants. SpeckSeq was validated using patients' cells and supported a reclassification of MEFV variant pathogenicity, leading to novel diagnoses. As a large-scale mutagenesis approach, using human genetics as a guide, SpeckSeq revealed structural and functional pyrin features, including a putative ligand-accommodating cavity in the B30.2 domain. Altogether, SpeckSeq classifies VUS to refine molecular diagnostics and improve our knowledge on the pyrin inflammasome.},
}

*Pyrin/genetics/chemistry
Humans
*Familial Mediterranean Fever/genetics
High-Throughput Nucleotide Sequencing/methods
Mutation/genetics
*Hereditary Autoinflammatory Diseases/genetics
Inflammasomes/metabolism

@article {pmid41334765,
year = {2025},
author = {Kmentová, N and Topić, M and Vanhove, MPM and Atkinson, SD},
title = {Monomyxum ligophori n. sp. in a ParasiteBlitz: monopisthocotylans as myxozoan hosts in South Carolina and monophyly of a cosmopolitan hyperparasitic clade.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e127},
doi = {10.1017/S0022149X25100904},
pmid = {41334765},
issn = {1475-2697},
support = {DIOS/OEYLRODE/2022/001//Universiteit Hasselt/ ; BOF20TT06//Universiteit Hasselt/ ; BOF21PD01//Universiteit Hasselt/ ; Prf-2022-049//Belgian Federal Science Policy Office/ ; NA22OAR4170114//U.S. Department of Commerce/ ; 2021H1D3A2A02081767//National Research Foundation of Korea/ ; Tartar Research Fund//Oregon State University/ ; F22AP01952//U.S. Fish and Wildlife Service/ ; 23KP05VHOM//Universiteit Hasselt/ ; },
mesh = {Animals ; *Myxozoa/genetics/classification/isolation & purification/physiology/growth & development ; *Fish Diseases/parasitology ; South Carolina ; Phylogeny ; Life Cycle Stages ; *Platyhelminths/parasitology ; *Smegmamorpha/parasitology ; Parasitic Diseases, Animal/parasitology ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; },
abstract = {A ParasiteBlitz event offers a brief, intense opportunity to discover diverse parasite species and to reveal life cycles of heteroxenous parasite taxa. In this study, we describe Monomyxum ligophori n. sp., a hyperparasitic myxozoan (Monomyxidae) proliferating in two dactylogyrid monopisthocotylan flatworms (Ligophorus saladensis, Ligophorus mugilinus) infecting mugilid fishes (Mugil cephalus, Mugil curema) on the Atlantic coast of North America. Furthermore, we used DNA barcoding to infer the parasite's complex life cycle, matching its hyperparasitic myxospore stages with actinospore stages infecting the polychaete Streblospio benedicti found in the same locality during the ParasiteBlitz and also reported previously from the same region. Thus we report the first life cycle of a myxozoan that most likely does not require a vertebrate host. Hyperparasitic myxozoans are rare with only five species reported worldwide to infect flatworms. This study provides more information on the previously discussed host specificity towards monopisthocotylan hosts of these monomyxid myxozoan hyperparasites. Notably, Monomyxum ligophori n. sp. was detected in two out of four gill-infecting parasitic flatworms (being absent in Ligophorus uruguayensis and Metamicrocotyla macracantha) found infecting the same fish individuals during the ParasiteBlitz. Our molecular data and phylogenetic analysis support the previously suggested common origin of Monomyxum species infecting monopisthocotylan flatworms, and contribute to understanding the life cycle and host interactions of this unique hyperparasitic myxozoan lineage.},
}

Animals
*Myxozoa/genetics/classification/isolation & purification/physiology/growth & development
*Fish Diseases/parasitology
South Carolina
Phylogeny
Life Cycle Stages
*Platyhelminths/parasitology
*Smegmamorpha/parasitology
Parasitic Diseases, Animal/parasitology
DNA Barcoding, Taxonomic
Host-Parasite Interactions

@article {pmid41333291,
year = {2025},
author = {Chávez-López, Y},
title = {A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20457},
pmid = {41333291},
issn = {2167-8359},
mesh = {Washington ; Animals ; Electron Transport Complex IV/genetics ; Phylogeny ; *Polychaeta/anatomy & histology/classification/genetics ; },
abstract = {Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster & Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.},
}

Washington
Animals
Electron Transport Complex IV/genetics
Phylogeny
*Polychaeta/anatomy & histology/classification/genetics

@article {pmid41332668,
year = {2025},
author = {Hartman, A and Takacsi-Nagy, O and Kernick, C and Theberath, NE and Lu, J and Wu, L and Mantilla, M and Mittra, S and McClellan, A and Johnson, N and Mohamad, L and Castillo-Colin, L and Hoque, F and Eapen, A and Chen, A and Moser, LM and Rogando, T and Hernandez, A and Santostefano, K and Satpathy, AT and Roth, TL},
title = {A unified genetic perturbation language for human cellular programming.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.20.689421},
pmid = {41332668},
issn = {2692-8205},
abstract = {Evolution simultaneously and combinatorially explores complex genetic changes across perturbation classes, including gene knockouts, knockdowns, overexpression, and the creation of new genes from existing domains. Separate technologies are capable of genetic perturbations at scale in human cells, but these methods are largely mutually incompatible. Here we present CRISPR-All, a unified genetic perturbation language for programming of any major type of genetic perturbation simultaneously, in any combination, at genome scale, in primary human cells. This is enabled by a standardized molecular architecture for each major perturbation class, development of a functional syntax for combining arbitrary numbers of elements across classes, and linkage to unique single cell compatible barcodes. To facilitate use, CRISPR-All converts high level descriptions of desired complex genetic changes into a single DNA sequence that can rewire genomic programs within a cell. Using the CRISPR-All language allowed for head-to-head functional comparisons across perturbation types in a comprehensive analysis of all previously identified genetic enhancements of human CAR-T cells. Combining CRISPR-All programs with single cell RNA sequencing revealed a greater diversity of phenotypic states, including improved functional performance, only accessible through distinct perturbation classes. Finally, CRISPR-All combinatorial genome scale screening of up to four distinct perturbations simultaneously revealed additive functional improvements in human T cells accessible only through iterative multiplexing of modifications across perturbation classes. CRISPR-All enables exploration of a combinatorial genetic perturbation space, which may be impactful for biological and clinical applications.},
}

@article {pmid41331945,
year = {2025},
author = {David, O and Munabi, IG and Joseph, O and Mwaka, E and William, B},
title = {A dataset of HLA-A allele sequences and periodontal disease status in people living with HIV.},
journal = {BMC research notes},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13104-025-07590-9},
pmid = {41331945},
issn = {1756-0500},
support = {R56DE032217/DE/NIDCR NIH HHS/United States ; },
abstract = {OBJECTIVES: This dataset was generated to investigate the distribution of HLA-A alleles in people living with HIV (PLWH) with and without periodontitis in Uganda. The data were collected as part of the parent study Oral papillomavirus, microbiota and cancer in people living with HIV (OHPVMC). The dataset provides valuable information about host genetic factors that may influence periodontal disease susceptibility in HIV-positive populations.

DATA DESCRIPTION: The dataset includes nanopore sequencing data (FASTQ format) for HLA-A alleles obtained from 64 PLWH participants (32 with periodontitis and 32 without). It also contains accompanying clinical metadata including periodontitis severity scores, age, sex, antiretroviral therapy duration, number of drinks per day and number of cigarettes per day. Processed files include HLA-A allele calls in CSV format, and file linking the barcodes to the unique identification numbers. All data files have been deposited in public repositories to facilitate reuse in immunogenetics and oral health research. The raw sequencing data are available through NCBI's Sequence Read Archive, while processed data and metadata are hosted on Figshare. This dataset will be particularly valuable for researchers studying genetic susceptibility to oral diseases, HLA diversity in African populations, and the application of nanopore sequencing for HLA typing.},
}

@article {pmid41331487,
year = {2025},
author = {Tan, H and Dong, X and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhang, X and Wang, H and Ding, Y and Liu, Y and Zhao, L},
title = {Molecular characterization of livestock-associated ticks and tick-borne bacteria in Xinjiang, northwestern China.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07178-z},
pmid = {41331487},
issn = {1756-3305},
support = {32260887//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; BR251303//Scientific Innovation Team Project/ ; },
abstract = {BACKGROUND: Xinjiang Uygur Autonomous Region represents a critical pastoral zone at the livestock-tick-human interface in northwestern China, yet molecular data on tick-borne pathogens in this region remain scarce.

METHODS: Between 2017 and 2018, 6172 ticks were collected from cattle, sheep, goats, horses, and dogs across 18 counties in Xinjiang. Tick species identification was performed through morphological examination and cytochrome oxidase I (COI) gene barcoding. Pooled samples (n = 55) were screened using polymerase chain reaction (PCR) and sequencing targeting Rickettsia (glutamate transporter A [gltA], outer membrane protein A [ompA] genes), Anaplasma (16S ribosomal RNA [16S rRNA]), Borrelia (heat shock protein GroEL [groEL]), and broad-range bacterial diversity (16S rRNA).

RESULTS: Seven tick species were identified: Alveonasus lahorensis (33.7%), Dermacentor marginatus (32.3%), Rhipicephalus turanicus (21.9%), Dermacentor silvarum (5.7%), Hyalomma asiaticum (4.0%), and Haemaphysalis sulcata (2.5%). Rickettsia DNA was detected in 28 of 55 pools (50.9%), with sequences showing relatedness to Rickettsia raoultii, Rickettsia massiliae, and Rickettsia barbariae. Anaplasma capra was identified in D. marginatus collected from goats (1.8% of pools), while Borrelia miyamotoi was detected in R. turanicus from sheep (1.8% of pools). Additional bacterial genera detected included Arsenophonus in D. marginatus, Coxiella in R. turanicus, and Francisella in H. asiaticum. Notably, R. massiliae was detected in both eggs and unfed larvae of R. turanicus, consistent with transovarial transmission.

CONCLUSIONS: This study represents the first comprehensive molecular survey of livestock-associated ticks in Xinjiang, revealing high prevalence of spotted fever group rickettsiae and the presence of emerging tick-borne pathogens. Our findings underscore potential zoonotic risks within pastoral systems and emphasize the critical need for enhanced One Health surveillance strategies at the livestock-human interface in this region.},
}

@article {pmid41329648,
year = {2025},
author = {Vihavainen, J and Kiljunen, N and Pohjola, P and McKeown, J and Oinonen, E and Mutanen, M and Pohjoismäki, J},
title = {Megabarcoding dark taxa - Assessing the utility of mass DNA barcoding for phorid fly species discovery.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0334948},
pmid = {41329648},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Diptera/genetics/classification/anatomy & histology ; Female ; Male ; Electron Transport Complex IV/genetics ; Phylogeny ; Finland ; Species Specificity ; },
abstract = {Many hyperdiverse, small-bodied insect families contain numerous undescribed species, generally termed "dark taxa". Scuttle flies (Diptera: Phoridae), being among the most diverse insect groups globally, are a prime example. DNA barcoding can help delineate dark taxa, particularly when integrated with morphology, and/or additional molecular evidence. We sequenced COI-barcodes from 9,120 Finnish phorid specimens and initially identified them using the BOLD database. Furthermore, species identifications of all 843 specimens, belonging to other genera than Megaselia, were confirmed morphologically. Initially, the BOLD-based identifications matched the morphological identifications only in 68% of the cases, primarily due to numerous misidentifications in BOLD. After adjusting the BOLD reference identifications based on morphological analyses of male features, we established a reliable framework for female identification. This is advantageous for future identification of females, as they are often excluded from traditional identification keys. Only two species were discovered as new to Finland, demonstrating that Finnish fauna is well-known, except Megaselia. Although DNA barcodes show great promise for identifying phorids, incorrectly identified reference sequences remain challenging, not the functionality of barcode gene Cytochrome c oxidase subunit I (COI) itself. The number of Megaselia BINs greatly exceeded the known Finnish species count, with many sequences lacking matches in BOLD. This further highlights Megaselia as a particularly dark group, for which genetic tools are essential for uncovering species identities and assessing diversity.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Diptera/genetics/classification/anatomy & histology
Female
Male
Electron Transport Complex IV/genetics
Phylogeny
Finland
Species Specificity

@article {pmid41328580,
year = {2025},
author = {Goodsell, C and Jung, P and Maslakova, S and Allen, J},
title = {Baseodiscus the Eldest: First Report of a Decades-Long Lifespan in a Nemertean Species.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70052},
pmid = {41328580},
issn = {2471-5646},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Nemertea is a speciose phylum of marine invertebrate predators ubiquitous in the world's oceans, which includes Lineus longissimus (Gunnerus, 1770)-the world's longest documented extant animal, yet much about the life histories of these remarkable animals remains poorly understood. For example, it is not known how long nemerteans live. We report a maximum known age of a nemertean individual, identified by morphology and DNA-barcoding as belonging to Baseodiscus punnetti (Coe, 1904), which has been kept in aquaria for at least 26 years. This finding confirms previous speculations that at least some species of nemerteans may live for many years and highlights a dearth of knowledge of the longevity of nemerteans and of marine invertebrates more broadly.},
}

@article {pmid41328418,
year = {2025},
author = {Hajri, S and Bahri, L and Harris, DJ},
title = {New Insights on Genetic and Morphological Divergence Among a Buthus Species Complex From Tunisia With the Identification of a New Species.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72556},
pmid = {41328418},
issn = {2045-7758},
abstract = {The taxonomy of the scorpion genus Buthus is complex due to the considerable increase in newly reported species, their high degree of similarity, and consequently, the great difficulty in their morphological differentiation. Tunisian species are not exempt from this issue, with several references highlighting the need for taxonomic revisions. This study integrates DNA sequence data and morphological assessments to investigate the diversity present in Tunisia and to provide morphological details that facilitate species identification. The results show that most Tunisian specimens are distributed within two clades. One clade comprises four subclades corresponding to B. tunetanus Herbst, 1800, B. paris C. L. Koch, 1839, B. chambiensis Kovařík 2006 and a southern group corresponding probably to B. lourencoi Rossi, Tropea & Yağmur, 2013. The second clade represents a new species described in this study as B. saidnouirai Hajri, Bahri & Harris, sp. nov. No evidence of B. dunlopi Kovařík 2006 have been recorded in the studied samples. Distances between all five species exceed the minimum divergence thresholds for Buthus species. The greatest distance was observed between B. saidnouirai. sp. nov. and the southern group, while the smallest distance was between B. tunetanus and B. paris. Although the genetic differences revealed considerable divergence of the new group from the four remaining species, the morphological assessment did not identify the same pattern. These five species demonstrate a morphological shape gradient in which B. paris and the southern group represent the two extremes, with B. paris being the most ornamented and the latter the least. The new species presents an intermediate morphology. The geographic distributions of the five reported species are discussed in this work according to the topography and orography of the region. Additional lineages known from Algeria may also enter the western fringes of Tunisia.},
}

@article {pmid41327488,
year = {2025},
author = {Song, Z and Klyuchnikov, E and Badbaran, A and Tan, L and Dress, RJ and Czajkowski, E and Weßler, S and Massoud, R and Wolschke, C and Schimrock, A and Zhang, Y and Ly, C and Gagelmann, N and Rathje, K and Fehse, B and Bonn, S and Ravens, S and Gagliani, N and Krebs, CF and Panzer, U and Ayuk, F and Kröger, N and Prinz, I},
title = {Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation.},
journal = {Biomarker research},
volume = {13},
number = {1},
pages = {155},
pmid = {41327488},
issn = {2050-7771},
abstract = {BACKGROUND: Alloreactive T cells mediate graft-versus-leukemia (GvL) reactions and acute graft-versus-host disease (aGvHD) in AML patients following allogeneic hematopoietic stem cell transplantation.

METHODS: To investigate biomarkers that identify alloreactive T cells associated with either beneficial GvL or detrimental aGvHD, we collected graft samples and two post-transplant follow-up blood samples (day 30 and day 100) of ten AML patients undergoing hematopoietic stem cell transplantation and profiled over 777,000 CD45[+] leukocytes in total by combinatorial barcoding-based mega-scale single-cell RNA sequencing.

RESULTS: Using immune receptor sequences as intrinsic clonal barcodes, we observed that especially CD8[+] graft-derived T cells persisted and displayed enhanced proliferation, clonal expansion, and likely alloreactivity. Notably, patient-derived peripheral leukocytes that survived the conditioning, as identified by sex-chromosome-related genes, were primarily CD4[+] T helper cells. MDGA1 expression on T cells and NK cells emerged as a novel biomarker potentially associated with aGvHD. Additionally, we observed a significant deficiency of ADGRG1 expression, a marker of alloreactive cytotoxic T cells, by αβ and γδ T cells from relapsed patients.

CONCLUSIONS: In conclusion, mega-scale single-cell monitoring of graft and hematopoietic immune cell reconstitution allowed us to demonstrate that MDGA1 and ADGRG1 may function as complementary biomarkers expressed by distinct circulating T cells that are associated with divergent outcomes in AML patients, enabling precise risk stratification of alloHSCT outcomes and presenting potential therapeutic targets.},
}

@article {pmid41325363,
year = {2025},
author = {Dvirnas, A and Leal-Garza, LM and Abbaspour, Z and Fröbrant, E and Frykholm, K and Wrande, M and Sandegren, L and Westerlund, F and Ambjörnsson, T},
title = {DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0335633},
pmid = {41325363},
issn = {1932-6203},
mesh = {*Algorithms ; *Chromosome Mapping/methods ; Escherichia coli/genetics ; *DNA/genetics ; Software ; },
abstract = {In optical genome mapping (OGM), large numbers of individual DNA maps-sequence-specific data series along single DNA molecules-are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in order to create consensus OGM maps for corresponding regions along the chromosomes. While there are several types of experimental OGM assays, not all of them have de novo OGM assembly tools available. In particular, in densely-labelled OGM there are no such tools. Here, we present and evaluate DOGMA, a de novo OGM assembly algorithm for densely labelled OGM data which uses matrix profiles. Matrix profile has transformed how data mining problems are approached in time series analysis. Yet, this algorithm has not been widely explored outside of the time series community- we here use it for OGM de novo assembly for the first time. Further novelties in our algorithm are the introduction of two scores for each individual alignment, use of p-values, a visual representation as barcode islands and the introduction of a method for generating consensus barcodes using amplitude adjustment. Utilizing p-values helps mitigate the risk of errors in the assemblies as caused by false positives. We demonstrate our algorithm by applying it for de novo OGM assembly of synthetic datasets and of an experimental dataset from an Escherichia coli genome. We validate the assemblies using corresponding reference genomes and investigate the strengths and limitations of the algorithm. De novo OGM assembly of dense optical DNA maps shows promise as a complement or an alternative to current OGM techniques for other types of genome mapping assays. The code is available at: https://github.com/dnadevcode/dogma.},
}

*Algorithms
*Chromosome Mapping/methods
Escherichia coli/genetics
*DNA/genetics
Software

@article {pmid41318587,
year = {2025},
author = {Platzgummer, K and Oerther, SI and Bečvář, T and Dvořák, V and Sádlová, J and Bečvářová, B and Volf, P and Obwaller, AG and Bakran-Lebl, K and Trájer, AJ and Walochnik, J and Kniha, E},
title = {The knowns and unknowns of phlebotomine sand flies (Diptera: Psychodidae) in selected countries of Central Europe.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07160-9},
pmid = {41318587},
issn = {1756-3305},
support = {bo/00896/24/5//Magyar Tudományos Akadémia/ ; 101057690//European Commission/ ; },
abstract = {BACKGROUND: Sand flies are vectors of the protozoan Leishmania spp. and phleboviruses. In Europe, several species are widely distributed in the Mediterranean region and a northward spread can be observed. They can be found regularly also in some regions of Central Europe, with Phlebotomus mascittii being the most cold-tolerant and northerly distributed species, but the knowledge on their distribution in countries such as Germany, Austria, Czechia, Slovakia, and Hungary remains fragmentary because of a lack of comprehensive field studies and a poor understanding of the ecological requirements and phylogeographic history.

METHODS: A comprehensive literature review of sand fly occurrence in five Central European countries was complemented by entomological surveys, including sand fly and rodent screening for sand fly-borne pathogens. Nucleic acid extraction, COI barcoding, blood meal analysis, and phylogenetic and environmental analyses incorporating unsupervised machine learning techniques were conducted.

