@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.},
}

@article {pmid41233332,
year = {2025},
author = {Comstock, WJ and Navarro, MVAS and Maybee, DV and Rho, Y and Wagner, M and Jaber, K and Wang, Y and Smolka, MB},
title = {Proteomic sensors for quantitative multiplexed and spatial monitoring of kinase signaling.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9902},
pmid = {41233332},
issn = {2041-1723},
support = {R35GM141159//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01HD095296//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31CA281247//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Proteomics/methods ; *Signal Transduction ; Humans ; Checkpoint Kinase 1/metabolism ; Ataxia Telangiectasia Mutated Proteins/metabolism/genetics ; Peptides/metabolism/chemistry ; *Biosensing Techniques/methods ; Protein Kinases/metabolism ; Mass Spectrometry ; DNA Damage ; },
abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we develop a proteomic kinase activity sensor technique (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a versatile system for systematically and spatially probing kinase action in cells.},
}

*Proteomics/methods
*Signal Transduction
Humans
Checkpoint Kinase 1/metabolism
Ataxia Telangiectasia Mutated Proteins/metabolism/genetics
Peptides/metabolism/chemistry
*Biosensing Techniques/methods
Protein Kinases/metabolism
Mass Spectrometry
DNA Damage

@article {pmid41232800,
year = {2025},
author = {Ma, P and Ma, H and Li, J and Bi, W and Zhang, S and Hou, W and Xu, H},
title = {Combinatorial chemistry and click chemistry for the optimization of lipid nanoparticles to enhance RNA delivery.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104532},
doi = {10.1016/j.drudis.2025.104532},
pmid = {41232800},
issn = {1878-5832},
abstract = {Lipid nanoparticle (LNP)-based gene therapy holds great promise to revolutionize modern medicine. To address the challenges associated with LNP-based mRNA delivery, we systematically examine combinatorial chemistry approaches that facilitate the rapid synthesis of ionizable lipid libraries for high-throughput LNP screening, the application of click and bioorthogonal chemistry for the surface modification of LNPs with targeting ligands, and recent advances in barcoding technologies enabling comprehensive in vitro and in vivo evaluation of LNP performance. Furthermore, we outline the key design considerations and crucial challenges associated with developing LNPs for effective mRNA delivery, and propose strategic approaches to expand lipid libraries and enhance high-throughput screening (HTS) capabilities.},
}

@article {pmid41229993,
year = {2025},
author = {Tongkerd, P and Janjai, T and Pholyotha, A and Gojšina, V and Panha, S and Sutcharit, C},
title = {The microsnail genera Clostophis and Acinolaemus (Eupulmonata, Pupilloidea, Hypselostomatidae) from central Thailand, with description of three new species.},
journal = {ZooKeys},
volume = {1258},
number = {},
pages = {35-71},
pmid = {41229993},
issn = {1313-2989},
abstract = {Hypselostomatid microsnails of the genera Clostophis and Acinolaemus from limestone hills in central Thailand were studied and three new species are described. Clostophis rhynchotes Tongkerd & Panha, sp. nov. is diagnosed by a conical spire, long and descending tuba, 14 spiral striations on the last whorl, and only a single parietal lamella. In addition, a previously known species, C. proboscideus, is redescribed, and variations in its apertural dentition are also documented. In the genus Acinolaemus, two new sympatric species that clearly differ in shell shape are described. Acinolaemus rhamphodontis Tongkerd & Panha, sp. nov. is characterised by a depressed conical spire with a long and descending tuba, and eight apertural dentitions, while A. corusticorus Tongkerd & Panha, sp. nov. possesses a conical shell without a tuba and nine apertural dentitions. Specimens from the type locality of A. ptychochilus (the type species), A. cryptidentatus and A. mueangonensis are re-described and compared with the new species. The living snails of A. mueangonensis and A. rhamphodontis Tongkerd & Panha, sp. nov. possess blackish to translucent bodies. In addition, COI barcoding data for Clostophis and Acinolaemus are provided for the first time.},
}