RESULTS: This study significantly advances the understanding of the current distribution of six sand fly species in Central Europe. Among them, only Ph. mascittii was present in all analyzed countries, except Czechia, with its seasonal activity peaking in July. Phlebotomus papatasi, Ph. perfiliewi and Ph. neglectus were recorded in Hungary, while Ph. perniciosus and Phlebotomus simici were found in Germany and Austria, respectively. Although Leishmania DNA was absent in sand flies and rodents, DNA from two distinct Trypanosoma lineages was detected in several specimens, suggesting Ph. mascittii feeds on both birds and ruminants. Trypanosomatid lineages identified in local rodents differed, indicating distinct lineages between sand flies and rodents. Environmental analysis identified 15 Corine land cover classes associated with sand fly presence, with urban locations being the most frequently occupied. Linear regression models comparing presence versus absence revealed significantly higher sand fly presence in forested and urban landscapes. Furthermore, Ph. mascittii populations formed four distinct ecological clusters, which broadly grouped into two main geographic groups: one in the Upper Rhine Valley of southwestern Germany and the other spanning the Carpathian Basin.

CONCLUSIONS: This study provides new insights into the current distribution, ecological preferences, seasonal activity, and potential vector capacity of sand fly species in Central Europe.},
}

@article {pmid41317321,
year = {2025},
author = {Shin, HJ and Sharma, S and Kronheim, S and Cheung, M and Nguyen, LV},
title = {Protocol to track single-cell-derived clones using DNA barcoding combined with single-cell RNA sequencing.},
journal = {STAR protocols},
volume = {6},
number = {4},
pages = {104229},
doi = {10.1016/j.xpro.2025.104229},
pmid = {41317321},
issn = {2666-1667},
abstract = {Clonal fitness and plasticity drive tumor heterogeneity contributing to disease progression and treatment resistance. Here, we provide a protocol to track the clonal outputs from uniquely marked cells. We describe steps for constructing and validating lentiviral DNA barcode libraries. We then detail procedures for single-cell RNA sequencing. This approach links clonal growth activity with transcriptomic profiles and enables permanent cellular labeling to track clonal dynamics in various model systems, which can provide insight into molecular processes underlying clone function. For complete details on the use and execution of this protocol, please refer to Nguyen et al.[1].},
}

@article {pmid41316409,
year = {2025},
author = {Leta, S and Mulatu, T and Yalew, B and Chibssa, TR and Paeshuyse, J},
title = {DNA barcoding and blood meal profiling of Ethiopian mosquitoes (Diptera: Culicidae): insights into species identification and host preferences.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {493},
pmid = {41316409},
issn = {1756-3305},
support = {4520196970//Global Minds PhD scholarship program, KU Leuven/ ; },
mesh = {Animals ; Ethiopia ; *DNA Barcoding, Taxonomic ; *Culicidae/classification/physiology/genetics ; *Mosquito Vectors/classification/physiology/genetics ; Phylogeny ; Feeding Behavior ; Host Specificity ; Genetic Variation ; Humans ; Female ; Aedes/classification/genetics/physiology ; Anopheles/classification/genetics/physiology ; },
abstract = {BACKGROUND: Arboviruses continue to threaten global health because of their rapid geographical expansion and significant disease burden. Of the over 500 recognized arboviruses, approximately 150 affect humans, and around 50 affect domestic animals and wildlife. The spread and impact of these viruses have increased significantly over the past three decades, driven by the proliferation of their vectors and the rise of global trade and travel.

METHODS: In this study, we used molecular methods to characterize mosquito species diversity and host feeding preferences across Ethiopia's Great Rift Valley. Mosquitoes were collected from diverse habitats in the Great Rift Valley of Ethiopia using Centers for Disease Control and Prevention (CDC) light traps, BG-Sentinel traps, and hand aspirators. The area was chosen for its high vector diversity, suitable breeding habitats, and the epidemiological importance of arboviruses. Morphological identification was conducted, and 204 blood-fed mosquitoes were selected. Genomic DNA was extracted, followed by polymerase chain reaction (PCR) amplification targeting the COI gene. Blood meal analysis was performed using vertebrate-specific primers targeting the 12S rRNA gene. Mosquito species identification, genetic diversity analysis, and phylogenetic analyses were conducted.

RESULTS: Of 6601 collected mosquitoes, 4977 were identified morphologically, comprising 399 Aedes, 2861 Culex, 1841 Anopheles, and 275 Mansonia species. COI DNA barcode analysis identified 142 mosquito specimens belonging to 16 species, with Anopheles coustani, Cx. tritaeniorhynchus, Cx. pipiens complex, Mansonia africana, and Ma. uniformis being the predominant species. Blood meal analysis (n = 71 successful amplifications) revealed a primary reliance on humans and cattle. Cx. pipiens complex showed a strong anthropophilic tendency, while Cx. tritaeniorhynchus and Ma. uniformis exhibited broader host ranges. Genetic diversity indices showed significant Fu's Fs statistics for Cx. pipiens complex, Cx. tritaeniorhynchus, Ma. africana, and Ma. uniformis.

CONCLUSIONS: This study offers valuable preliminary insights into the diversity of mosquito species, genetic variation, and host-feeding preferences within the Ethiopian Rift Valley. The findings emphasize the potential of molecular techniques to enhance traditional entomological methods and improve the accuracy of mosquito identification. While the study is limited in both geographic and temporal scope, it highlights mosquito species of medical and veterinary significance and suggests implications for arboviral disease surveillance.},
}

Animals
Ethiopia
*DNA Barcoding, Taxonomic
*Culicidae/classification/physiology/genetics
*Mosquito Vectors/classification/physiology/genetics
Phylogeny
Feeding Behavior
Host Specificity
Genetic Variation
Humans
Female
Aedes/classification/genetics/physiology
Anopheles/classification/genetics/physiology

@article {pmid41315888,
year = {2025},
author = {van der Windt, N and Paix, B and Biesmeijer, JC and Ambo-Rappe, R and Huang, YM and Nirbadha, KGS and Sipkema, D and de Voogd, NJ},
title = {Host Evolutionary History Drives Prokaryotic Diversity in the Globally Distributed Sponge Family Petrosiidae.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70186},
doi = {10.1111/mec.70186},
pmid = {41315888},
issn = {1365-294X},
support = {101000392//Horizon 2020 Framework Programme/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //European Regional Development Fund/ ; //Collectivité Territoriale de Martinique/ ; CRG-1-814 2012-BER-002//King Abdullah University of Science and Technology/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology/ ; MNPH104403//Marine National Parks Headquarters/ ; },
abstract = {Sponge microbial communities play a crucial role in marine ecosystem functioning and serve as a rich source of bioactive compounds. While host identity is recognised as a major determinant of microbiome diversity, the underlying evolutionary mechanisms remain poorly understood. This study aimed to comprehensively assess phylosymbiosis patterns within the sponge family Petrosiidae. In total 21 sponge species, collected across a broad geographic scale, were examined to investigate how host phylogeny influences microbiome composition. Using 28S rRNA, 18S rRNA and COI gene barcoding to identify host sponges, combined with 16S rRNA gene amplicon sequencing to characterise prokaryotic communities, we provide evidence of phylosymbiosis through multiple analytical approaches, including distance-based metrics and topological congruence. Our results show that host phylogeny and identity play a significant role in structuring sponge microbiomes, even at finer taxonomic resolutions. However, we observed notable incongruencies, where closely related sponge species exhibit divergent microbial communities that appear to be associated with depth or geographical location. This study represents the first large-scale investigation of phylosymbiosis in sponges at the family level, providing valuable insights into the evolutionary and ecological drivers shaping sponge microbiomes, particularly in the sponge family Petrosiidae.},
}

@article {pmid41315366,
year = {2025},
author = {Sahu, A and Singh, M and Sarkar, UK},
title = {Building a DNA barcode library of commercially exploited fish genetic resources (FGR) of the Gomti River, Ganga basin, implications for conservation and management.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42721},
pmid = {41315366},
issn = {2045-2322},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Rivers ; Phylogeny ; *Conservation of Natural Resources ; India ; Biodiversity ; Electron Transport Complex IV/genetics ; *Gene Library ; },
abstract = {The Gomti River is a vital tributary of the largest Gangetic Riverine system, flowing in the northern part of Uttar Pradesh, India. This habitat serves as one of India's most precious repository for fish genetic resources (FGR), contributing significantly to regional biodiversity, and is a source of livelihood. It has diverse climatic conditions, which have led to a distinctive fish community structure and the presence of native species. The application of DNA barcoding for assessing FGR in the north Himalayan region, particularly in UP, presents a notable research gap. This study established the first DNA barcodes of voucher specimens identified through classical taxonomy, creating a molecular catalogue of commercially important fish species. DNA barcoding was accomplished using the cytochrome oxidase subunit I gene (COI) for species identification and phylogenetic analysis. We identified 37 commercially important fish species (34 native & 3 exotics) using classical taxonomy and molecular biology, which belonged to 8 orders, 18 families, and 29 genera. The IUCN conservation status revealed that 30 species (81.08%) were categorized as Least Concern (LC), followed by 4 species (10.81%) as Near Threatened (NT), 2 species (5.41%) as Vulnerable (VU), and 1 species (2.70%) as Endangered (EN). Cypriniformes order and Cyprinidae family emerged as the most dominant groups, contributing 40.54% and 29.73%, respectively. Average read lengths of all sequences were 630.82 bp (range 578-655 bp). Overall nucleotide composition of Adenine (A) = 25.81%, Thymine (T) = 28.88%, Cytosine (C) = 27.53%, and Guanine (G) = 17.78%. Average GC content (54.69%) was higher than AT content (45.31%). As expected, the uncorrected p-genetic distances showed a progressive increase in genetic divergence from lower to higher taxonomic levels. p-distance values ranged from 0-0.48% (mean 0.06%) within species, 0-11.37% (1.56%) within genera, 0-12.27% (5.00%) within families, and 0-15.31% (8.88%) within orders. Among families, Cyprinidae (12.27%) and Danionidae (11.57%) exhibited the highest genetic divergence. Whereas at the order level, the greatest divergence was observed in Perciformes (15.31%), followed by Siluriformes (15.22%). The constructed phylogenetic tree shows that all species are clearly separated based on similar groups and clustered into independent clades. Assemble Species by Automatic Partitioning (ASAP) analysis identified ten partitions with the best ASAP score (4.00). It reveals a barcode gap of 1-9% (0.01-0.09) and delimits approximately 31-37 putative fish species. The GTR + G + I model revealed a strong transition bias in the COI gene of the barcoded fishes, with higher pyrimidine substitutions and transition/transversion ratios (k1 = 10.80; k2 = 26.98; R = 3.09). Our dataset comprised 110 COI nucleotide sequences with 592 positions in the final alignment, including 236 polymorphic sites and 39 distinct haplotypes. We also estimated haplotype diversity (Hd = 0.975) and nucleotide diversity (π = 0.194). Our findings highlighted that efficacy of traditional taxonomy and DNA barcoding method (also known as integrative taxonomy) is complementary to each other for identifying and authenticating fish taxa. Additionally, the developed COI library will be valuable for future environmental DNA (eDNA) studies for detecting indigenous and exotic fish species and useful for nature conservation. We conclude that it serves as an effective tool for sustainable conservation, fishery management, and future monitoring of freshwater fish genetic resources.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
Rivers
Phylogeny
*Conservation of Natural Resources
India
Biodiversity
Electron Transport Complex IV/genetics
*Gene Library

@article {pmid41310420,
year = {2025},
author = {Al-Andal, A},
title = {Plastome diversity and phylogenetic insights among modern Egyptian wheat cultivars: Genome-Wide and Gene-Level perspectives.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07739-5},
pmid = {41310420},
issn = {1471-2229},
support = {RGP2/310/46//Deanship of Research and Graduate Studies at King Khalid University/ ; },
abstract = {This study presents a genome-wide and gene-level characterization of plastome diversity and phylogenetic relationships among ten modern Egyptian wheat cultivars, representing both hexaploid and tetraploid lineages. Raw sequencing data for all cultivars were retrieved from NCBI BioProject PRJNA1290394, and plastome assemblies were generated using the published wheat chloroplast genome (GenBank accession MW889057.1) as the seed reference under default settings. Comprehensive plastome sequencing revealed an exceptionally conserved genome structure and gene content across cultivars, yet identified distinct mutation hotspots, with the rps2 gene exhibiting the highest single-gene SNP burden (up to 21 SNPs in cultivar Sahel 1). SNP profiling demonstrated clear differentiation between genetically divergent cultivars such as Sahel 1 and GMZ9, and documented variation in overall mutational load-ranging from 7 to 74 SNPs per cultivar-mirroring phylogenetic clade structure. Chloroplast heteroplasmy analysis uncovered cultivar-specific genome stability patterns, informing breeding decisions and highlighting cytoplasmic diversity. SSR motif analysis confirmed predominant AT-rich homopolymers and subtle motif-length differences distinguishing tetraploid and hexaploid genotypes. Codon usage analysis showed a highly conserved AT-bias and effective translational optimization across ploidy levels. Phylogenetic reconstruction using complete plastome sequences resolved finer relationships than gene-based approaches, while matK emerged as a superior biomarker for distinguishing Poaceae lineages. mVISTA comparison revealed conserved plastome structure with divergence hotspots at atpH-atpI and atpA regions, underscoring their value as potential molecular markers for phylogenetic and barcoding applications. Taken together, these findings provide deep insights into plastome-driven genetic diversity, robust cultivar identification, and the evolutionary context for Egyptian wheat breeding and conservation programs. (253 words).},
}

@article {pmid41309703,
year = {2025},
author = {Salamon, S and Mikołajczak, K and Basińska-Barczak, A and Banachewicz, P and Błaszczyk, L},
title = {Intergenerational and horizontal transmission of wheat endophytic fungi.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42275},
pmid = {41309703},
issn = {2045-2322},
support = {2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; },
mesh = {*Triticum/microbiology ; *Endophytes/genetics/physiology/classification ; *Fungi/genetics/classification ; Mycobiome ; Seedlings/microbiology ; },
abstract = {Understanding the mechanisms of endophytic fungal transmission is crucial for deciphering plant-microbe interactions and leveraging microbiomes in crop improvement. In this study, we examined the potential for intergenerational inheritance and external recruitment of endophytic fungi in common wheat. Fungal community structure was compared in generation G1 and parental G0 plants using ITS2 metabarcoding data and culture-based identification in four tissues (roots, stems, leaves, and seeds) in ten cultivars. A set of 27 operational taxonomic units (OTUs) was consistently detected in both generations, suggesting the presence of a core mycobiome dominated by genera such as Fusarium, Trichoderma, Penicillium, Cladosporium, Sarocladium and Lecanicillium. Experimental inoculation of axenic wheat seedlings with fungi Fusarium proliferatum, Penicillium expansum, Trichoderma hamatum originating from the wheat endosphere confirmed the ability of these species to recolonize host tissues and thus their role in stable association with plants. However, several other taxa (Engyodontium album, Sarocladium spinificis, Clonostachys candelabrum, and Nigrospora gorlenkoana) originating from internal wheat tissues failed to recolonize axenic plants, suggesting transient colonization via horizontal pathways. These findings highlight the dual contribution of vertical inheritance and environmental recruitment in shaping the wheat endomycobiome, offering a foundation for targeted manipulation of beneficial fungi in cereal crops.},
}

*Triticum/microbiology
*Endophytes/genetics/physiology/classification
*Fungi/genetics/classification
Mycobiome
Seedlings/microbiology

@article {pmid41309632,
year = {2025},
author = {Hosogane, T and Santana, LS and Eling, N and Moch, H and Bodenmiller, B},
title = {Compressed sensing expands the multiplexity of imaging mass cytometry.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66629-4},
pmid = {41309632},
issn = {2041-1723},
support = {310030_205007//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_213512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; UC4 DK108132/DK/NIDDK NIH HHS/United States ; IMAXT Grand Challenge//Cancer Research UK (CRUK)/ ; 866074//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The multiplexity of current antibody-based imaging is limited by the number of reporters that can be detected simultaneously. Compressed sensing can be used to reconstruct high-dimensional information from low-dimensional measurements. Previously, compressed sensing using composite in situ imaging (CISI) of transcriptomic data leveraged gene co-regulation structure to recover spatial expression of 37 RNA species from images of 11 composite channels. Here, we extend the CISI framework to protein expression data measured by imaging mass cytometry (IMC). CISI-IMC accurately recovers spatial expression of 16 immune and stromal marker proteins from images of 8 composite channels with an average Pearson's correlation of 0.8 across protein. Training the CISI-IMC framework using data collected on multiple human tissues enables universal decompression of composite data from a wide range of tumor and healthy tissue types. The expression dictionary and barcoding matrix described here are immediately implementable for general immune and stromal cell type classification, but CISI-IMC can in principle be applied to other markers or other antibody-based imaging methods. Our work lays the foundation for much higher plex protein imaging.},
}

@article {pmid41307211,
year = {2025},
author = {Ramsey-Coleman, C and Youngner, C and Singletary, T and Wright, D and Payton, C and Sargent, M and Kettel Khan, L and Lavinghouze, SR},
title = {Scanning for Wellness: QR Code Strategies to Promote Public Health Programs.},
journal = {Health promotion practice},
volume = {},
number = {},
pages = {15248399251391141},
doi = {10.1177/15248399251391141},
pmid = {41307211},
issn = {1524-8399},
abstract = {This article discusses the importance of effective communication tools in public health, highlighting innovations like Quick Response (QR) codes and QR wallet reference cards (QR cards) for enhancing outreach and education. QR codes are scannable barcodes that link to digital content. QR cards are compact cards, similar to business cards, with codes that lead to relevant health information. To our knowledge, there is little published literature on using QR codes and cards for public health programs and health communication outside of health care clinics and education settings. The North Carolina Department of Health and Human Services, Division of Public Health, Community and Clinical Connections for Prevention and Health Branch has successfully implemented QR codes in various public health programs, particularly in diabetes management and nutrition, physical activity, and obesity initiatives. Key lessons learned include using reputable QR code generators, ensuring visibility and scanability of the codes, testing links before use, providing clear calls to action, and considering dynamic versus static codes based on needs. QR codes can be leveraged in public health practice for program promotion, evaluation sharing, and community resource accessibility. However, limitations such as smartphone dependency among some populations should be acknowledged. In conclusion, while QR codes are a simple tool, they hold significant potential for improving public health communication. Research on QR code use in public health settings could help inform best practices for public health programs and health promotion across different contexts.},
}

@article {pmid41304618,
year = {2025},
author = {Djebaili, R and Farda, B and Gialdini, O and Vaccarelli, I and Rezaee Danesh, Y and Pellegrini, M},
title = {Microbial Consortium of Streptomyces spp. from Mining Environments Enhances Phytoremediation Potential of Lemna minor L.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223467},
pmid = {41304618},
issn = {2223-7747},
abstract = {The presence of substantial amounts of heavy metals in the environment can result in various significant ecological issues and human health risks. Currently, bioremediation employing microorganisms is garnering significant interest due to its effectiveness. The present investigation aimed to isolate actinobacterial strains from an Italian mine and to characterise them for heavy metals resistance and plant growth-promoting characteristics. The different samples were processed for DNA extraction and 16S rRNA gene metabarcoding to investigate the bacteria and archaea communities. Cultivable microbiota were isolated and evaluated for heavy metals tolerance and different PGP traits. The most pertinent strains were tested for compatibility, merged into a consortium, and tested on Lemna minor L. Metabarcoding analysis revealed that amplicon sequence variants (ASVs) at the phylum level were mostly assigned to proteobacteria and bacteroidota. Uncultured and unknown taxa were the most prevalent in the samples at the genus level. A total of ten strains were obtained from the culture-dependent approach exhibiting interesting heavy metals tolerance and plant growth-promoting traits. The best strains (MTW 1 and MTW 5) were selected and further characterised by 16S barcoding. These strains were identified as Streptomyces atratus (99.57% identity). An in planta experiment showed that the metal-tolerant consortium MTW 1-5 improved plant physiology by significantly optimising plant growth and tolerance to heavy metals. The experiment conducted provided evidence for the possibility of using actinobacteria as bioaugmentation agents to improve the phytoextraction abilities of L. minor.},
}

@article {pmid41303671,
year = {2025},
author = {Jang, W and Lee, SH and Kim, WJ and Yang, S and Moon, BC},
title = {PCR-Based Molecular Authentication Method for Sources of Agrimoniae Herba via Comparative Analyses of Complete Chloroplast Genomes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211189},
pmid = {41303671},
issn = {1422-0067},
support = {KSN2511030//Korea Institute of Oriental Medicine/ ; },
mesh = {*Genome, Chloroplast ; Phylogeny ; Polymorphism, Single Nucleotide ; *Polymerase Chain Reaction/methods ; DNA Barcoding, Taxonomic/methods ; *Agrimonia/genetics/classification ; INDEL Mutation ; Plants, Medicinal/genetics ; Species Specificity ; Drugs, Chinese Herbal ; },
abstract = {Accurate species identification is essential for the quality control and standardization of herbal medicines. Agrimonia species, the authentic sources of Agrimoniae Herba, have long been used in traditional medicine, yet limited genomic resources have hindered the establishment of reliable molecular approaches for accurate species discrimination within this genus. Here, we report the newly assembled complete chloroplast genomes (155,156-155,302 bp) of four Agrimonia species, which exhibit the typical quadripartite structure and contain 112 unique genes. Comparative analysis revealed 684 variable sites, including 497 single nucleotide polymorphisms (SNPs) and 187 insertions/deletions (InDels), predominantly located in the single-copy regions. Based on these species-specific variations, we developed nine PCR-based molecular markers that distinguished the four species. The markers were validated using herbarium specimens and commercial herbal products, demonstrating reproducibility and practical applicability. Phylogenetic analysis supported the monophyly of the genus Agrimonia and resolved each species into distinct clusters within the subtribe Agrimoniinae. These results showed that chloroplast genome sequences of the genus Agrimonia can serve as effective super DNA barcodes for species identification. Our study provides fundamental genomic resources for Agrimonia and reliable molecular tools for species authentication, providing a basis for ensuring the authenticity and safety of Agrimoniae Herba.},
}

*Genome, Chloroplast
Phylogeny
Polymorphism, Single Nucleotide
*Polymerase Chain Reaction/methods
DNA Barcoding, Taxonomic/methods
*Agrimonia/genetics/classification
INDEL Mutation
Plants, Medicinal/genetics
Species Specificity
Drugs, Chinese Herbal

@article {pmid41302919,
year = {2025},
author = {Yakimenko, EV and Romanovich, AE and Lukhtanov, VA},
title = {Questionable Species Names for Distinct Species Clusters: An Empirical Test of the BOLD Molecular Identification Engine.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111172},
pmid = {41302919},
issn = {2075-4450},
support = {24-14-00047//Russian Science Foundation/ ; },
abstract = {DNA barcoding is an effective method for species identification, but its practical application, as implemented in the Barcode of Life Data System (BOLD), faces numerous challenges. In our work, we conducted an empirical test of this approach using butterflies of the Volga River region in eastern Europe as a model system. We demonstrate that DNA barcoding is a powerful tool for identifying species clusters of the local fauna studied. However, assigning the identified clusters to scientific species names using BOLD was problematic for more than half of the species analyzed. The reasons for these problems are numerous errors in (1) species and even (2) generic identifications of DNA barcodes in the BOLD database (30% and 26% of all problematic cases, respectively), (3) similarity of DNA barcodes in different species (22%), (4) unresolved taxonomic problems associated with the species names that BOLD suggests as identifications (18%), (5) anomalous barcodes (2%), and (6) incompleteness of the BOLD database (2%). Solving problems 1, 2 and 5 requires improving the DNA barcode curation system and minimization of the identification errors in the BOLD database. Problems 3 and 6 can be partly solved by accumulating DNA barcodes, especially barcodes of local faunas, since populations of different species with identical DNA barcodes often have non-overlapping areas. Problem 4 is the most difficult and requires further intensive taxonomic research to solve it.},
}

@article {pmid41302916,
year = {2025},
author = {Stonis, JR and Remeikis, A and Orlovskytė, S},
title = {New Discoveries Supporting the Exceptional Species Diversity of Opostegidae in Central America and the Caribbean, Alerting on Misidentified Barcodes.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111170},
pmid = {41302916},
issn = {2075-4450},
abstract = {The aim of this study was to supplement current knowledge on the species diversity of Opostegidae in Central America and the Caribbean and to compare this diversity with that of other regions. We examined historical material and conducted fieldwork in Honduras during 2023-2025, a true tabula rasa in terms of Opostegidae diversity. Collected specimens were dissected, with genitalia photographed and analyzed. Molecular divergence was assessed using Neighbor-Joining and Maximum Likelihood methods, as well as Bayesian inference; creation of a mitotype network (TCS algorithm) and species delimitation (bPTP method) were also performed. The study of historical material revealed that Pseudopostega saltatrix (Walsingham) is not conspecific with taxa previously published under the same name, resulting in the description of one new Pseudopostega species. Fieldwork in Honduras yielded 11 additional Pseudopostega species-all new national records, six of which are new to science. The paper introduces 33 new molecular sequences, bringing the total to 114 mtDNA COI-5' sequences currently deposited in the National Genomics Data Center (China). With these discoveries, the number of Opostegidae in Central America and the Caribbean rises to 63 species, representing 30.9% of the global fauna. The Neotropical realm (103 spp.) exhibits markedly higher Opostegidae diversity than other biogeographical regions, underscoring its importance as a center of diversification. Our analysis also revealed an alarmingly high proportion of doubtful molecular barcodes-nearly one-third (27%) appear erroneous due to species misidentification in Neotropical Opostegidae.},
}

@article {pmid41302912,
year = {2025},
author = {Liu, Y and Triapitsyn, SV and Zhang, D and Wang, J and Aishan, Z},
title = {Integrative Taxonomy of Polynema (Doriclytus) (Hymenoptera: Mymaridae) from Oriental China: Three New Species and Five New Records Revealed by Morphological and Molecular Analyses.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111166},
pmid = {41302912},
issn = {2075-4450},
support = {32260123//Zhulidezi Aishan/ ; },
abstract = {Polynema Haliday, 1833 (Hymenoptera: Chalcidoidea: Mymaridae), one of the most species-rich genera in the family, comprises egg parasitoids with diverse hosts across multiple insect orders, some serving as biological control agents for agricultural and forestry pests. The subgenus Polynema (Doriclytus Foerster, 1847), characterized by pronounced morphological conservatism, has historical taxonomic challenges due to reliance on external morphological characteristics. This study employed an integrative taxonomic approach, combining morphological and molecular analyses, to investigate P. (Doriclytus) diversity in the Oriental region of China. Eight species were identified, including three new species-P. (Doriclytus) acutum Wang & Aishan, sp. nov., P. (Doriclytus) daliense Wang & Aishan, sp. nov., and P. (Doriclytus) longicornia Wang & Aishan, sp. nov.-and five species newly recorded from China: P. (Doriclytus) alalatum Rehmat & Anis, 2016, P. (Doriclytus) bicolorigastra Rehmat & Anis, 2016, P. (Doriclytus) dhenkunde Mani & Saraswat, 1973, P. (Doriclytus) dunense Hayat & Anis, 1999, and P. (Doriclytus) tyakshiense Irfan & Anis, 2023. Comprehensive morphological descriptions and diagnostic illustrations are provided for all new taxa, with key diagnostic features detailed for the newly recorded species. Molecular analysis of COI sequences using both the Assemble Species by Automatic Partitioning (ASAP) and Generalized Mixed Yule Coalescent (GMYC) models yielded congruent species delimitation results, with genetic distances between delimited species showing maximum intraspecific divergence of 1.51% and interspecific divergences of 3-12% within the 470 bp COI barcode region. The deposition of 32 novel COI sequences in GenBank significantly enhances molecular resources for Mymaridae systematics.},
}

@article {pmid41302893,
year = {2025},
author = {Liang, F and Zeng, W and Li, S and Liu, X},
title = {Species Delimitation in the Bark Louse Genus Neostenopsocus Liang & Liu, 2024 (Psocodea: Stenopsocidae) Based on DNA Barcoding.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111147},
pmid = {41302893},
issn = {2075-4450},
support = {32100362, 32200366//National Natural Science Foundation of China/ ; 23B0490//Scientific Research Fund of Hunan Provincial Education Department/ ; },
abstract = {The family Stenopsocidae exhibits a rich biodiversity in China, yet species identification based on morphological characters remains problematic due to insufficient study and absent molecular data. DNA barcoding has been widely employed for rapid species identification in insects, particularly through standardized COI gene sequencing. In this study, we conducted species delimitation for Neostenopsocus in China based on the morphological characters and DNA barcodes, comprising 20 morphological species with 110 barcodes. We redescribed 13 species from China and proposed 39 new synonyms. This study supports the applicability of DNA barcoding for species identification in Neostenopsocus. The K2P distance between the morphological species of Neostenopsocus ranges from 0.0051 to 0.2040, with most exceeding 0.10. The maximum intraspecific divergence reaches 0.0778 in N. nepalensis. The external morphology of Neostenopsocus shows considerable structural uniformity, and the genitalia provide limited diagnostic value for species identification. Instead, the marking patterns of the head and forewing are considered to be useful for species identification. Therefore, delimiting closely related species demands an integrated taxonomy approach that combines extensive geographical sampling, detailed morphological analysis, and nuclear DNA data.},
}

@article {pmid41302869,
year = {2025},
author = {Toševski, I and Caldara, R and Jović, J and Baviera, C and Ugarte San Vicente, I and Krstić, O},
title = {An Integrative Revision of the Genus Rhamphus (Curculionidae) from the Western Palearctic: Morphological and Molecular Data Reveal the Radiation of Multiple Species.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111123},
pmid = {41302869},
issn = {2075-4450},
support = {451-03-136/2025-03/200010//Ministry of Science, Technological Development, and Innovation of the Republic of Serbia/ ; },
abstract = {Here, we report on the complexity of the taxonomy and species evolution within the monophyletic genus Rhamphus, which includes some of the smallest members of the Curculionidae family and whose species are morphologically almost indistinguishable from each other. Despite their similar appearance, we found high divergence and varying evolutionary rates among observed species groups living both in sympatry and allopatry in the western Palearctic. On the basis of subtle morphological differences and molecular evidence, we defined eight morphotypic groups and 14 species, of which 6 are newly described in this paper: R. diottiisp. nov. and R. ibericussp. nov. (monzinii-group), R. cypricussp. nov. and R. macedonicussp. nov. (cypricus-group), R. betulaesp. nov. and R. crypticussp. nov. (pulicarius group). Rhamphus morphotypic groups showed intense species radiation and cryptic speciation, with an estimated genetic divergence of 4.2-18.8% (uncorrected) in the barcoding region of the mitochondrial COI gene. The estimated divergence of the two nuclear markers, nEF-1α and nCAD, ranged from 1 to 11.9% and 0.5 to 15%, respectively. Phylogenetic analyses using both single and partitioned multigene adequately resolved the relationships between Rhamphus species and identified all groups and the species with high nodal support. According to our study, Rhamphus species cluster into monophyletic groups that are partly defined by their host plant associations and by subtle differences in penis shape. No substantial differences in female genitalia were found. Most of the species exhibit relatively rapid species radiation, which is cryptic by nature.},
}

@article {pmid41302845,
year = {2025},
author = {Xun, H and Jiang, K and Zhu, W},
title = {Review of the Genus Mictis (Hemiptera: Heteroptera: Coreidae: Coreinae) from China, with Description of a New Species.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111099},
pmid = {41302845},
issn = {2075-4450},
support = {32400356//Biological Resources Programme, Chinese Academy of Sciences, and National Natural Science Foundation of China/ ; },
abstract = {Species of the genus Mictis Leach, 1814, notable for their large body size and wide distribution, have attracted significant attention in physiological and phylogenetic studies. However, taxonomic issues surrounding these insects have long been overlooked, with the validity and taxonomic status of several species remaining unresolved. This study systematically reviews the nomenclatural and taxonomic issues of the genus Mictis within China, resulting in the proposal of two new synonyms and one new combination: Mictis serina (Dallas, 1852) = Mictis fuscipes (Hsiao, 1963) syn. n., Mictis longicornis (Westwood, 1842) = Mictis tuberosa (Hsiao, 1965) syn. n., and Ochrochira falloui (Reuter, 1888) comb. n. All known Mictis species from the region are diagnosed, and a new species, Mictis arcuatasp. n., is described. An identification key and DNA barcoding data for the Mictis species are provided. The intra-specific chromatic variation and distribution of the genus are also discussed.},
}

@article {pmid41302835,
year = {2025},
author = {Lukhtanov, VA},
title = {Integrative Taxonomic Analysis Doubles Number of Species in the Central Asian Butterfly Genus Lyela (Lepidoptera, Nymphalidae, Satyrinae).},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111089},
pmid = {41302835},
issn = {2075-4450},
support = {24-14-00047//Russian Science Foundation/ ; },
abstract = {Lyela Swinhoe, 1908 is a small Central Asian butterfly genus, in which three species were previously recognized based on comparison of wing patterns. The present study, based on an extensive population sample across the entire range of Lyela and using integrative taxonomy methods, confirmed the monophyly of the genus and revealed the paraphyly of the most widespread species, Lyela myops sensu auct. The genus is shown to include six species, L. myops (Staudinger, 1881) (Kazakhstan, northern Kyrgyzstan, northwestern China, and southwestern Mongolia), L. tashkumirica Lukhtanov, 2024, stat. nov. (Fergana Valley in Kyrgyzstan), L. babatagi Tshikolovets, 1998, stat. nov. (southern Uzbekistan and eastern Turkmenistan), L. tekkensis (Staudinger, 1886), stat. nov. (southwestern Turkmenistan and northeastern Iran), L. macmahoni Swinhoe, 1908 (Pakistan and Afghanistan), and L. amirica Wyatt, 1961 (Afghanistan). Each of these species represents a monophyletic unity with respect to the COI gene and is separated from the other species by a distinct barcoding gap and structural differences in the male genitalia.},
}

@article {pmid41300814,
year = {2025},
author = {Karbarz, M and Grzyb, F and Szlachcikowska, D and Leśko, A},
title = {Untangling Coelogyne: Efficacy of DNA Barcodes for Species and Genus Identification.},
journal = {Genes},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/genes16111361},
pmid = {41300814},
issn = {2073-4425},
support = {Agreement No. RID/SP/0010/2024/1.//Minister of Science of the Republic of Poland under the Program "Regional initiative of excellence"./ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; Phylogeny ; DNA, Plant/genetics ; Species Specificity ; },
abstract = {Background/Objectives: While morphological similarity and incomplete specimens pose a challenge to the precise identification of Coelogyne orchids, accurate species and genus assignment is essential for conservation and CITES enforcement. This study evaluated the efficacy of five DNA barcode regions-rbcL, matK, trnH-psbA, atpF-atpH, and ITS2-and their combinations for species- and genus-level discrimination within the genus Coelogyne, aiming to develop a rapid and simple diagnostic tool for use by customs officers and trade inspectors. This is the first comprehensive comparative analysis of these five barcode regions specifically within Coelogyne, a genus underrepresented in molecular identification studies, and the first to propose multi-locus combinations for potential practical use. This study identified DNA barcode regions with high resolution and reliability, providing a solid basis for practical identification kits. Such tools will enhance CITES enforcement by enabling rapid detection of Coelogyne species in trade, directly supporting their conservation and contributing to the reduction in illegal orchid trade. Methods: Using a CTAB protocol, genomic DNA was extracted from leaf samples belonging to 19 Coelogyne species. Sanger sequencing was performed after PCR amplification using published primer sets for every barcode region. Sequences were modified in BioEdit, and BLASTn (accessed 15 June 2025) was used to compare them to GenBank (NCBI Nucleotide). Amplification efficiency was calculated per locus. Species and genus identification success rates were determined by the congruence of top BLAST hits with morphologically pre-identified taxa. Multi-barcode combinations (matK + rbcL, ITS2 + matK, matK + trnH-psbA, rbcL + trnH-psbA, and matK + rbcL + trnH-psbA) were also assessed. Results: With rbcL, atpF-atpH, and ITS2 yielding ≤11%, the highest single-locus species identification rates were for trnH-psbA (21%) and matK (16%). Among single-locus barcodes, matK showed the highest performance, with 84% genus assignment. ITS2 reached 27%, but genus-level resolution remained limited for the rbcL, trnH-psbA and atpF-atpH barcodes. Multi-barcode approaches maintained species resolution: matK + rbcL + trnH-psbA, matK + rbcL, and matK + trnH-psbA correctly identified 16% of species and achieved 74-79% genus assignment. Conclusions: No single locus achieves robust species discrimination in Coelogyne, but trnH-psbA, matK and atpF-atpH provide the best single-marker performance. Using the matK locus alone, in combination with either trnH-psbA or rbcL, or all three together ensures consistent genus-level identification and significantly improves taxonomic resolution. This study introduces a novel multi-locus barcode strategy tailored to Coelogyne, offering a practical solution for identification and enforcement. While promising, this approach represents a potential application that requires further validation before routine implementation.},
}

*DNA Barcoding, Taxonomic/methods
*Orchidaceae/genetics/classification
Phylogeny
DNA, Plant/genetics
Species Specificity

@article {pmid41300785,
year = {2025},
author = {Chen, Z and Zeng, Q and Gong, M and Wu, H and Chen, W and Xu, X},
title = {DNA Barcoding Identification of Angelicae Sinensis Radix and Its Adulterants Based on Internal Transcribed Spacer 2 Region and Secondary Structure Prediction.},
journal = {Genes},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/genes16111333},
pmid = {41300785},
issn = {2073-4425},
support = {No. 2023YFD1601400//the National Key Research and Development Program for Young Scientists of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Angelica sinensis/genetics/classification ; *DNA, Ribosomal Spacer/genetics/chemistry ; DNA, Plant/genetics ; Nucleic Acid Conformation ; Drug Contamination ; },
abstract = {Background: Morphological similarities among Angelicae Sinensis Radix and related species often lead to market substitution. This study develops a DNA barcoding method to authenticate these herbs and identify adulterants derived from Angelica, Heracleum, and Peucedanum genera. Methods: Phylogenetic analysis was conducted using MEGA 11.0 software with ITS2 sequences from Angelicae Sinensis Radix, Ligusticopsis Pubescens Radix, Angelicae Pubescens Radix, and their related species within the genera Angelica, Peucedanum, and Heracleum. Additionally, ITS2 secondary structures were predicted for the three herbs to provide supplementary evidence for identification. Results: The amplification success rate was 86.67%, and the interspecific genetic distance, ranging from 0.009~0.220, was significantly greater than the intraspecific genetic distance range from 0.000~0.062, indicating that the ITS2 sequence is suitable for differentiating three herbs and their related species. Additionally, their ITS2 secondary structures exhibited significant differences, which can also serve as a reliable criterion for their identification. Conclusions: This study not only validated the identification efficacy of ITS2 sequences and their secondary structures for the three herbs, but more importantly, enabled precise traceability of adulterants through the construction of a comprehensive phylogenetic framework.},
}

*DNA Barcoding, Taxonomic/methods
Phylogeny
*Angelica sinensis/genetics/classification
*DNA, Ribosomal Spacer/genetics/chemistry
DNA, Plant/genetics
Nucleic Acid Conformation
Drug Contamination

@article {pmid41300772,
year = {2025},
author = {Xiang, P and Phua, YW and Rosli, AR and Loh, KJ and Syn, CK},
title = {Forensic Identification of Cannabis with Plant DNA Barcodes and Cannabinoid Synthesis Genes.},
journal = {Genes},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/genes16111320},
pmid = {41300772},
issn = {2073-4425},
mesh = {*Cannabis/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Cannabinoids/biosynthesis/genetics ; *DNA, Plant/genetics ; Humans ; Plant Proteins/genetics ; },
abstract = {Background/Objectives: According to the World Drug Report 2025, cannabis is the most abused drug in the world, being sold in illicit markets in various physical forms ranging from herbal cannabis to cannabis resin and liquid cannabis. Currently, the methods used for cannabis identification are largely based on the morphological features and chemical content of the product. In this respect, identification could be severely impacted if the product is highly fragmented or pulverised. As such, DNA-based molecular techniques offer a viable alternative detection approach. In this study, we have developed a robust DNA testing method for cannabis identification, with high sensitivity and specificity. Methods/Results: Two plant DNA barcode regions, rbcL and matK, were successfully amplified in a cohort of 54 cannabis plant samples. DNA sequences obtained from these samples were blast-searched against GenBank and resulted in returned matched identity of at least 99% compared to their corresponding Cannabis sativa reference sequences. In addition, the amplification of two cannabis-unique markers, the tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes, produced amplicons with expected sizes only in cannabis samples; these amplicons were not detected in those plants closely related to cannabis. Sequence comparison of the majority of samples yielded at least 97% matched identity against C. sativa reference sequences in GenBank. The THCAS and CBDAS markers detected only the cannabis DNA in varying levels of cannabis-hops and cannabis-tobacco DNA mixtures. Lastly, the use of the four markers could effectively differentiate between cannabis and non-cannabis in 27 blinded samples, including 18 actual casework samples. Conclusions: In conclusion, these four genetic markers can be used to discriminate cannabis from other plant species at the genus level, especially in challenging forensic samples lacking morphological features which therefore cannot be determined by traditional detection methods. As such, this method can complement existing techniques to identify a myriad of cannabis samples.},
}