@article {pmid41227545,
year = {2025},
author = {Xue, F and Zhu, X and Qin, L and Guo, Y and Sun, J and Dang, Z and Hua, L and Chu, B and Hua, R},
title = {Sex-Based Dietary Divergence in Plateau Pikas (Ochotona curzoniae) but Not Plateau Zokors (Eospalax baileyi).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227545},
issn = {2076-2615},
support = {GAU-QDFC-2024-02//Bin Chu/ ; 32201478//Bin Chu/ ; },
abstract = {Quantifying sex-specific dietary differences in small mammals reveals the internal resource allocation mechanisms within a species and provides new insights for ecosystem management and conservation practices. The plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi) are dominant small mammals that exhibit distinct lifestyles and social structures on the Qinghai-Tibetan Plateau. Despite the fact that the diets of both species have been extensively studied, sex-specific dietary differences have rarely been investigated. This study employed DNA metabarcoding combined with a self-constructed plant DNA barcode database to analyze the diet composition and trophic niche of male and female plateau pika and plateau zokor during the growing season. The results showed that male and female plateau pika consumed 39 and 37 plant species, respectively, and male and female plateau zokor consumed 38 and 39 plant species, respectively. With respect to the plateau pika, males showed a significantly higher intake of Phlomoides umbrosa than females (p < 0.05), whereas females consumed a significantly greater proportion of tuberous plants (p < 0.05). Females also exhibited a significantly greater dietary diversity and trophic niche breadth than males. But there was no significant difference in dietary diversity and trophic niche breadth between the sexes in the plateau zokor. In conclusion, our results show that dietary differences between males and females depend on each species' lifestyle. Social, surface-living pikas show apparent sex-based differences, while solitary, underground-living zokors do not.},
}

@article {pmid41223485,
year = {2025},
author = {Zhao, M and Song, H and Zheng, Y and Qin, L and Liu, X and Deng, S and Liu, J and Chen, L and Du, W and Wang, Z},
title = {A proof-of-principle study: Species identification based on mitochondrial 12S rRNA gene using QNome nanopore sequencing.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103388},
doi = {10.1016/j.fsigen.2025.103388},
pmid = {41223485},
issn = {1878-0326},
abstract = {Accurate species identification can provide crucial evidence to aid criminal investigations and preserve species diversity. DNA barcoding is an effective tool to ascertain the origin of degraded, trace, or processed samples, and the mitochondrial 12S rRNA gene serving as a potential marker due to its low intraspecific variation and high interspecific variation. QNome nanopore sequencing, with its flexible read lengths, real-time analysis, and portable device size, offers new means for species identification. In this proof-of-principle study, we collected 12S rRNA gene reference sequences of 120 common species from Genbank genetic sequence database and conducted sequence similarity analysis to evaluate the applicability of this genetic marker. The automated species identification pipeline, ClassIdent, based on QNome nanopore sequencing of the 12S rRNA gene, was subsequently developed as an open-source tool. We sequenced 60 tested samples from different animals using the QNome sequencer, and ClassIdent was employed to detect matching proportions and generate consensus sequences. Out of the 60 tested samples, 53 matched the sequences of their corresponding species, while the remaining seven matched sequences from closely related species within the same genus or family. The average proportion of sequencing reads assigned to the reference sequence was 95.66 %, with an average sequence similarity of 99.11 %. The consensus sequences generated by ClassIdent demonstrated high accuracy, showing an average sequence similarity of 99.34 % compared to Sanger sequences. Overall, this pipeline demonstrated the potential of using 12S rRNA gene for species identification via Qnome nanopore sequencing. However, further research is needed to incorporate more DNA barcoding markers or to detect the whole mitochondrial genome based on long read sequencing technology.},
}