*Cannabis/genetics/classification
*DNA Barcoding, Taxonomic/methods
*Cannabinoids/biosynthesis/genetics
*DNA, Plant/genetics
Humans
Plant Proteins/genetics

@article {pmid41300762,
year = {2025},
author = {Wang, Y and Xiang, Z and Liu, K and Lin, Y and Dong, S},
title = {Complete Chloroplast Genome and Phylogenomic Analysis of Davallia trichomanoides (Polypodiaceae).},
journal = {Genes},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/genes16111310},
pmid = {41300762},
issn = {2073-4425},
support = {QDZK112022022//National Natural Science Foundation of China Cultivation Project/ ; },
mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; *Polypodiaceae/genetics/classification ; Evolution, Molecular ; },
abstract = {Background/Objectives: Chloroplast genomes (plastomes) are valuable for fern systematics, yet the epiphytic lineages have remained underexplored. Methods: The Davallia trichomanoides plastome was de novo assembled from Illumina data and annotated. Results: The plastome measures 154,217 bp with a GC content of 40.82% and contains 115 genes. Comparative analysis reveals two inverted repeat (IR) size classes (~24.0-24.6 kb vs. ~27.4-27.5 kb) and lineage-specific shifts at the IR junctions. For instance, the ndhF gene remains in the small single copy (SSC) region in D. trichomanoides and Drynaria acuminata, but it crosses into the IRb region in other species. We observed nucleotide diversity hotspots in the large single copy (LSC) and SSC regions. The IR regions are highly conserved. The ratios of nonsynonymous to synonymous substitutions (Ka/Ks) are mostly less than 1, indicating purifying selection. Phylogenetic analysis places D. trichomanoides as the sister to D. acuminata. Conclusions: This study highlights the stable plastome structure of D. trichomanoides and identifies candidate loci for barcoding. It also supports the stable placement of Davallia within the epiphytic Polypodiineae.},
}

*Genome, Chloroplast/genetics
*Phylogeny
*Polypodiaceae/genetics/classification
Evolution, Molecular

@article {pmid41300739,
year = {2025},
author = {Yin, D and Li, X and Xiao, Z and Zhou, L},
title = {Chloroplast Genome Features and Phylogeny of Two Nationally Protected Medicinal Plants, Euchresta tubulosa and Euchresta japonica: Molecular Resources for Identification and Conservation.},
journal = {Genes},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/genes16111286},
pmid = {41300739},
issn = {2073-4425},
mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *Plants, Medicinal/genetics/classification ; Endangered Species ; DNA Barcoding, Taxonomic/methods ; },
abstract = {[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of E. tubulosa and E. japonica-two medicinal plants belonging to the genus Euchresta-this study aims to identify their differential genes, thereby providing fundamental research for screening candidate genes as DNA barcodes for species identification and facilitating the conservation of these endangered species. [Methods]: Illumina PE150 sequencing was performed. Chloroplast genomes (plastomes) were assembled and annotated with GetOrganelle/SPAdes. Comparative analyses assessed gene content, IR/LSC/SSC structure, repeat profiles, and codon-usage bias. Using related Fabaceae as references, we conducted mVISTA alignments and sliding-window nucleotide diversity (Pi) analyses to identify candidate DNA barcodes. Phylogenies from whole-plastome sequences were inferred with Maximum Likelihood, Bayesian Inference, and Maximum Parsimony. [Results]: The plastomes measured 153,960 bp (E. japonica) and 150,146 bp (E. tubulosa), with GC contents of 36.30% and 36.20%, respectively, each exhibiting a typical quadripartite structure. IR/SC boundaries were highly conserved without evident expansion or contraction. Repeat statistics were 20/30 palindromic repeats, 57/64 tandem repeats, and 156/159 simple sequence repeats (SSRs) in E. japonica/E. tubulosa, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci-rps19, psbA, trnK, matK, and rps16 (Pi > 0.03)-were identified as candidate DNA barcodes. All trees consistently placed both species within Papilionoideae (Fabaceae) and recovered the closest relationship to Sophora macrocarpa. [Conclusions]: This study provides, for the first time, complete plastomes and candidate barcoding regions for two protected Euchresta species, supplying foundational resources for species identification, resource assessment, and conservation planning.},
}

*Genome, Chloroplast/genetics
Phylogeny
*Plants, Medicinal/genetics/classification
Endangered Species
DNA Barcoding, Taxonomic/methods

@article {pmid41299646,
year = {2025},
author = {Bunchom, N and Saijuntha, W and Andrews, RH and Agatsuma, T and Valencia, J and Revolteado, MJ and Prasayasith, P and Soundala, P and Sannikone, S and Hansana, P and Sato, MO and Banouvong, V and Buchy, P and Iwagami, M},
title = {Molecular insights into seasonal trematode infections in Bithynia Snails: host lineages, parasite diversity, and Opisthorchis viverrini susceptibility in southern Lao PDR.},
journal = {Tropical medicine and health},
volume = {53},
number = {1},
pages = {173},
pmid = {41299646},
issn = {1348-8945},
support = {Grant No. 6518003/2565//Mahasarakham University/ ; Grant No. JP25jm0110028; 2022-2028//Japan International Cooperation Agency (JICA) and the Japan Agency for Medical Research and Development (AMED) through the SATREPS project, titled "Project for Malaria and Neglected Parasitic Diseases Control and Elimination using Advanced Research Technique, Communication Tools, and Eco-Health Education"/ ; },
abstract = {BACKGROUND: Opisthorchiasis, caused by Opisthorchis viverrini, is a major public health concern in Southeast Asia. Despite control programs, O. viverrini infection persists and contributes to severe liver diseases, including cholangiocarcinoma. This study aimed to assess seasonal variation in trematode prevalence and diversity, evaluate the susceptibility of Bithynia siamensis sensu lato lineages II and III to O. viverrini infection, and examine the phylogenetic and haplotype network of identified trematode and their snail hosts in Champasak Province, southern Lao PDR.

METHODS: Snail samples were collected quarterly in 2024 (February, May, August, and November) from Khong and Mounlapamok Districts using handpicking and scooping. Trematode infections were detected by the crushing method, identified morphologically, and confirmed by molecular analysis. DNA barcoding of nuclear and mitochondrial genes was used to verify trematode species and snail lineages.

RESULTS: Of 1,764 Bithynia snails examined, 169 (9.58%) were infected. Five cercarial types were identified: amphistome (3.40%), xiphidiocercariae (2.78%), monostome (2.61%), mixed monostome and amphistome (0.34%), cystophorous (0.28%), and O. viverrini (0.17%). Infection rates of O. viverrini did not differ between lineages II and III, but other trematodes were significantly more frequent in lineage III (76.67%).

CONCLUSIONS: Trematode infection rates and species diversity in B. s. goniomphalos show marked seasonal variation in Champasak Province, southern Lao PDR. These findings highlight the complexity of host-parasite interactions and the role of environmental factors shaping transmission, providing insights for targeted prevention and control.},
}

@article {pmid41297683,
year = {2025},
author = {Zheng, M and Zhao, Y and Gao, M and Huang, M and Song, X},
title = {Chloroplast structure, codon usage bias, and machine learning-based molecular identification using DNA barcoding of Sophorae Tonkinensis Radix et Rhizoma(Shan Dou gen) and its analogues.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {107005},
doi = {10.1016/j.fitote.2025.107005},
pmid = {41297683},
issn = {1873-6971},
abstract = {To investigate the complete chloroplast genome sequences and codon usage bias of "Shan Dou Gen" (Sophorae Tonkinensis Radix et Rhizoma) and its six easily confused species, analyze their evolutionary patterns, and evaluate the identification efficiency of four DNA barcodes combined with two machine learning methods for these seven plant species. Chloroplast gene structures of the seven species were aligned to construct phylogenetic trees. Codon usage bias was analyzed using CodonW and CUSP. Genetic distances were calculated based on the Kimura-2-Parameter model to assess the barcoding gap and reconstruct phylogenetic trees.Species discrimination capabilities of four DNA barcodes (ITS2, matK, psbA-trnH, and rbcL) were compared. Species identification was performed using BLOG and WEKA machine learning algorithms. Single-nucleotide SSRs predominated in chloroplast genomes, primarily composed of A/T bases. Complete species differentiation was achieved using cpDNA. Natural selection was the primary factor influencing codon usage bias, followed by mutation pressure. Among synonymous codons, A > T and G > C in base composition, with optimal codons ending in A/U at the third position across all seven species. All four DNA barcodes successfully discriminated Shandougen from its confusable species. The BLOG algorithm achieved >85 % identification accuracy, outperforming WEKA. This research provides a theoretical foundation for ensuring clinical medication safety, elucidating plant phylogeny, facilitating species identification, and guiding resource conservation and utilization of Shandougen and its analogues.},
}

@article {pmid41296748,
year = {2025},
author = {Prudente, ALC and Silva, FM and Santos, MMD and Vasconcelos, S and Rojas-Runjaic, FJM and Becerra-Rondón, AC and Maciel, AO and Sarmento, JF and Graboski, R and Teixeira, C and Guimarães, AC and Nascimento, A and Oliveira, AMS and Molina, M and Silva, P and Carvalho Neto, CS and Nunes, GL},
title = {Unraveling the herpetofauna diversity in canga and forest ecosystems of the Eastern Amazon.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0332753},
pmid = {41296748},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Brazil ; *Forests ; *Reptiles/genetics/classification ; *Amphibians/genetics/classification ; Phylogeny ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Conservation of Natural Resources ; Lizards/genetics/classification ; },
abstract = {Species inventories are essential for discovering new taxa, improving knowledge of species' geographic distributions, characterizing local richness, evaluating biodiversity loss, and contributing to the conservation of endangered areas, including those with endemic and rare species. The southeastern region of Pará, Brazil, encompasses a transitional zone between the Amazon and Cerrado biomes, marked by a mosaic of natural environments with high variability in relief, substrates, and geological attributes. We conducted a comprehensive survey of the region's herpetofauna, combining taxonomic surveys with molecular characterization, with a particular focus on species associated with savanna-like environments known as canga. We selected four sampling sites: one within the Serra dos Carajás mosaic of protected areas and three in the surrounding region, including São Geraldo do Araguaia, Conceição do Araguaia, and Ourilândia do Norte/São Félix do Xingu. Our inventory recorded a total of 242 species (99 amphibians and 143 squamate reptiles), including ten new records for the state of Pará and two notable range extensions. We also generated a DNA barcode reference library of 860 sequences (436 COI and 424 16S rRNA) from 500 specimens. Approximately 58.4% of amphibian species and 32.2% of squamate reptile species were supported by at least one reference barcode. Our dataset includes five novel COI and two novel 16S rRNA records for amphibians, and 25 novel COI and 13 novel 16S rRNA records for squamate reptiles.},
}

Animals
*Biodiversity
Brazil
*Forests
*Reptiles/genetics/classification
*Amphibians/genetics/classification
Phylogeny
DNA Barcoding, Taxonomic
RNA, Ribosomal, 16S/genetics
Ecosystem
Conservation of Natural Resources
Lizards/genetics/classification

@article {pmid41295111,
year = {2025},
author = {Sun, Y and Wang, J and Yin, R},
title = {RepSAU-Net: Semantic Segmentation of Barcodes in Complex Backgrounds via Fused Self-Attention and Reparameterization Methods.},
journal = {Journal of imaging},
volume = {11},
number = {11},
pages = {},
pmid = {41295111},
issn = {2313-433X},
abstract = {In the digital era, commodity barcodes serve as a bridge between the physical and digital worlds and are widely used in retail checkout systems. To meet the broader application demands for product identification, this paper proposes a method for locating, semantically segmenting barcodes in complex backgrounds, decoding hidden information, and recovering these barcodes in wide field-of-view images. This method integrates self-attention mechanisms and reparameterization techniques to construct a RepSAU-Net model. Specifically, this paper first introduces a barcode image dataset synthesis strategy adapted for deep learning models, constructing the SBS (Screen Stego Barcodes) dataset, which comprises 2000 wide field-of-view background images (Type A) and 400 information-hidden barcode images (Type B), totaling 30,000 images. Based on this, a network architecture (RepSAU-Net) combining a self-attention mechanism and RepVGG reparameterization technology was designed, with a parameter count of 32.88 M. Experimental results demonstrate that this network performs well in barcode segmentation tasks, achieving an inference speed of 4.88 frames/s, a Mean Intersection over Union (MIoU) of 98.36%, and an Accuracy (Acc) of 94.96%. This research effectively enhances global information capture and feature extraction capabilities without significantly increasing computational load, providing technical support for the application of data-embedded barcodes.},
}

@article {pmid41294086,
year = {2026},
author = {Vu, D and de Vries, M and van den Ende, BG and Houbraken, J and Nilsson, RH and Brankovics, B and Hernández-Restrepo, M and Groenewald, JZ and Crous, PW and Hagen, F and Meyer, W and Verkley, GJM and Groenewald, M},
title = {Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70082},
doi = {10.1111/1755-0998.70082},
pmid = {41294086},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Yeasts/classification/genetics/isolation & purification ; DNA, Fungal/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Yeast identification is essential in fields ranging from microbiology and biotechnology to food science and medicine. While DNA barcoding has become the standard for identifying cultured strains, environmental DNA (eDNA) metabarcoding has revolutionised microbial community profiling, providing deeper insights into yeast communities across diverse ecosystems. A major challenge in DNA (meta)barcoding remains the limited availability of high-quality reference sequences, which are critical for accurate species identification and comprehensive taxonomic profiling of both environmental and clinical samples. To address this gap, the Westerdijk Fungal Biodiversity Institute (WI) launched a DNA barcoding initiative in 2006 to generate high-quality, often type-derived ITS and LSU barcodes for all ~100,000 fungal strains preserved in the CBS culture collection, including approximately 15,000 yeasts. Building on the yeast barcode dataset released in 2016, we now present an expanded set of 2856 ITS and 3815 LSU sequences, representing 911 and 1137 yeast species, respectively. Notably, 27%-29% of these sequences are derived from ex-type cultures. Using both newly generated and previously published barcodes, we assess the taxonomic resolution of commonly used yeast metabarcoding markers (ITS, ITS1, ITS2 and LSU) and propose marker-specific similarity cutoffs for different yeast taxonomic groups. These results provide actionable guidance for marker selection and improve the interpretation of metabarcoding data. We further demonstrate the impact of well-curated reference databases with up-to-date taxonomy by reanalyzing Human Microbiome Project data, revealing how diet and environment shape the gut mycobiota.},
}

*DNA Barcoding, Taxonomic/methods
*Yeasts/classification/genetics/isolation & purification
DNA, Fungal/genetics/chemistry
High-Throughput Nucleotide Sequencing/methods
DNA, Ribosomal Spacer/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41292861,
year = {2025},
author = {Unverdorben, LV and Mason, S and Wu, W and Noda, M and Castaneda, S and Vornhagen, J and Snitkin, ES and Rao, K and Bachman, MA},
title = {A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.686704},
pmid = {41292861},
issn = {2692-8205},
abstract = {UNLABELLED: Klebsiella pneumoniae and related species are a common cause of healthcare-associated infections. The gut is a major Klebsiella reservoir and gut colonization is a risk factor for developing an extraintestinal Klebsiella infection. Patients can be colonized by multiple Klebsiella strains or even species in the gut simultaneously, and there is high concordance between the gut colonizing- and infection causing-strains. The detection and characterization of colonizing strains is critical for a better understanding of the progression to infection and for developing interventions for colonized patients. However, the association between mixed or mono-colonization and subsequent infection is unknown. In this study, we developed an amplicon-based sequencing method called wzi -Seq that enables the detection and quantification of Klebsiella strains from complex samples and mixtures using the conserved capsule gene wzi as a molecular barcode. This method is highly accurate and precise with a sensitivity of 93% and specificity of 99.8% in mixtures containing as many as 58 unique wzi types. The assay was validated analytically and applied to an established case and control cohort. We determined that 63.2% (108/171) patients were mono-colonized with a single Klebsiella strain while 36.8% (63/171) had mixed colonization with multiple Klebsiella strains. Controlling for patient variables in multivariate analysis, we determined that mono-colonization was significantly (p = 0.034) associated with infection. Characterization of Klebsiella colonizing populations could improve the accuracy of assessing infection risk and enable targeted interventions to prevent these healthcare-associated infections.

IMPORTANCE: Klebsiella gut colonization is a major risk factor the development of extraintestinal Klebsiella infections in hospitalized settings. However, it is unknown if patients are colonized by one or multiple strains of Klebsiella and how the population structure of Klebsiella in the gut impacts infection risk. Here we describe the development of a novel technique, wzi -Seq, to detect and quantify multiple Klebsiella strains from complex samples using standard techniques and rapid DNA sequencing. We applied wzi -Seq to rectal swabs from a well-characterized patient cohort and found that Klebsiella colonization with a single strain was more prevalent than colonization with multiple strains. Furthermore, mono-colonized patients had a significantly higher risk of developing a Klebsiella infection than mixed colonized patients. This work validates a new tool to study Klebsiella populations and reveals that population structure in the gut influences the risk of healthcare associated infections.},
}

@article {pmid41292775,
year = {2025},
author = {Stuart, H and McKenna, A},
title = {SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage trees.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.12.688020},
pmid = {41292775},
issn = {2692-8205},
abstract = {Understanding the evolutionary dynamics of clonal populations is essential for uncovering the principles of development, disease progression, and therapeutic resistance. Recent advances in single-cell lineage tracing and transcriptomics enable such analyses by combining heritable barcodes with cell-state information. Here, we present SCOUT (s ingle- c ell O rnstein- U hlenbeck t rees), a framework that models gene expression dynamics along single-cell lineage trees using Ornstein-Uhlenbeck processes to distinguish neutral drift from selective pressure. Using simulations, we demonstrate that SCOUT accurately classifies genes based on their underlying evolutionary models. We further validate SCOUT in Caenorhabditis elegans development, identifying biological processes under selection across distinct developmental contexts. Finally, we apply SCOUT to a lung adenocarcinoma xenograft model, revealing key regulators of metastatic progression and tumor microenvironmental adaptation. By integrating lineage and transcriptomic data, SCOUT provides a powerful evolutionary lens for dissecting the forces that shape cell fate.},
}

@article {pmid41292737,
year = {2025},
author = {Choudhary, K and McManus, MT},
title = {Scalable imaging-based profiling of CRISPR perturbations with protein barcodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.11.687767},
pmid = {41292737},
issn = {2692-8205},
abstract = {Imaging-based CRISPR screens enable high-content functional genomics by capturing phenotypic changes in cells after genetic perturbation. Protein barcodes provide cost-effective, easy-to-implement, and imaging-compatible barcoding for pooled perturbations, yet their scalability has been constrained by the need for arrayed cloning, lentiviral recombination between barcodes and guides, and difficulties in decoding barcodes with high confidence. Here, we introduce poolVis and cellPool, an integrated experimental and computational platform designed to address these limitations. poolVis uses Cre-lox-mediated reconfiguration to position barcode-sgRNA pairs in proximity during viral integration, which greatly reduces barcode shuffling during pooled cloning and delivery. cellPool leverages a scalable computational workflow and the unique aspects of protein barcodes to produce unpooled image galleries from multi-terabyte scale datasets. Applying this platform to single- and double-CRISPRi profiling of cell-cycle genes and chromokinesins in the MCF10A cells uncovered established and previously unrecognized phenotypes, including nuclear morphology changes and reciprocal sign epistasis in DNA damage.},
}

@article {pmid41292433,
year = {2025},
author = {Lan, F and Chen, A and Ding, Y and Yang, C and Zhang, P and Fang, X},
title = {Sensitive and Specific Analysis of miRNAs in Single Tumor-Derived Extracellular Vesicles Using CRISPR-Based Nanoflow Cytometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c04700},
pmid = {41292433},
issn = {1520-6882},
abstract = {Tumor-derived extracellular vesicle (TEV) microRNAs (miRNAs) are promising cancer biomarkers but pose detection challenges due to their low abundance and sequence homology. Here, we present a CRISPR/Cas13a-based nanoflow cytometry (nFCM) platform integrated with a DNA-guided orthogonal membrane fusion strategy for ultrasensitive miRNA detection of TEVs at the single particle level. TEVs were identified with aptamers against CD63 and EpCAM markers to create an orthogonal barcode-anchored TEV (Orth-TEV). Meanwhile, liposomes preloaded with CRISPR/Cas13a molecular sensing components were modified with cholesterol-tagged DNA probes to produce Tags-CRISPR/Cas13a@Lipo. The complementary DNA sequences on the Orth-TEV and Tags-CRISPR/Cas13a@Lipo vesicles facilitated zipper-like hybridization, thereby achieving specific membrane fusion to effectively eliminate the interference of nontarget vesicles or free molecules. The resulting TEV-CRISPR/Cas13a@Lipo vesicles allow in situ detection of three prostate cancer (PCa)-associated miRNAs in a single TEV via nFCM with a low detection limit (LOD) of 14.7 (miR-153), 16.0 (miR-183), and 23.7 (miR-940) particles/mL, respectively. The approach was further applied to plasma samples from PCa patients and healthy donors, showing significantly elevated miRNA signals in PCa-derived TEV. ROC analysis yielded AUC values of 0.931, 0.923, and 0.869 for the three target miRNAs, confirming excellent diagnostic performance. To enhance classification accuracy, we conducted a statistical multivariate analysis based on the PCA-LDA model, which achieved perfect group separation and a diagnostic accuracy of 91.3%. Overall, this CRISPR/Cas13a-based nFCM platform offers a robust, accurate, and clinically applicable platform for single-vesicle miRNA profiling with broad potential in liquid biopsy-based cancer diagnosis.},
}

@article {pmid41290749,
year = {2025},
author = {Silva, MI and Viegas, MB and Sousa, F and Gordo, LS and Paulo, OS and Vieira, AR},
title = {Identification of tuna species used by the Portuguese canning industry through a DNA-based approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41802},
pmid = {41290749},
issn = {2045-2322},
support = {CEECIND/01528/2017//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Tuna/genetics/classification ; Portugal ; *DNA Barcoding, Taxonomic/methods ; Seasons ; *Food Preservation/methods ; Seafood ; Fisheries ; *DNA/genetics ; Species Specificity ; },
abstract = {Despite the popularity of canned tuna in Portugal, limited research has explored how tuna species vary across brands and seasons. Accurate species identification is crucial to preserve both the economy and ecology of global tuna fisheries, as mislabelling and the use of certain species can have far-reaching implications. Our study analysed the diversity of tuna species used by the Portuguese tuna canning industry, focusing on brand-specific and seasonal variations, using molecular barcoding methods. In this industry, the occurrence of different species was observed only in products using water as a preservation medium. Skipjack tuna was predominant across all preservation media and brands analysed. Nonetheless, other species like Thunnus obesus and T. albacares, or Auxis spp. (not considered true tuna) were also detected. The use of different species was limited to cans produced during the second quarter of the year, which could reflect differences in seasonal availability of different tuna species or in sourcing strategies/market preferences of each company. Finally, more than one species was detected inside the same container in four brands, violating current European legislation. These results provide the first broad assessment of species used in the Portuguese tuna canning industry and showed the inclusion of vulnerable species is limited.},
}

Animals
*Tuna/genetics/classification
Portugal
*DNA Barcoding, Taxonomic/methods
Seasons
*Food Preservation/methods
Seafood
Fisheries
*DNA/genetics
Species Specificity

@article {pmid41290175,
year = {2025},
author = {Pakrashi, A and Thompson, KA and Hebert, PDN},
title = {Haplodiploidy accelerates mitogenome evolution in insects.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2059},
pages = {20251813},
doi = {10.1098/rspb.2025.1813},
pmid = {41290175},
issn = {1471-2954},
support = {//Canada Foundation for Innovation (MSI)/ ; //Ontario Ministry of Colleges and Universities/ ; //Government of Canada through Genome Canada and Ontario Genomics/ ; //The New Frontiers in Research Fund/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *Insecta/genetics ; *Evolution, Molecular ; Phylogeny ; *Diploidy ; *Haploidy ; Electron Transport Complex IV/genetics ; },
abstract = {Rates of mitogenome evolution differ among animal lineages, and this variation has been linked to life history, to ecological traits and-potentially-to the sex-determination system. Insects are a compelling model for examining the latter factor because haplodiploid (HD) has evolved on multiple occasions from a diplodiploid (DD) ancestral state. We tested for rate differences between DD and HD taxa by examining sequence change in a sentinel segment of the mitogenome, the 658 bp barcode region of the cytochrome c oxidase subunit I (COI) gene. Specifically, we investigated if amino acid substitutions and indels are more frequent in HD than DD lineages by inspecting COI sequences from over 86 000 BINs (a species proxy) representing 783 insect families and 26 orders. Among them, 10 lineages, varying in rank from tribe to order, are HD. Our analysis, which accounts for phylogeny, indicates that HD lineages have higher rates (1.7×) of amino acid substitution, higher Ka/Ks (3.5×) and far more indels than DD taxa. While our results demonstrate that HD accelerates mitogenome evolution, future work is needed to clarify its mechanistic basis. We hypothesize that HD facilitates positive selection for mitochondrial mutations which encode proteins that interact with nuclear gene products. Such coevolutionary interactions should be facilitated because recessive mutations in the nuclear genome are fully exposed to selection in males of the HD but not the DD lineages.},
}

Animals
*Genome, Mitochondrial
*Insecta/genetics
*Evolution, Molecular
Phylogeny
*Diploidy
*Haploidy
Electron Transport Complex IV/genetics

@article {pmid41288610,
year = {2025},
author = {Shu, L and Zhuang, D and Tang, J and Zhao, J and Shao, W and Guan, X and Zhang, D},
title = {DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
pmid = {41288610},
issn = {1367-4811},
support = {62136004//National Natural Science Foundation of China/ ; 62276130//National Natural Science Foundation of China/ ; 2023YFF1204803//National Key R&D Program of China/ ; BE2022842//Key Research and Development Plan of Jiangsu Province/ ; },
mesh = {*Nanopore Sequencing/methods ; *Deep Learning ; *Sequence Analysis, RNA/methods ; *Software ; Nanopores ; },
abstract = {MOTIVATION: Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches struggle to accurately demultiplex raw nanopore signals, failing to capture both local patterns and long-range dependencies. This limitation underscores the requirement for advanced solutions to improve accuracy, efficiency, and adaptability in sequencing workflows. We present DemuxTrans, a hybrid deep learning framework that integrates Multi-Layer Feature Fusion, Transformers, and Temporal Convolutional Networks (TCN) for precise barcode demultiplexing.

RESULTS: DemuxTrans achieves state-of-the-art performance across multiple datasets by effectively balancing local feature extraction, global context modeling, and long-term dependency capture, excelling in metrics such as accuracy, recall and F1-score. These results demonstrate DemuxTrans as a scalable, efficient solution for barcode demultiplexing in nanopore sequencing, enabling precise identification of multiplexed RNA samples and improving throughput in transcriptomic and epigenomic analyses.

The code and datasets are publicly available on https://github.com/LiyuanShu116/Demuxtrans.},
}

*Nanopore Sequencing/methods
*Deep Learning
*Sequence Analysis, RNA/methods
*Software
Nanopores

@article {pmid41288389,
year = {2025},
author = {Taheri, S and Schwarzkopf, E and Berman, HL and Brandt, N and McNeill, J and Sevier, N and Ruffieux, M and Dunn, RR and Smukowski Heil, C},
title = {The role of flour type and feeding schedule on the sourdough microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238025},
doi = {10.1128/spectrum.02380-25},
pmid = {41288389},
issn = {2165-0497},
abstract = {Sourdough starters are fermentations of various grains by bacteria and yeast and are of worldwide economic and cultural importance. Sourdoughs are sometimes spontaneously inoculated, and their resident microbial communities are in part shaped by environmental factors, potentially including flour, water, air, human microbiota, equipment, geography, and temperature. The number of different genera of bacteria and yeast found in sourdoughs is large; however, only a handful of species typically dominate an individual sourdough starter. Understanding how and why certain species form a mature climax community in a particular environment is a key question in microbial ecology. To investigate this question, we used a meta-barcoding approach and tested whether different baking flours (all-purpose, bread, and whole wheat) and frequency of feeding, also known as backslopping, shape the sourdough starter microbial community over the course of one month. We found that the yeast genus Kazachstania rapidly rose in frequency and became the most abundant yeast in all starters, regardless of flour type or feeding schedule. In contrast, flour type did affect the bacterial community. Mature sourdoughs all contained the bacterial genera Companilactobacillus, Levilactobacillus, Lactiplantibacillus, Furfurilactobacillus, and Acetobacter, with Companilactobacillus detected at higher relative abundance in whole wheat flour and Levilactobacillus detected at higher relative abundance in bread flour. We conclude that flour can shape the microbial community of sourdough and has potential implications for functional traits.IMPORTANCEHow organisms disperse and colonize new environments is central to our understanding of biodiversity. Sourdough, the often spontaneously inoculated fermentation of grains by bacteria and yeast, represents a great system to test and observe how microorganisms come to inhabit a particular niche. In our study, we investigate how environmental parameters such as flour type and feeding frequency influence the microbial community. We find that the common sourdough yeast genus Kazachstania is most abundant in all starters regardless of treatment, but we also find a significant effect of flour type on the lactic acid bacteria composition of the sourdough starters. This work shows how the environment can impact the presence and abundance of particular microorganisms and prompts future studies to test how particular lactic acid bacteria species can specialize on certain resources.},
}

@article {pmid41288263,
year = {2025},
author = {Creedy, TJ and Ding, Y and Gregory, KM and Swaby, L and Zhang, F and Vogler, AP},
title = {Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf031},
pmid = {41288263},
issn = {1076-836X},
support = {//NHM Biodiversity Initiative (2013-2017)/ ; //iBioGen consortium/ ; 810729//EU Horizon 2020/ ; //Chinese Scholarship Council/ ; IAF-2018-038//Leverhulme International Fellowship/ ; },
abstract = {Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank's Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.},
}

@article {pmid41284889,
year = {2025},
author = {Shang, F and Nizharadze, T and Thiele, R and Cirovic, B and Frank, L and Busch, K and Pei, W and Feyerabend, TB and Höfer, T and Wang, X and Rodewald, HR},
title = {Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2505510122},
doi = {10.1073/pnas.2505510122},
pmid = {41284889},
issn = {1091-6490},
support = {32170742 and 92374117//MOST | National Natural Science Foundation of China (NSFC)/ ; SFB 873-B11//Deutsche Forschungsgemeinschaft (DFG)/ ; SFB 873-B11//Deutsche Forschungsgemeinschaft (DFG)/ ; Helmholtz I & I Initiative program//Helmholtz Association ()/ ; Leibniz Award//Deutsche Forschungsgemeinschaft (DFG)/ ; Advanced Grant 742883//EC | European Research Council (ERC)/ ; },
mesh = {Animals ; *Hematopoietic Stem Cells/cytology/metabolism ; *Cell Lineage ; Mice ; *Transcriptome ; *Multipotent Stem Cells/cytology/metabolism ; *Hematopoiesis/physiology ; Cell Differentiation ; Biomarkers/metabolism ; Mice, Inbred C57BL ; },
abstract = {Multipotent progenitors (MPP) are the quantitative source of native hematopoiesis that have been thought to be replenished slowly by hematopoietic stem cells (HSC). However, recent fate mapping studies have revealed two developmentally distinct populations of MPP, HSC-derived MPP (hMPP), and HSC-independent, embryonic MPP (eMPP). These data raise fundamental questions on the distinctions and functions of these progenitors. Here, we mapped the clonal dynamics of the two independent MPP systems, using in situ barcoding, and barcode linkage (hMPP), or disconnect (eMPP), with HSC. The cumulative output of eMPP to hematopoiesis was 35%, and their output was enriched for lymphoid fates. Conversely, hMPP output was enriched for myeloid-restricted fates. Distinguishing HSC from eMPP outputs revealed that only ~15% of adult HSC clones underwent multilineage differentiation (lymphoid, myeloid, and erythroid). To prospectively identify eMPP, we developed PolySMART for joint profiling of PolyloxExpress RNA barcodes, surface markers, and transcriptomes, and we found that the plasma cell marker CD138 enriches for eMPP. CD138[+] MPP are primed for self-renewal and toward lymphoid fate, and become largely but not completely replaced by CD138[-] MPP over time, which may contribute to the loss of lymphoid output with age. Taken together, adult hematopoiesis consists of two distinct lineage trees. The source of the "eMPP tree" substantially contributes to hematopoiesis before it declines, while the HSC-hMPP tree supplies hematopoiesis life-long. Our molecular determinants distinguishing the two MPP systems may open avenues to further explore these unexpected layers of hematopoiesis.},
}

Animals
*Hematopoietic Stem Cells/cytology/metabolism
*Cell Lineage
Mice
*Transcriptome
*Multipotent Stem Cells/cytology/metabolism
*Hematopoiesis/physiology
Cell Differentiation
Biomarkers/metabolism
Mice, Inbred C57BL

@article {pmid41282751,
year = {2025},
author = {Fu, Y and English, AC and Paulin, LF and Jhangiani, SN and Weissenberger, G and Vee, V and Han, Y and Mehta, HH and Muzny, DM and Gibbs, RA and Posey, JE and Calame, DG and Sedlazeck, FJ},
title = {Enriching for Answers in Rare Diseases.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.21.25338483},
pmid = {41282751},
abstract = {We present Trio-barcoded ONT Adaptive Sampling (TBAS), a cost-efficient long-read sequencing strategy combining sample barcoding and adaptive enrichment to sequence rare-disease trios on a single PromethION flow cell. TBAS achieved near-complete variant phasing and detection of small variants, structural variants, and tandem repeats with high accuracy and 77% potential solve rate. This scalable approach retains methylation data and enables clinically relevant, phenotype-guided long-read diagnostics at a fraction of current costs.},
}

@article {pmid41282438,
year = {2025},
author = {Jin, YL and Bu, Y},
title = {Four new species of Symphylella (Symphyla, Scolopendrellidae) from Chongqing, southwest China with DNA barcoding analysis.},
journal = {ZooKeys},
volume = {1259},
number = {},
pages = {349-379},
pmid = {41282438},
issn = {1313-2989},
abstract = {The symphylans from Chongqing, Southwest China were investigated and studied for the first time. Four new species of the genus Symphylella, S. obtusa sp. nov., S. yintiaolingensis sp. nov., S. flabella sp. nov., and S. micropora sp. nov., are identified and described. They were compared with similar species in detail. The DNA barcodes for all new species were sequenced and analyzed together with other congeners and the genetic distance analysis further support our morphological determination. In addition, two groups, the isabellae group and oligosetosa group, of the genus Symphylella are proposed based on the pattern of inserted setae on the tergal processes, and their respective species are listed.},
}

@article {pmid41282325,
year = {2025},
author = {},
title = {Correction to Application of Invertebrate-Derived DNA Barcoding (iDNA) in Blood-Sucking Leeches From West Sumatra: A Discovery of Blue-Eyed Litter Frog Leptobrachium waysapuntiense.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72553},
doi = {10.1002/ece3.72553},
pmid = {41282325},
issn = {2045-7758},
abstract = {[This corrects the article DOI: 10.1002/ece3.72235.].},
}

@article {pmid41280501,
year = {2025},
author = {Kamra, J and Saini, P and Prakash, O and Kumar, V and Tiwari, R},
title = {A comprehensive review on biotechnological approaches for improvement of medicinal plants: techniques for qualitative and quantitative production.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {435},
pmid = {41280501},
issn = {2190-572X},
abstract = {Recent advancements in biotechnology have opened new avenues for enhancing both the qualitative and quantitative production of medicinal plants. This review highlights various genetic modification approaches, including transgenesis, recombinant DNA technology (RDT), and gene amplification through polymerase chain reaction (PCR), which enable the targeted improvement of plant traits. Complementary techniques such as omics technologies and RNA interference (RNAi) further allow precise regulation of gene expression, elucidation of metabolic pathway and enhancement of metabolite biosynthesis (e.g., alkaloids, terpenoids). In addition, this review discusses innovative strategies to improve plant yield and quality, including genetic marker-based identification, cryopreservation for long-term conservation, plant tissue culture for large-scale propagation, nanotechnology-based delivery systems, bio-fortification, DNA barcoding, and metabolomics for sustainable utilization. The integration of these biotechnological tools signficantly contributes to the production of high-value bioactive compounds, secondary metabolites, and recombinant proteins, while also facilitating drug discovery pipelines. Moreover, these interventions enhance tolerance to environmental stresses, promoting adaptation under adverse conditions.},
}

@article {pmid41280488,
year = {2025},
author = {Barman, R and Banik, D},
title = {DNA barcoding clubbed with morphomatrix of commonly distributed species of Myristicaceae from North East India.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {424},
pmid = {41280488},
issn = {2190-572X},
abstract = {UNLABELLED: The depauperate and paleopolyploid family Myristicaceae face challenges for correct species identification. Majority rule consensus trees of morphomatrix of NER species reflected diagnostic group traits (ca. 41.70%) and variable traits (ca. 58.30%) respectively. Amplification and sequencing success rates with DNA barcode loci rbcL, matK and, trnL-F were > 90% while 45% and 76% with psbA-trnH, respectively in Horsfieldia and Knema. 178 sequences of 8 species of the region were submitted to GenBank including trnL-F spacer mostly for the first time. The highest parsimony informative sites were exhibited by trnL-F and highest variable sites by matK. Mean inter-specific distances with trnL-F, matK + trnL-F in Horsfieldia and with psbA-trnH, rbcL + trnL-F in Knema were ≥ 2 times mean intraspecific distances. trnL-F in Horsfieldia and rbcL + trnL-F in Knema, and trnL-F + psbA-trnH in Horsfieldia and Knema showed barcode gaps. Identification success by 'best match' was 98% with matK + trnL-F and 96-97% with trnL-F + psbA-trnH in Horsfieldia and Knema. The Maximum Parsimony and Bayesian Inference (BI) trees with trnL-F and BI tree with trnL-F + psbA-trnH was monophyletic and resolved 100% and 60% species. Dynamic DNA QR codes generated with Knema erratica-matK, Horsfieldia kingii-psbA-trnH, Endocomia macrocoma subsp. prainii-trnL-F. The loci trnL-F, trnL-F + psbA-trnH were exhibited as candidate barcodes, additionally matK + trnL-F for Horsfieldia and rbcL + trnL-F for Knema. The DNA barcode library of NER Myristicaceae would aid in species identification, ecological variation and conservation biology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04625-7.},
}

@article {pmid41280400,
year = {2025},
author = {Ensing, DJ and Nelson, TD and Moffat, CE and Joslin, L and Eckert, L and Kraml, MM and Eckert, CG},
title = {Together again: the invasive mustard Hesperis matronalis suffers devastating seed predation by a recently adventive specialist weevil.},
journal = {BioControl (Dordrecht, Netherlands)},
volume = {70},
number = {6},
pages = {835-847},
pmid = {41280400},
issn = {1386-6141},
abstract = {UNLABELLED: The enemy release hypothesis underpins classical (or importation) biocontrol as a management technique for invasive species. Classical biocontrol has had resounding success when prospective control agents have been subject to appropriate screening before release. Occasionally, however, natural enemies have been reunited with their hosts accidentally. Such adventive agents may provide effective control but have also avoided the careful screening characteristic of modern importation biocontrol programmes. We were studying the invasive mustard, Hesperis matronalis L. (Dame's rocket; Brassicaceae: Hesperidae), when we discovered rampant seed predation by an unknown seed predator. Using DNA barcoding, we identified this seed predator as Ceutorhynchus inaffectatus Gyllenhal (Coleoptera: Curculionidae), a recently (2018) detected species in North America. Comparing potential and realised seed production, we found that seed predation by C. inaffectatus strongly reduces H. matronalis fecundity, and that this effect was not moderated by infection with turnip mosaic virus (TuMV), a commercially important pathogen hosted by H. matronalis and transmitted by polyphagous aphid species. C. inaffectatus is expected to be highly host-specific, and the absence of native Hesperidae species in North America suggests the potential for C. inaffectatus as a classical, but adventive, biocontrol agent of H. matronalis. We suggest population genetic research to identify the origin of C. inaffectatus, and host specificity testing before any intentional redistribution of this species for H. matronalis biocontrol. More generally, this system acts as a model for biocontrol prospects with adventive insect herbivore species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10526-025-10338-w.},
}

@article {pmid41280082,
year = {2025},
author = {Mosadeghi, R and Foyt, D and Sharp, L and Taylor, C and Tay, N and Oberlin, S and Fan, J and Bourke, S and Kattah, M and Huang, B and McManus, MT},
title = {RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.686676},
pmid = {41280082},
issn = {2692-8205},
abstract = {High-throughput pooled screening has advanced functional genomics, but most existing methods rely on endpoint sequencing and are blind to dynamic, time-resolved phenotypes. We developed RainBar (Rainbow Barcodes), an optical barcoding system that supports pooled live-cell imaging with single-cell resolution. RainBar uses lentiviral co-delivery of spectrally distinct nuclear and cytoplasmic fluorescent proteins to encode up to 64 unique perturbations per well. To mitigate barcode recombination and improve decoding accuracy, we employed single-template viral production, codon diversification, and a ratio-based spectral unmixing pipeline tailored to overlapping fluorophores. An inverted cytoplasmic segmentation approach and multilayer perceptron classifier enabled accurate barcode identification in both arrayed and pooled formats. As a proof of concept, we applied RainBar to dissect NF-κB signaling dynamics in epithelial cells. Live imaging of RelA translocation uncovered stimulus-specific kinetics: IL-1β triggered rapid recovery, while TNF induced prolonged nuclear localization. In pooled CRISPRi screens, RainBar recovered known NF-κB regulators (e.g., IL1R1, MYD88, TNFRSF1A) and highlighted additional modulators, including the Ino80 chromatin remodeling complex subunits and KAT2A acetyltransferase. Together, these results position RainBar as a flexible platform for multiplexed, image-based functional genomics, with potential to reveal dynamic signaling architectures across diverse cellular contexts in live cells.},
}

@article {pmid41279805,
year = {2025},
author = {Leyson, CM and Vargas-Maldonado, N and Gaddy, M and Raghunathan, V and Ferreri, LM and Sethi, M and Patatanian, K and Carnaccini, S and Ganti, K and VanInsberghe, D and Lowen, AC},
title = {Viral lineage and mode of exposure modulate within host spatial dynamics of influenza A viruses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.03.686270},
pmid = {41279805},
issn = {2692-8205},
abstract = {UNLABELLED: The upper and lower respiratory tracts (URT and LRT) present distinct environments for influenza A virus (IAV) replication. Their differential features have major implications for viral evolutionary dynamics, transmission potential, and pathogenesis. To investigate the implications of differential viral replication in the URT and LRT, we assessed dispersal of IAVs throughout the guinea pig respiratory system. Guinea pigs were inoculated intranasally with a 300 μL volume to deliver inoculum to both the URT and LRT. Two strains were used to represent the circulating seasonal IAV lineages: influenza A/TX/50/2012 (H3N2) and influenza A/CA/07/2009 (H1N1) virus. The inclusion of a diverse genetic barcode enabled high-resolution tracing of viral dispersal for the H1N1 virus. While infectious virus was consistently detected in the URT, the H1N1 virus could be detected in LRT while the H3N2 virus could not. To determine whether replication of the H1N1 virus in the LRT extends to other modes of infection, virus distribution was evaluated following infection via aerosol exposure or transmission. Infectious virus in lung homogenates was observed in both cases, confirming the LRT tropism of the H1N1 virus. Sequencing genetic barcodes revealed that diversity was largely maintained in nasal samples and trachea but contracted upon dispersal to the lungs. This loss of diversity was associated with increased distance to and branching from the major airways, implicating long distance dispersal through the airways in imposing within-host population bottlenecks. These data underline the implications for within-host viral dynamics of the distinct environments of the upper and lower respiratory tracts.

IMPORTANCE: The upper (URT) and lower (LRT) respiratory tracts create different conditions for influenza A virus (IAV) spread and evolution. We studied how the virus moves through guinea pigs' airways after infection with H3N2 or H1N1 strains of IAV. Whether delivered intranasally, by aerosol or by transmission, the H1N1 virus replicated in the nasal cavity, trachea, and lungs. By contrast, the H3N2 virus stayed mostly in the nasal cavity. Genetic barcodes were used to track how the H1N1 virus moved and changed. The populations replicating in the nasal cavity and trachea maintained high diversity but those sampled from the lungs showed low diversity. This bottlenecking effect was stronger for viral populations present deeper in the lungs. These findings show that the different environments of the URT and LRT strongly shape how influenza spreads and evolves inside a host.},
}

@article {pmid41279755,
year = {2025},
author = {Hickey, JW and Li, H and Caraccio, C and Yan, Y and Marx, K and Martin, P and Leng, HT and Fayiah, J and Towalid, E and Dighero-Kemp, B and Nolan, GP and Prakash, M and McIlwain, DR},
title = {Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.09.680291},
pmid = {41279755},
issn = {2692-8205},
abstract = {Recent advances in multiplexed single-cell characterization have revolutionized our insight into cell biology, but many available technologies remain limited by high costs or a lack of customizability. To address these challenges, we developed Fluid-Squid, a cost-effective, quantitative imaging platform that integrates automated fluidics to support customizable, do-it-yourself multiplexed imaging workflows. Using Fluid-Squid, we successfully imaged fresh frozen human intestinal tissues with a 36-plex oligonucleotide-barcoded antibody panel and further demonstrated the feasibility of lyophilizing such multiplexed panels. We also adapted existing multiplexed imaging workflows to characterize individual cells to identify immune cell populations, phenotype, and antigen-specific cells from mouse splenocytes and human peripheral blood mononuclear cells (PBMCs) with a 39-antibody panel. To further expand its utility, we developed a barcoding strategy that allows for the pooling and simultaneous staining of multiple samples, reducing time, costs, and batch effects in single-cell experiments. This approach facilitated rapid titration to optimize antibody concentrations and assess the impact of various blood preparation methods on cell type retention. Overall, our work provides a new open-source framework for automated fluidics and microscopy in a flexible, cost-effective platform, empowering adaptable multiplexed characterization of both single cells and tissues.},
}

@article {pmid41279741,
year = {2025},
author = {Bradley, NJ and Pendyala, S and Partington, K and Fowler, DM},
title = {STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.31.685785},
pmid = {41279741},
issn = {2692-8205},
abstract = {UNLABELLED: Fluorescent in situ sequencing involves imaging-based sequencing by synthesis in intact cells or tissues to reveal target nucleotide sequences inside each cell. Often, the target sequences are barcodes that indicate a perturbation (e.g. CRISPR guide or genetic variant) delivered to the cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images with millions of cells, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing, a software package that analyzes raw in situ sequencing images to produce a genotype-to-phenotype mapping for each cell. STAR-Call improves upon previous solutions by combining stitching and alignment of images into a single step that minimizes both inter-cycle and intra-cycle alignment error. STARCall also improves detection and extraction of sequencing reads, incorporating filters and normalization to combat background fluorophore signal. We compare STARCall to other methods using a diverse set of images that include commonly encountered imaging problems such as variable intensity across channels and cycles and high levels of background. Specifically, this comprises ∼250,000 images from a pooled screen of ∼3,500 barcoded LMNA variants expressed in U2OS cells and ∼1,200 bar-coded PTEN variants in induced pluripotent stem cells (iPSC) and iPSC-derived neurons. Overall, STARCall aligned more than 50% of tiles with <1 pixel error on all nine image sets while alternative packages had higher error on four. STARCall also yielded an 8-40% increase in genotyped cells due to improved filtering and normalization methods that address background fluorescence. STARCall can call tools like CellPose to segment cells and CellProfiler to compute cell features from the phenotyping images. STARcall is open-source and freely available, providing a robust solution for the analysis of in situ sequencing data.

AUTHOR SUMMARY: Short regions of RNA or DNA can be sequenced inside intact cells or tissues (i.e. in situ) by combining a microscope and sequencing by DNA synthesis. Multiple cycles of sequencing are performed, in which incorporation of a single fluorescently labeled nucleotide is imaged, and the corresponding base detected. Recently, in situ sequencing has proved useful in optical pooled screens, where a library of perturbations such as CRISPR-mediated gene knockouts or genetic variants is introduced into cells, and in situ sequencing is used to reveal the specific perturbation in each cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing. STARCall uses a novel stitching algorithm that minimizes both inter-cycle and intra-cycle alignment error, and improved filters and normalization for base calling. When applied to a set of 9 in situ sequencing image sets, STARCall yielded an 8-40% increase in genotyped cells. STARCall is open-source and applicable to a variety of experiments, providing a robust pipeline for in situ sequencing data.},
}

@article {pmid41279580,
year = {2025},
author = {Yoon, CJ and Nam, CH and Lee, SM and Choi, ES and Bae, JH and Kim, H and Jung, YM and Lim, J and Kim, R and Derom, C and Meireson, E and Weyers, S and Park, JW and Lee, J and Sung, J and Griffith, OL and Griffith, M and Jun, JK and Ju, YS},
title = {Clonal dynamics of monozygotic twinning in early human embryogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.05.680569},
pmid = {41279580},
issn = {2692-8205},
abstract = {Monozygotic twins are derived from the split of a single zygote early in embryogenesis. Although it was hypothesized that the timing of twining is overall associated with fetal membrane configuration of twins, i.e., chorionicity and amnionicity, our understanding of early embryonic clonal dynamics underlying human twinning is limited. Here we explored the segregations of early embryonic lineages in 7 dichorionic diamniotic (DCDA), 7 monochorionic diamniotic (MCDA), 8 monochorionic monoamniotic (MCMA) monozygotic twins, and 1 dichorionic triamniotic (DCTA) monozygotic triplets, using post-zygotic early embryonic mutations (EEMs) as endogenous lineage barcodes. Patterns of the early lineage distributions among monozygotic twins revealed three apparent clonal categories, referred to as para-identical, sub-identical, and full-identical twins, which largely correlated with the amnionicity of the twins. Rather, despite conventional wisdom, chorionicity was not substantially associated with early clonal compositions, but with blood exchanges in utero . In sub-identical twins, where one co-twin was clonally a part of the other, our data suggested that the foundation of the latter co-twin was established after acquisition of a median of 6 additional post-zygotic mutations (range: 2-13), corresponding to ∼5 early cell divisions. Additional in-depth analysis on the matched placenta from an MCDA twin suggested that separation of two co-twins can precede the separation of the placenta and embryonic proper, and a single chorion can be formed even with multiclonal origin. Our findings provide insights into the clonal dynamics, twinning processes, and cell fate decisions in early human embryogenesis.},
}

@article {pmid41279260,
year = {2025},
author = {Wu, YC and Schwartz, D and Khalil, EA and Upadhye, A and Rehman, J and Lee, SS},
title = {NicheProt : Cell-type-resolved proteomics of tissue compartments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.23.684231},
pmid = {41279260},
issn = {2692-8205},
abstract = {Spatial proteomics uncovers the molecular underpinnings of cellular function in intact tissues. Laser capture microdissection coupled with mass spectrometry enables comprehensive proteomic profiling of selected tissue regions, but typically does not support cell-type-specific proteomic analysis. We present NicheProt , a 3D optical microscopy-guided, photobleaching-mediated cell barcoding approach for isolating intact specific cell types from defined microanatomical tissue compartments or niches. Using sequential bottom-up proteomic analysis, we defined two distinct phenotypes of CD11c[+] dendritic cells based on their spatial locations in the inflamed mouse spleen. These two compartment-specific dendritic cell populations were characterized by proteomic signatures differing in the levels of 54 proteins. This 3D tissue microscopy-guided method offers cell-type and microregion-resolved proteomic analysis, facilitating the proteomic discovery of previously unrecognized cell subtypes and their functional roles in distinct tissue compartments.},
}

@article {pmid41279235,
year = {2025},
author = {Baranowska, P and Lam, T and Herr, AE},
title = {Deterministic DNA barcoding using vacuum-driven loading of free oligonucleotides to microwell arrays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.29.684720},
pmid = {41279235},
issn = {2692-8205},
abstract = {Achieving high-throughput and cost-effective next-generation sequencing requires sample (samples, cells/beads) pooling. A key approach to pooling samples while maintaining unambiguous sample identification is to employ DNA barcoding, which assigns each specimen a unique nucleotide (index) sequence. For barcoding in droplets and microwells, one widely used approach is to randomly seed a unique oligo-coated bead into each compartment. Synthesis of oligonucleotide-coated beads (e.g., split-pooling) is exceptionally intensive and random seeding can result in errors. As an alternative, we present deterministic, aqueous barcoding of 512 arrayed microwells using a multi-layer, vacuum-driven microfluidic network. To uniquely barcode each of the 512 microwells, the oligonucleotide solutions are designed using a Combinatorial Dual Indexing (i5, i7) scheme with the deterministic loading. Deterministic loading of the solutions is achieved by sequentially mating two bifurcated and complementary microchannel-network layers to the microwell array. Vacuum-assisted flow and dead-end channel design yields uniform barcode patterning in the microwell array (∼20% CV), reasonable barcode loading times (30 - 40 min per one step), and reduced reagent use (∼ 8-16 µL at 25 µM oligos vs. 10-50 µL at 100 µM for bead systems). Cross-contamination occurred in ∼4% of the microwells, well within the acceptable range. Following DNA barcode delivery, on-chip PCR of nuclear DNA from a breast cancer cell line having the characteristics of the differentiated mammary epithelium (MCF7) was successfully performed, with off-chip quality control of the amplified breast cancer DNA. Overall, we describe a deterministic and bead-free DNA barcoding strategy for efficient barcoding of widely used microwell arrays.},
}

@article {pmid41278540,
year = {2025},
author = {Twa, GM and Phillips, RA and Robinson, NJ and Day, JJ},
title = {Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf156},
pmid = {41278540},
issn = {2631-9268},
mesh = {Animals ; Male ; Female ; Rats ; *RNA, Small Nuclear/genetics ; Machine Learning ; *RNA-Seq/methods ; *Sequence Analysis, RNA/methods ; *Gene Expression Profiling/methods ; Sex Characteristics ; },
abstract = {Single-nucleus RNA sequencing (snRNA-seq) technology offers unprecedented resolution for studying cell type-specific gene expression patterns. However, snRNA-seq poses high costs and technical limitations, often requiring the pooling of independent biological samples and the loss of individual sample-level data. Deconvolution of sample identity using inherent features would enable the incorporation of pooled barcoding and sequencing protocols, thereby increasing data throughput and analytical sample size without requiring increases in experimental sample size and sequencing costs. In this study, we demonstrate a proof of concept that sex-dependent gene expression patterns can be leveraged for the deconvolution of pooled snRNA-seq data. Using previously published snRNA-seq data from the rat ventral tegmental area, we trained a range of machine learning models to classify cell sex using genes differentially expressed in cells from male and female rats. Models that used sex-dependent gene expression predicted cell sex with high accuracy (93%-95%) and generalizability and outperformed simple classification models using only sex chromosome gene expression (88%-90%). This work provides a model for future snRNA-seq studies to perform sample deconvolution using a two-sex pooled sample sequencing design and benchmarks the performance of various machine learning approaches to deconvolve sample identification from inherent sample features.},
}

Animals
Male
Female
Rats
*RNA, Small Nuclear/genetics
Machine Learning
*RNA-Seq/methods
*Sequence Analysis, RNA/methods
*Gene Expression Profiling/methods
Sex Characteristics

@article {pmid41277841,
year = {2025},
author = {Gopal, K and Burnett, C and Kharytonchyk, S and Emery, A and Atindaana, E and Swanstrom, R and Kidd, JM and Telesnitsky, A},
title = {RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0133425},
doi = {10.1128/jvi.01334-25},
pmid = {41277841},
issn = {1098-5514},
abstract = {UNLABELLED: Accurately quantifying virus release from HIV-1-infected cells is central to predicting infection outcomes and evaluating treatment strategies. Recent studies suggest that viral shedding can vary strikingly among infected cells. To identify predictors of virus release levels, a previously developed high-throughput molecular barcoding system was used to track the expression properties of individual infected clones within a polyclonal population. Consistent with previous reports, virus release spanned four orders of magnitude among clonal integrants. While reporter gene expression correlated poorly with virus release, intracellular viral RNA levels correlated well, and levels of unspliced HIV-1 RNA correlated most closely. Comparing clones with different virus release levels showed that they varied not only in total intracellular HIV-1 RNA levels but also in levels of viral RNA splicing. Remobilizing proviruses revealed that splicing differences were largely due to cell-intrinsic properties, although splicing differences were due to heritable features of the parent provirus for at least one clone. This clone displayed high levels of reporter gene expression from an HIV-1spliced RNA, but low levels of unspliced viral RNA and virus release. This over-splicing clone, which contained a non-synonymous substitution in rev, did not respond to treatment with the latency-reversing agent JQ1 but displayed increased virus release in response to treatment with pladienolide B, a splicing inhibitor. These findings demonstrate that splicing differences can contribute to virus production levels and suggest that future studies on proviral populations that include expanded clones may benefit from assessing clone-specific splicing properties.

IMPORTANCE: Many models of HIV-1 infection rely on the assumption that actively infected cells release similar amounts of virus, despite recent reports that suggest shedding differs drastically among infected cells. In this study, the expression phenotypes of hundreds of integrant clones were analyzed to identify factors contributing to burst size variation. In agreement with previous reports, virus release spanned over four orders of magnitude within the infected pool. Both proviral expression levels and variation in splicing contributed to these burst size differences. While cell-intrinsic factors appeared to be the primary contributors to heterogeneous shedding patterns, viral point mutations were also observed and, in at least one case, contributed to particle release levels. Together, these findings demonstrate that expression variation among proviruses is both large and multifaceted and suggest that clone-specific differences in HIV-1 expression properties may contribute to unpredicted responses to treatment interventions.},
}

@article {pmid41277803,
year = {2025},
author = {Guðmundsson, T and Randhawa, HS},
title = {Parasite diversity in haddock (Melanogrammus aeglefinus) from Icelandic waters.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e125},
doi = {10.1017/S0022149X2510076X},
pmid = {41277803},
issn = {1475-2697},
support = {//Háskóli Íslands/ ; },
mesh = {Animals ; Iceland/epidemiology ; *Fish Diseases/parasitology/epidemiology ; *Biodiversity ; *Gadiformes/parasitology ; *Parasites/classification/isolation & purification/genetics ; DNA Barcoding, Taxonomic ; *Helminths/isolation & purification/classification/genetics ; },
abstract = {It is assumed that the biology and ecology of commercial fish species are relatively well-known, given that many of these parameters are key for stock assessment in fisheries management. Surprisingly (or not), several new parasite species are described annually from fish that are of commercial and cultural importance. Haddock (Melanogrammus aeglefinus) is an important commercial fish species in the North Atlantic with more than 50 parasite species having been reported from it. Despite its commercial importance in Icelandic waters, only 11 parasite species have been reported from Icelandic haddock. In February and March 2023, 26 haddock were sampled, including 16 and 10 from the north and south of Iceland, respectively. Fish were examined for parasites, with a focus on macroparasites (large, usually visible to the eye). Parasites were identified morphologically with identifications of helminths confirmed using DNA barcoding (Sanger sequencing). Overall, 19 different parasite species were recovered with 17 being shared between haddock sampled from the north and south of Iceland. Of these, eight represent new geographical records for parasites of haddock in Icelandic waters. Our study indicates that monitoring for parasites remains important, regardless of how well a species has been studied. Furthermore, reporting parasites per organ and per region, especially when areas are known to be influenced by different abiotic and physical features, is important in the context of parasites as biological tags for stock identification. Despite a small sample size, our study suggests that some parasites might act as potential biological tags for stock identification of haddock in Icelandic waters.},
}

Animals
Iceland/epidemiology
*Fish Diseases/parasitology/epidemiology
*Biodiversity
*Gadiformes/parasitology
*Parasites/classification/isolation & purification/genetics
DNA Barcoding, Taxonomic
*Helminths/isolation & purification/classification/genetics

@article {pmid41273043,
year = {2025},
author = {González, ML and Camps, GA and Sérsic, AN and Cosacov, A and Acosta, MC and Aguilar, DL and Almirón, NEA and Chiapero, AL and Lauenstein, DL and Scaldaferro, M and Sosa-Pivatto, M and do Pico, GV and Moreno, EMS and Vega, C and Neffa, VS and Baranzelli, MC},
title = {Mind the Gaps: Shortfalls in Studies of the Intraspecific Genetic Diversity of Plants Across the Gran Chaco.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70187},
doi = {10.1111/mec.70187},
pmid = {41273043},
issn = {1365-294X},
support = {PIBAA-28720210100101CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PIP-11220210100320CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PIP-11220210100536CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 2020-00602//Fondo para la Investigación Científica y Tecnológica/ ; PICT-3050//Fondo para la Investigación Científica y Tecnológica/ ; PICT-2021-273//Fondo para la Investigación Científica y Tecnológica/ ; PIP-33620230100570CB//Secretaria de Ciencia y Tecnología - Universidad Nacional de Córdoba/ ; },
abstract = {Intraspecific genetic diversity (IGD) is a fundamental component of biodiversity, essential for understanding the evolutionary histories and demographic processes of species, and is key to effective conservation planning. However, ecologically important regions such as the Gran Chaco, South America's second-largest forested biome, remain largely underexplored. Encompassing diverse vegetation across climatic and altitudinal gradients, it harbours more than 3400 vascular plant species, 11% of which are endemic. Despite its ecological importance, genetic research in the region is limited and often biased. We reviewed IGD studies on vascular plants in the Gran Chaco from 1985 to 2024, identifying 85 studies covering 74 species. Coverage remains alarmingly low, with only 2.14% of species and 9.95% of the phylogenetic diversity represented. Research is skewed towards perennial (91%) and tree (46%) species, with limited representation of annuals and herbaceous taxa. Most studies relied on nuclear DNA (66%), fewer used chloroplast DNA (27%) and only 7% combined both genomes. Geographically, 33% of the Gran Chaco has no IGD data, and a further 22% includes data from a single species. Genetic sampling is concentrated in more accessible areas with higher road density and proximity to research institutions, particularly at higher altitudes. We found that in the Argentine Chaco ecoregions, 4.4 species have been genetically studied for every 100 species recorded, while in the Bolivia and Paraguay Chaco ecoregions, this proportion drops to 1.1 species for every 100 in each country. Future research on IGD in the Gran Chaco should broaden its taxonomic scope, diversify genomic tools and expand geographic coverage. Addressing these gaps will provide critical insights into the biogeographic history of the Gran Chaco and strengthen conservation strategies in this threatened and understudied biome.},
}

@article {pmid41272223,
year = {2025},
author = {Atsma, H and Burkett-Cadena, ND and Wisely, SM and Urlaub, A and Botero-Cañola, S and Reeves, LE},
title = {Monitoring biodiversity and detection of diverse vertebrate species with mosquito blood meal analysis at the DeLuca Preserve, Florida, USA.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28062-x},
pmid = {41272223},
issn = {2045-2322},
abstract = {Biodiversity monitoring is essential to conservation, yet field surveys are expensive, labor-intensive, and require substantial taxonomic expertise. DNA-based approaches are increasingly implemented to indirectly detect the presence of species at diverse types of field sites. In terrestrial ecosystems, invertebrate-derived DNA (iDNA) has potential to contribute to monitoring efforts that aim to characterize the diversity of vertebrate communities or to detect the presence of vertebrate species. We investigated the feasibility of using mosquito blood meals to detect vertebrate animals, focusing on the diversity of species detected by mosquitoes collectively and by individual species. Mosquitoes were collected at the DeLuca Preserve, Osceola County, Florida, USA over an eight-month period using sampling methods known to be effective for blood-fed mosquitoes. Blood-fed mosquitoes were identified and screened for host DNA using DNA barcoding-based blood meal analysis. From a sample of 2,051 identified blood meals, representing 21 mosquito species, mosquitoes collectively detected 86 vertebrate species. This assemblage of vertebrates was taxonomically diverse with species from all four terrestrial vertebrate classes, 22 orders, including large- and small-bodied species, and species that are nocturnal, diurnal, migratory, resident, fossorial, arboreal, and semiaquatic, and those that are imperiled, invasive, and cryptic. The host detection efficiency, a measure of the number of detected vertebrate species relative to the number of identified blood meals, varied among mosquito species, indicating that species do not contribute equally to detecting vertebrate species within a community. Our results demonstrate the feasibility of mosquito-based iDNA as a detection method for vertebrates, capable of detecting diverse vertebrate species with a single sampling technique. Because of variation in mosquito diversity patterns between geographic sites and habitats, and in the host associations and host detection efficiency among mosquito species, preliminary surveys to identify and target mosquito species appropriate to the goals of the monitoring effort would be expected to optimize return on investment in mosquito-based vertebrate surveys.},
}

@article {pmid41271826,
year = {2025},
author = {Sugi, T and Reteng, P and Gaithuma, AK and Kawai, N and Namangala, B and Mutengo, MM and Ishiguro, N and Hayashida, K and Yamagishi, J},
title = {Enhanced blood parasite species identification using V4-V9 18S rDNA barcoding by universal primers on a nanopore platform.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41249},
pmid = {41271826},
issn = {2045-2322},
support = {JP24ym0126801//Japan Agency for Medical Research and Development/ ; JP20wm0125008//Japan Agency for Medical Research and Development/ ; JPJSCCB20230007//Japan Society for the Promotion of Science Core-to-Core program/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *RNA, Ribosomal, 18S/genetics ; Cattle ; Humans ; *DNA Primers/genetics ; *Nanopores ; Plasmodium falciparum/genetics/isolation & purification ; *DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Parasites/genetics/classification ; DNA, Protozoan/genetics ; },
abstract = {Microscopic examination is commonly used for blood parasite detection in resource-limited settings due to its low cost and simplicity. However, it requires microscopy experts and has poor species-level identification. This study proposes a targeted next-generation sequencing (NGS) approach using a portable nanopore platform to enable accurate and sensitive parasite detection in such settings. To improve species identification on the error-prone nanopore sequencer, we designed a DNA barcoding strategy targeting the 18S rDNA V4-V9 region, which outperformed the commonly used V9 region. To enrich parasite DNA and reduce host contamination, two blocking primers were developed: a C3 spacer-modified oligo competing with the universal reverse primer and a peptide nucleic acid (PNA) oligo that inhibits polymerase elongation. These were combined to selectively reduce the amplification of host's DNA from blood samples. The developed targeted NGS test successfully detected Trypanosoma brucei rhodesiense, Plasmodium falciparum, and Babesia bovis in human blood samples spiked with as few as 1, 4, and 4 parasites per microliter, respectively. Validation study using field cattle blood samples revealed that this test could detect multiple Theileria species co-infections in the same cattle. The established parasite targeted NGS test using a portable nanopore platform enables comprehensive parasite detection with high sensitivity and accurate species identification.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*RNA, Ribosomal, 18S/genetics
Cattle
Humans
*DNA Primers/genetics
*Nanopores
Plasmodium falciparum/genetics/isolation & purification
*DNA, Ribosomal/genetics
High-Throughput Nucleotide Sequencing/methods
*Parasites/genetics/classification
DNA, Protozoan/genetics

@article {pmid41267691,
year = {2025},
author = {Kaltenbach, T},
title = {Mayflies of the Fiji Islands (Ephemeroptera).},
journal = {ZooKeys},
volume = {1259},
number = {},
pages = {205-276},
pmid = {41267691},
issn = {1313-2989},
abstract = {Material collected in 2024 in nine different rivers on the two main islands of Fiji, Viti Levu and Vanua Levu, is the basis for this taxonomic study of mayflies of the Fiji Islands. Apart from one larva of Caenidae, not treated in this study, all other larvae and three female imagos belong to two genera of the family Baetidae (Baetis Leach and Papuanatula Lugo-Ortiz & McCafferty). A new subgenus of Papuanatula, Fijifiliola subgen. nov., based on the larvae of ten new species, and the larva and female imago of one new species of Baetis are described and illustrated. DNA barcodes (COI) were obtained for most species, and their genetic distances were analysed (Kimura-2 parameter). A key to all species of Papuanatula (Fijifiliola)subgen. nov. is provided. Amongst the new species of Papuanatula (Fijifiliola)subgen. nov., a case of parthenogenesis and likely ovoviviparity is discussed.},
}

@article {pmid41263605,
year = {2025},
author = {Terra, M and Brescovit, A and Dias, A and Rincão, M and da Rosa, R},
title = {Cryptic diversity identified by DNA barcoding reveals the impact of pleistocene climate oscillations on a forest interior spider.},
journal = {Genome},
volume = {68},
number = {},
pages = {1-12},
doi = {10.1139/gen-2025-0028},
pmid = {41263605},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Genetic Variation ; Forests ; Brazil ; Haplotypes ; *Spiders/genetics/classification ; DNA, Mitochondrial/genetics ; Phylogeography ; Climate Change ; },
abstract = {Quaternary climate oscillations significantly influenced the configuration of the Brazilian Atlantic Forest. In this study, mitochondrial DNA analysis of Enoploctenus cyclothorax (Bertkau, 1880) was conducted to investigate potential cryptic diversity within populations across the state of Paraná, Brazil. Two divergent genetic lineages were identified based on genetic distances, haplotype network, and phylogenetic inference. A phylogeographical break separates the lineages into two geographic regions; one lineage is found exclusively in the eastern region and the other is found mainly in the northern and western regions of the state. The coalescence tree estimates the divergence time between 1.8 million years and 500 000 years ago, period marked by glaciation, suggesting historical forest fragmentation as a potential isolating mechanism. These findings support the hypothesis of independently evolving units within E. cyclothorax, possibly representing cryptic species, though broader sampling and integrative approaches are necessary for taxonomic validation.},
}

Animals
*DNA Barcoding, Taxonomic
Phylogeny
*Genetic Variation
Forests
Brazil
Haplotypes
*Spiders/genetics/classification
DNA, Mitochondrial/genetics
Phylogeography
Climate Change

@article {pmid41262462,
year = {2025},
author = {Lewis, JH and Kojima, H and Campbell, EO},
title = {A Japan-focused review of East Asian Acicnemis Fairmaire, 1849 (Coleoptera, Curculionidae) reveals cryptic diversity in a well-studied region.},
journal = {ZooKeys},
volume = {1259},
number = {},
pages = {103-167},
pmid = {41262462},
issn = {1313-2989},
abstract = {The East Asian species of Acicnemis Fairmaire, 1849 (Coleoptera: Curculionidae: Molytinae) are reviewed using a combination of traditional morphological approaches (microscopy, dissections) and DNA barcoding. Three new species, A. cryptica Lewis & Kojima, sp. nov., A. koguma Lewis & Kojima, sp. nov. and A. squamata Lewis & Kojima, sp. nov. are described from mainland Japan. The former two species are cryptic and sister to more widespread, previously described taxa. Based on examination of name-bearing type material and morphological considerations Acicnemis cruciata Kleine, 1924 syn. nov. is a junior subjective synonym of Acicnemis postica Hubenthal, 1919, Acicnemis yakushimana Morimoto & Miyakawa, 1995 syn. nov. is a junior subjective synonym of A. dividicincta Morimoto & Miyakawa, 1995, and Acicnemis dorsonigrita Voss, 1941 syn. nov. is a junior subjective synonym of Acicnemis palliata Pascoe, 1872. Lectotypes are designated for Acicnemis albofasciata (Ter-Minasian, 1953), A. laeta Hubenthal, 1919, A. postica Hubenthal, 1919 and A. sauteri Hubenthal, 1919. Important morphological characters used in Acicnemis species identification are reviewed and a key to the East Asian species is provided. DNA (CO1) barcoding is used to supplement our morphology-based species hypothesis, and the first published barcodes for most species covered here are presented.},
}

@article {pmid41259660,
year = {2025},
author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A},
title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf620},
pmid = {41259660},
issn = {1367-4811},
abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.

RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.

raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.},
}

@article {pmid41256401,
year = {2025},
author = {Rosen, JD and Vasanthakumari, AD and Salomon, K and de Lange, N and Dash, PM and Keukeleire, P and Hassan, A and Barrera, A and Kircher, M and Love, MI and Schubach, M},
title = {Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.25.678548},
pmid = {41256401},
issn = {2692-8205},
abstract = {As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of non-coding genomic variation remains a major challenge due to the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively Parallel Reporter Assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, and systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing and visualization. Using diverse MPRA datasets, we characterize technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.},
}

@article {pmid41255016,
year = {2025},
author = {Li, X and Zhang, X and Zhai, J and Lei, R and Li, H},
title = {DNA barcode-targeted triplex droplet digital PCR for three high-risk soybean fungal pathogens in soybean seeds.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70388},
pmid = {41255016},
issn = {1526-4998},
support = {2021YFD1400100//National Key Research and Development Program of China/ ; 2021YFD1400103//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Soybean crops face significant threats from the fungal pathogens Diaporthe aspalathi, Diaporthe caulivora, and Cadophora gregata, which cause stem canker and brown stem rot leading to substantial yield losses. Current detection methods rely on time-consuming isolation and culturing, underscoring the need for rapid, sensitive, and direct diagnostic tools. This study aimed to develop a triplex droplet digital polymerase chain reaction (ddPCR) assay for simultaneous detection of these three pathogens without requiring fungal cultivation.

RESULTS: A triplex ddPCR assay was designed using specific regions of the translation elongation factor 1-α (EF-1α) and β-tubulin (TUB2) genes, which were identified via comparative DNA barcode analysis of fungi infecting soybean plants. The assay achieved high sensitivity with absolute quantification limits of 0.20 copies/μL for D. aspalathi, 0.34 copies/μL for D. caulivora, and 2.58 copies/μL for C. gregata. Recovery rates from fungal-mycelium-spiked soybean seed samples ranged from 58.8% to 91.7%. When applied to field samples, the assay detected the target pathogens in 60% of imported soybean seeds.

CONCLUSION: The triplex ddPCR method enables accurate, sensitive, and rapid simultaneous detection of three high-risk fungal pathogens in soybean seeds. This assay supports large-scale screening of imported commodities, facilitates early disease management, and has the potential to reduce significant economic losses in soybean production. © 2025 Society of Chemical Industry.},
}

@article {pmid41254144,
year = {2025},
author = {Abu El-Hassan, GMM and Abo El-Ela, RH and Sawaby, R and El-Hamouly, H and El Sawaf, BM and Ghallab, EH},
title = {Morphology, molecular phylogeny and record verification of Sarcophaga ruficornis Fabricius (Diptera: Sarcophagidae) from Egypt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40357},
pmid = {41254144},
issn = {2045-2322},
mesh = {Animals ; *Sarcophagidae/genetics/anatomy & histology/classification ; Egypt ; *Phylogeny ; DNA Barcoding, Taxonomic/methods ; Male ; Female ; Electron Transport Complex IV/genetics ; Forensic Entomology/methods ; },
abstract = {In forensic entomology, accurate species identification is essential for calculating the exact minimum postmortem interval (minPMI), as insect developmental rates are highly species-specific. Sarcophaga (Liopygia) ruficornis (Fabricius, 1794) is a species of medical and forensic significance. Recently, it was recorded from Egypt for the first time. The current study aimed to conclusively identify S. ruficornis in Egypt through DNA barcoding and morphological examination of both adult males and females, for the first time, to our knowledge. A segment of the mitochondrial cytochrome oxidase subunit one gene (COI) of S. ruficornis was amplified, and a sequence length of 817 bp was obtained and submitted to GenBank. The genitalia of both sexes and the diagnostic morphological characters of the species were examined and illustrated. In addition, the phylogenetic relationship of the Egyptian population of S. ruficornis was investigated. This study demonstrates the utility of DNA barcoding for investigating the genetic composition and variation of S. ruficornis populations and provides essential data for the identification of S. ruficornis in Egypt, which makes it possible to identify a specimen correctly even when only limited morphological evidence is available.},
}

Animals
*Sarcophagidae/genetics/anatomy & histology/classification
Egypt
*Phylogeny
DNA Barcoding, Taxonomic/methods
Male
Female
Electron Transport Complex IV/genetics
Forensic Entomology/methods

@article {pmid41249436,
year = {2025},
author = {Zhuo, W and Liu, Y and Wang, H and Lu, S and Xiao, B and Yang, M and Xiong, C and Zhou, N and Zhang, G and Qi, J and Zhu, J and Wang, L and Ren, F},
title = {Chloroplast genome analysis reveals intraspecific variation and phylogenetic conflicts in Bletilla.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40297},
pmid = {41249436},
issn = {2045-2322},
support = {2024jbky-032//Basic Research Expenses of Chongqing Science and Technology Bureau/ ; cstc2022ycjh-bgzxm0029//Chongqing Talent Program/ ; CQYC20210309793//Chongqing Talent Program/ ; 2Y201402128//Chongqing Traditional Chinese Medicine Technology Projec/ ; },
mesh = {*Genome, Chloroplast ; *Phylogeny ; *Orchidaceae/genetics/classification ; *Genetic Variation ; DNA Barcoding, Taxonomic ; Chloroplasts/genetics ; },
abstract = {The genus Bletilla Rchb.f., an endangered taxon of Orchidaceae Juss. with significant medicinal value, faces persistent controversies in taxonomic identification and phylogenetic relationships. In this study, we analyzed a dataset of 57 complete chloroplast genomes (CPGs) from five subfamilies of Orchidaceae, including five newly sequenced Bletilla CPGs and publicly available data. These CPGs were combined with corresponding nuclear ribosomal internal transcribed spacer (nrITS) sequences obtained from public databases to resolve taxonomic uncertainties and phylogenetic relationships within Bletilla. Our results revealed significant intraspecific variation in Bletilla CPGs with overlapping intraspecific and interspecific genetic distances (GDs), alongside non-monophyletic clades of B. striata, B. ochracea, and B. formosana in species-level phylogenies. Consequently, the CPG 'super barcodes'-proposed as high-resolution markers for plant identification-demonstrated limited discriminatory power in Bletilla, challenging their universal reliability. Phylogenetic analysis revealed conflicting placements between Bletilla and B. sinensis in CPG and nrITS trees: while nrITS data supported a monophyletic Bletilla within the subtribe Coelogyninae Benth., CPG data placed B. sinensis outside Bletilla, forming a sister clade with Calanthe triplicata and Tainia dunnii. Collectively, this study provides new evidence for the taxonomic identification and phylogenetic relationships of Bletilla through chloroplast-nuclear genome integration, offering a preliminary framework for taxonomic re-evaluation of complex plant groups.},
}

*Genome, Chloroplast
*Phylogeny
*Orchidaceae/genetics/classification
*Genetic Variation
DNA Barcoding, Taxonomic
Chloroplasts/genetics

@article {pmid41248424,
year = {2025},
author = {Af Geijerstam, P and Johansson, E and Fägerstam, S and Wu, JH and Ghafouri, B and Karlsson, K and Hebib, L and Kastbom, L and Wennberg, P and Gustafson Hedov, E and Storgärds, M and Sundström, J and Rådholm, K},
title = {Effect of the FoodSwitch application on type 2 diabetes in Sweden: a study protocol for the randomised controlled DIgitAl diabeTES Treatment - the Healthy Eating, heaLthy Patients trial (DIATEST-HELP).},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e110141},
doi = {10.1136/bmjopen-2025-110141},
pmid = {41248424},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy ; Sweden ; *Mobile Applications ; *Diet, Healthy ; Randomized Controlled Trials as Topic ; Glycated Hemoglobin/analysis ; Quality of Life ; Adult ; Female ; *Food Labeling/methods ; Male ; Middle Aged ; Smartphone ; },
abstract = {INTRODUCTION: A healthy diet improves glycaemic control and reduces cardiovascular risk in type 2 diabetes (T2D). However, access to dietitians is limited. Several countries have implemented mandatory interpretive front-of-pack labelling to guide consumers towards healthier food choices, but Sweden has not. Smartphone applications may offer an alternative platform to provide such information. This study evaluates the dietary and clinical impact of a novel application providing interpretive labelling to Swedish adults with T2D.

METHODS AND ANALYSIS: This is a fully decentralised randomised controlled trial. 900 individuals with T2D for ≥2 years who regularly shop for groceries will be recruited via general practices and community advertisements. Participants will be randomised to receive either: (1) access to the FoodSwitch mobile application plus standard written dietary advice, or (2) standard written dietary advice only. The FoodSwitch application allows users to scan barcodes on packaged foods to receive recommendations of healthier alternatives within the same category. The primary outcome is the difference in change in mean self-measured glycated haemoglobin between groups after 6 months. Secondary outcomes include differences in changes in waist circumference, body weight, quality of life, medication use, hospitalisations and all-cause mortality at 26 weeks. Exploratory outcomes include omics analyses. Recruitment is ongoing. Expected study completion on 31 December 2026.

ETHICS AND DISSEMINATION: The trial has received ethical approval from the Swedish Ethical Review Authority (2023-06622-01, 2024-06668-02, 2024-07357-02 and 2025-01095-02) and is performed in line with World Medical Association Declaration of Helsinki and the General Data Protection Regulation. Results will be published in a peer-reviewed international journal.

TRIAL REGISTRATION NUMBER: NCT05977218.},
}

Humans
*Diabetes Mellitus, Type 2/diet therapy
Sweden
*Mobile Applications
*Diet, Healthy
Randomized Controlled Trials as Topic
Glycated Hemoglobin/analysis
Quality of Life
Adult
Female
*Food Labeling/methods
Male
Middle Aged
Smartphone

@article {pmid41248068,
year = {2025},
author = {Casasent, AK and Stolley, DL and Gamal, BT and Dahay, A and Mok, S and Rocha, L and Li, V and Nguyen, AT and Zhang, B and Brasuell, CT and Thompson, EJ and Huynh, T and Burks, JK and Ferri-Borgogno, S},
title = {Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {224},
pages = {},
doi = {10.3791/68619},
pmid = {41248068},
issn = {1940-087X},
mesh = {*Transcriptome ; Animals ; *Gene Expression Profiling/methods ; Paraffin Embedding/methods ; Mice ; Humans ; *Sequence Analysis, RNA/methods ; },
abstract = {The spatial composition of cells within the host, as well as the bacteria or viral loads within the tissue, can impact the interaction of cell types and analytes that drive the cell through cell-type-specific processes. Stereo-seq for FFPE tissues uses random priming to spatial barcodes, which is different from standard spatial transcriptomics methods, which use A'tailing to capture messenger RNA (mRNA) or probe-based to capture species-specific transcripts. These methods do not embrace the more current knowledge about the impact and importance of other types of RNA from long non-coding RNA, mitochondrial RNA, microRNA, or other species, RNA, such as microbial, viral, and fungal. Outlined here is a step-by-step procedure from tissue sectioning through library preparation for spatial species-agnostic stereo-seq application with RNA detection using a randomer probe methodology, which is compatible with formalin fixed paraffin embedded (FFPE) tissues. This Stereo-seq method has a random capture bead of 0.22 µm in size that reoccurs in an array every 0.5 µm, allowing for subcellular resolution from a sequencing-based technology. As this method detects both host and non-host RNA, the protocol requires specific considerations to allow for the determination of what is inside the tissue versus what was deposited on the tissue during the collection, preservation, cutting, and detection process (i.e., environmental and handling contaminants). Lastly, this protocol allows one to have high (single-cell) level resolution of multi-RNA species within a spatial context, providing insight into the intra- and inter-actome of cell types and pathological species.},
}

*Transcriptome
Animals
*Gene Expression Profiling/methods
Paraffin Embedding/methods
Mice
Humans
*Sequence Analysis, RNA/methods

@article {pmid41247050,
year = {2025},
author = {Inman, B and Butler, J and George-Nichol, S and Kovalenko, G and Savidge, T and Vergnetti, Y and Pongratz, C and Bee, E and DiNardo, AR and Kay, A and Mandalakas, A and Bortz, E and Ness, TE},
title = {Application of FreezeTB, a targeted nanopore sequencing assay, for identification of drug resistance and lineages among pulmonary tuberculosis cases in Alaska.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0233525},
doi = {10.1128/spectrum.02335-25},
pmid = {41247050},
issn = {2165-0497},
abstract = {Alaska has the highest incidence of tuberculosis (TB) in the United States, with 8% mortality while undergoing TB treatment. With a quarter of TB cases lacking sputum culture to enable drug resistance testing, FreezeTB aimed to develop tools tailored to meet the challenges in Alaska while being translatable to other settings. We designed a rapid and cost-effective laboratory workflow and software to identify drug-resistant mutations in Mycobacterium tuberculosis using targeted next-generation sequencing (tNGS). FreezeTB, a Fast, Reliable, Economical Evaluation tool to Zap Endemic Tuberculosis, amplifies 22 gene loci associated with resistance to 16 anti-tuberculosis drugs. M. tuberculosis isolates from Alaska (2011-2024) were blinded and underwent analysis with FreezeTB, then compared with phenotypic drug susceptibility testing (pDST) and whole genome sequencing (WGS). Compared with WGS (n = 79), FreezeTB provided the same mutations in 96% (n = 76/79) of samples with 100% lineage agreement (n = 79/79). Compared with pDST using Cohen's kappa, FreezeTB had almost perfect agreement for rifampin (RIF, 0.90; n = 97/98) and ethambutol (EMB, 1.00; n = 98/98), strong agreement for isoniazid (INH, 0.80; n = 88/98), moderate agreement for ethionamide (ETO, 0.78; n = 95/98), weak agreement for streptomycin (STR, 0.56; n = 95/98), and no agreement for pyrazinamide (PZA, 0.20; n = 91/98). Using a portable nanopore sequencer, each sample cost under $30 for sequencing, which included a flow cell, a barcoding kit, a flow cell wash kit, a polymerase, and primers. FreezeTB provides a portable, 1-day laboratory and bioinformatic workflow for sequencing M. tuberculosis. Freeze TB can accurately determine mycobacterial lineage and resistance for RIF, INH, ETH, and ETO at a low cost.IMPORTANCEGlobally, tuberculosis is the leading infectious cause of mortality with 10.8 million new cases and 1.25 million deaths occurring in 2024. Targeted next-generation sequencing (tNGS) is a rapid, cost-effective method for identifying mutations in the Mycobacterium tuberculosis genome associated with drug resistance. FreezeTB was created to provide low-cost, portable sequencing and tNGS analysis for drug resistance. FreezeTB selectively amplifies and sequences 24 targets of the M. tuberculosis genome that cover regions the WHO has designated as containing mutations conferring drug resistance, as well as provides species confirmation and rapid lineage determination. Freeze TB is a laboratory workflow and free, open-source (OS) low dependency bioinformatic software that can be downloaded onto a computer with no further need for internet access. Using M. tuberculosis isolates from Alaska, FreezeTB provided the same mutations in 96% (n = 76/79) of samples with 100% lineage agreement (n = 79/79) compared with whole genome sequencing.},
}

@article {pmid41246444,
year = {2025},
author = {Park, J and Ra, DK and Kim, S},
title = {A newly-recorded species, Roeslerstammia erxlebella (Fabricius, 1787) (Lepidoptera, Roeslerstammiidae) from Korea, with a key to species of the genus and DNA barcoding analysis.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e171683},
doi = {10.3897/BDJ.13.e171683},
pmid = {41246444},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Roeslerstammia Zeller, 1839, the type genus of the family Roeslerstammiidae, comprises a total of four species on a global scale. The type species, Roeslerstammia erxlebella (Fabricius, 1787) is distributed across the Palaearctic Region, from Europe to Japan. However, the presence of this species has only been confirmed in European countries, Russia and Japan.

NEW INFORMATION: The present study reports the first record of Roeslerstammia erxlebella in Korea, specifically from Odae-san National Park. This paper constitutes a review of the taxonomic history of the family Roeslerstammiidae and the genus Roeslerstammia. A thorough taxonomic account of the recently documented species, R. erxlebella, is presented, accompanied by a taxonomic key and an illustrated map delineating the geographical distribution of the genus Roeslerstammia. Furthemore, the DNA Barcode data of a Korean individual was made available, alongside public data from BOLD systems. The DNA Barcoding analysis further indicates that the Korean individual is R. erxlebella.},
}

@article {pmid41245217,
year = {2025},
author = {Ojeda-Perez, I and Bustos, A and Selvaraj, S and Fañanas-Baquero, S and Alberquilla-Fernandez, O and Serrano, LJ and Bonafont, J and Garcia-Torralba, A and Torres-Ruiz, R and Rodriguez-Perales, S and Lang, V and Trigueros, C and Mayo-Garcia, R and Quintana-Bustamante, O and Porteus, M and Sánchez-Dominguez, R and Segovia, JC},
title = {Harnessing DNA barcoding to enhance and sustain polyclonality in gene-edited hematopoietic stem cells.},
journal = {Molecular therapy. Methods & clinical development},
volume = {33},
number = {4},
pages = {101615},
doi = {10.1016/j.omtm.2025.101615},
pmid = {41245217},
issn = {2329-0501},
abstract = {A challenge in gene editing for hematopoietic stem and progenitor cells (HSPCs) is achieving efficient editing while preserving long-term engraftment and clonal diversity. Tracking edited clones with high resolution is essential to understand the impact of editing on hematopoiesis. We developed a barcoded AAV6 donor template (BC-AAV) to precisely monitor the fate of edited HSPCs following transplantation. Our findings reveal that, despite initial barcode diversity in vitro, human hematopoiesis generated by edited HSPCs transplanted in immunodeficient mice is driven by a limited number of dominant clones. The engraftment of gene-edited cells follows an oligo/polyclonal pattern, indicating that editing does not alter clonal dynamics in this model. Using BC-AAV, we optimized a gene editing protocol for correcting the PKLR gene, responsible for pyruvate kinase deficiency, a rare disorder that causes severe anemia due to red blood energy imbalance. We implemented key improvements. GMP-grade StemSpan AOF medium and StemRegenin-1 increased clonal diversity while maintaining hematopoietic potential. NHEJ inhibitor AZD-7648, significantly boosted editing efficiency in vitro, and a shorter transduction period enhanced engraftment and clonal balance without compromising editing outcomes. This refined strategy for gene editing in human HSPCs optimizes both efficiency and long-term polyclonal dynamics and has important implications for clinical applications.},
}

@article {pmid41239062,
year = {2025},
author = {Ayadi, ZEM and Rebah, MA and Gey, D and Tazerouti, F},
title = {Morphological and Molecular Characterization of Hexostoma auxisi Palombi, 1943 (Polyopisthocotylea: Hexostomatidae) from Auxis rochei (Risso, 1810) (Teleostei: Scombridae) off Algerian Waters, Western Mediterranean.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {222},
pmid = {41239062},
issn = {1896-1851},
mesh = {Animals ; Mediterranean Sea ; *Trematoda/genetics/anatomy & histology/classification/isolation & purification ; Algeria ; *Fish Diseases/parasitology/epidemiology ; *Trematode Infections/veterinary/parasitology ; Electron Transport Complex IV/genetics ; Gills/parasitology ; Phylogeny ; *Perciformes/parasitology ; },
abstract = {INTRODUCTION: Hexostoma auxisi Palombi, 1943 was originally described by Palombi (1943) from Auxis thazard off Italy, Mediterranean Sea. The original description of this species lacks morphological and morpho-metrical data. In addition, no published sequence of this species is available in molecular engines.

MATERIALS AND METHODS: Specimens of Hexostoma auxisi were collected from the gills of Auxis rochei (Risso, 1810) off the Algerian coast, Western Mediterranean. Monogenean were stained with acetic carmine, measured and drawn. Furthermore, molecular study was conducted using partial fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) of parasites and a tissue sample of the fish's gills on which the monogeneans were found.

RESULTS: In this study, we provide morpho-anatomical and morpho-metrical data of Hexostoma auxisi. Our specimens are morphologically close to those described by Palombi (1943) off Italy, Mediterranean Sea. The morphological study was supported by a molecular analysis of cox1 gene that reveals that our sequence of H. auxisi is distinct from its congener H. thynni by 20.51%.

CONLUSION: The present study allowed us to confirm the taxonomic status of Hexostoma auxisi which belongs to the genus Hexostoma and the family Hexostomatidae.},
}

Animals
Mediterranean Sea
*Trematoda/genetics/anatomy & histology/classification/isolation & purification
Algeria
*Fish Diseases/parasitology/epidemiology
*Trematode Infections/veterinary/parasitology
Electron Transport Complex IV/genetics
Gills/parasitology
Phylogeny
*Perciformes/parasitology

@article {pmid41238550,
year = {2025},
author = {Yadav, RP and Xing, P and Zhao, M and Hollander, P and Strell, C and Xie, M and Salehi, M and Torell, E and Sjöblom, T and Enblad, G and Amini, RM and Swartling, FJ and Glimelius, I and Micke, P and Hellström, M and Chen, X},
title = {scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10022},
pmid = {41238550},
issn = {2041-1723},
support = {2024-03756//Vetenskapsrådet (Swedish Research Council)/ ; 24 3484 Pj//Swedish Cancer Foundation/ ; 22 0491 JIA//Swedish Cancer Foundation/ ; KAW 2023.0046//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2024.0166//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {Humans ; *Chromatin/metabolism/genetics ; Animals ; *Paraffin Embedding/methods ; Formaldehyde/chemistry ; Mice ; *Single-Cell Analysis/methods ; Tissue Fixation/methods ; Transposases/metabolism/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Epigenesis, Genetic ; Lung Neoplasms/genetics/pathology ; Lymph Nodes/pathology/metabolism ; Spleen ; Lymphoma, Large B-Cell, Diffuse/genetics/pathology ; },
abstract = {Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.},
}

Humans
*Chromatin/metabolism/genetics
Animals
*Paraffin Embedding/methods
Formaldehyde/chemistry
Mice
*Single-Cell Analysis/methods
Tissue Fixation/methods
Transposases/metabolism/genetics
*High-Throughput Nucleotide Sequencing/methods
Epigenesis, Genetic
Lung Neoplasms/genetics/pathology
Lymph Nodes/pathology/metabolism
Spleen
Lymphoma, Large B-Cell, Diffuse/genetics/pathology

@article {pmid41236296,
year = {2025},
author = {Albogami, A},
title = {Genetic diversity and phylogenetic structure of Marawh and Bidah pomegranate landraces from Al-Baha, Saudi Arabia, using ITS DNA barcoding.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {10},
pages = {89-93},
doi = {10.14715/cmb/2025.71.10.12},
pmid = {41236296},
issn = {1165-158X},
mesh = {Saudi Arabia ; *Phylogeny ; *Pomegranate/genetics/classification ; *Genetic Variation ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; },
abstract = {Pomegranate (Punica granatum L.) plays a vital cultural and economic role in the Al-Baha region of Saudi Arabia. Despite its significance, limited molecular data exist on the genetic structure of local landraces, particularly the distinct red and green fruit colour variants of the Marawh and Bidah cultivars. This study investigates the genetic diversity and phylogenetic relationships among these landraces using the nuclear internal transcribed spacer (ITS) DNA region. Maximum likelihood phylogenetic tree construction and network analysis (SplitsTree) were employed. Results reveal that red- and green-fruited landraces cluster into distinct clades, with red variants exhibiting reticulate patterns suggestive of introgression or incomplete lineage sorting. Genetic distance analysis confirmed a high similarity (~99.15%) between the green variants, despite their placement in separate clades. The findings provide crucial insights into the evolutionary history, cultivar authentication, and conservation strategies for pomegranate germplasm in Al-Baha. Future directions include genome-wide SNP analyses and expanded sampling to refine our understanding of these valuable genetic resources.},
}

Saudi Arabia
*Phylogeny
*Pomegranate/genetics/classification
*Genetic Variation
*DNA Barcoding, Taxonomic/methods
DNA, Plant/genetics

@article {pmid41234542,
year = {2025},
author = {Lapeva-Gjonova, A and Pramatarova, M and Borowiec, L and Gjonov, I and Kostova, R and Bekchiev, R and Borissov, S},
title = {DNA barcoding of Messor ants of Bulgaria with insights into their taxonomic diversity.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e168586},
pmid = {41234542},
issn = {1314-2828},
abstract = {BACKGROUND: Despite ongoing efforts to catalogue European ant species, studies focusing on the genetic diversity of Balkan ants remain limited. An integrative approach combining morphology, genetics, ecology and biogeography is preferable for accurately identifying species and resolving taxonomic uncertainties, particularly amongst challenging insect taxa, such as the ants in the genus Messor (Hymenoptera, Formicidae).

NEW INFORMATION: In this study, we analyse ants of the genus Messor using DNA barcode sequences, with a particular focus on the Bulgarian fauna. A total of 85 COI sequences were examined, including 84 from Messor specimens and one from Aphaenogaster, which was used as an outgroup. Of these, 81 sequences were newly generated, while four were retrieved from GenBank. The majority of specimens were collected in Bulgaria (61), with additional samples from Greece (13), Türkiye (4), Albania (1) and North Macedonia (2), providing broader genetic and geographic representation.Althogether, 11 Messor morphospecies were identified, based on specimens used for molecular analysis. To assess the degree of congruence between morphological and molecular data, six species delimitation analyses were conducted: RESL, GMYC, ASAP, ABGD, bPTP and mPTP. In addition, haplotype network analysis of all sequences identified 35 distinct and coherently clustered haplotypes, providing insights into genetic diversity.The COI barcode region successfully distinguished Messor wasmanni Krausse, 1910, M. oertzeni Forel, 1910 and M. ibericus Santschi, 1931. In contrast, species pairs, such as M. atanassovii Atanassov, 1982 and M. creticus Salata & Borowiec, 2019, as well as M. ponticus Steiner et al., 2018 and M. hellenius Agosti & Collingwood, 1987, could not be reliably differentiated using COI data. Furthermore, Messor structor (Latreille, 1798) showed high intraspecific genetic diversity. Finally, the structor and instabilis species groups were recovered with moderate to high support in both Maximum Likelihood and Bayesian Inference analyses, confirming that M. oertzeni and M. hellenius belong to the structor group.Our results provide a reference for future research and underscore the value of integrative taxonomic approaches in ant biodiversity studies.},
}

@article {pmid41233723,
year = {2025},
author = {Ollivier, M and Marquisseau, A and Dufrêne, E and Rudelle, R and Rougerie, R and Perrard, A and Pichon, M and , },
title = {CODABEILLES: a reliable reference library of COI DNA barcodes for French wild bees monitoring (Apoidea: Anthophila).},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {121},
pmid = {41233723},
issn = {2730-7182},
support = {ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; },
abstract = {UNLABELLED: In the Anthropocene, the decline of insect pollinators poses a significant threat to ecosystem services, particularly to wild bee populations essential for plant biodiversity and agricultural productivity. France, with 983 species, hosts one of the most diverse bee faunas in Europe, yet these species face growing pressures from habitat loss, climate change, and intensive agriculture. Addressing this crisis requires robust taxonomic frameworks and efficient species identification methods to support long-term monitoring initiatives such as the European Pollinator Monitoring Scheme, EU-PoMS. DNA barcoding, utilizing the COI-5P gene, has proven effective for species delineation and biodiversity monitoring, particularly in detecting cryptic diversity among genera with large numbers of species such as Andrena, Nomada or Lasioglossum. However, significant gaps remain in reference libraries, particularly for the species from the Mediterranean Basin. To bridge this gap, the CODABEILLES initiative was launched in 2021 to enhance barcode data for the French bee fauna. Initially, only 25% of species had barcodes from French voucher specimens, increasing to 62% when considering voucher specimens from other countries. By 2025, thanks to collaboration with sixteen specialists and institutions, CODABEILLES contributed 1477 reference barcodes, covering approximately 560 species and raising barcode coverage to 82%. When integrating data published under other initiatives over the same period the coverage reaches 94% of the French bee fauna. This dataset significantly enhances species identification accuracy and supports large-scale pollinator monitoring through metabarcoding and environmental DNA approaches. Despite the success of COI-5P barcoding, taxonomic inconsistencies persist, necessitating further integrative research. This study underscores the need for continued collaboration among taxonomists, molecular biologists, and conservationists to refine species classifications and ensure comprehensive reference databases. The improved barcode coverage provided by CODABEILLES paves the way for more accurate DNA-based monitoring of wild bee populations and their ecological interactions, crucial for guiding conservation strategies in the face of ongoing environmental change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-025-02429-0.},
}