@article {pmid41223244,
year = {2025},
author = {Pontes, A and Silva, MR and Rutkowski, D and Carvalho, C and Coito, J and Capela, N and Groenewald, M and Brito, PH and Gonçalves, C and Vannette, RL and Sampaio, JP},
title = {Zygosaccharomyces progenitor sp. nov., a new yeast species associated with bees of the genera Apis and Bombus.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006957},
pmid = {41223244},
issn = {1466-5034},
mesh = {Animals ; *Phylogeny ; Bees/microbiology ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; Mycological Typing Techniques ; *Zygosaccharomyces/classification/genetics/isolation & purification ; Japan ; DNA Barcoding, Taxonomic ; Portugal ; United States ; Honey/microbiology ; Genome, Fungal ; },
abstract = {A novel ascomycetous yeast species of the genus Zygosaccharomyces is proposed, based on isolates obtained in Japan, Portugal and the USA, and on a combination of conventional DNA barcode sequence analyses and whole-genome phylogenies. The new species is described as Zygosaccharomyces progenitor sp. nov. (PYCC 7198[T]) and was found in association with bees (Apis mellifera and Bombus spp.) and their honey, besides being found in plants and soil. The novel species belongs to a Zygosaccharomyces subclade that also harbours Zygosaccharomyces rouxii. Although the two species can be differentiated at the sequence level, they cannot be distinguished at the phenotypic level. As is typical of the genus, Z. progenitor sp. nov. produces spherical ascospores after cell conjugation.},
}

Animals
*Phylogeny
Bees/microbiology
DNA, Fungal/genetics
Sequence Analysis, DNA
Mycological Typing Techniques
*Zygosaccharomyces/classification/genetics/isolation & purification
Japan
DNA Barcoding, Taxonomic
Portugal
United States
Honey/microbiology
Genome, Fungal

@article {pmid41222779,
year = {2025},
author = {Wei, R and Li, Q},
title = {Comparative plastomes and phylogenetic relationships of Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon from plastomes and ITS.},
journal = {Genetica},
volume = {153},
number = {1},
pages = {33},
pmid = {41222779},
issn = {1573-6857},
mesh = {*Phylogeny ; *Genome, Plastid ; Evolution, Molecular ; *Phyllanthus/genetics/classification ; RNA, Transfer/genetics ; *Plastids/genetics ; RNA, Ribosomal/genetics ; },
abstract = {Phylogenomic approaches effectively minimize topological incongruences caused by heterogeneous gene evolutionary rates among lineages. The taxonomic status of Breynia, Glochidion, Synostemon, and Sauropus-whether they should be merged into Phyllanthus or retain their separate generic status-remains controversial. Moreover, these taxonomic revisions lack evidences from phylogenomic evidence. In this study, we assembled the first complete plastid genomes of Breynia disticha, Glochidion eriocarpum, G. hirsutum, G. lanceolarium, Phyllanthus fluitans, Sauropus androgynus, and Synostemon bacciformis to elucidate plastome evolutionary dynamics and resolve phylogenetic relationships among these five genera. The plastomes ranged in size from 152,927 to 157,460 bp, encoding a conserved set of 78 protein-coding genes, 35-36 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes, totaling 117-118 unique genes. Notably, 12 novel tRNA secondary structures were identified, potentially linked to lineage-specific adaptations. Structural variation at the LSC/IRb boundary, driven by IRb expansion-contraction dynamics, resulted in significant gene length and content heterogeneity. Divergence hotspot analyses identified petA-psbJ, rpl22, ndhF-rpl32, and ycf1 as hypervariable loci suitable for DNA barcoding applications. Positive selection signals were detected in five genes (ndhB, rpl33, rps15, ycf2, ycf4), suggesting their critical roles in environmental adaptation. Phylogenomic discordance between plastid and nuclear ribosomal DNA (nrDNA) datasets was pervasive across Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon, likely attributable to historical hybridization or chloroplast capture events. Given that the intergeneric boundaries among Breynia, Glochidion, Phyllanthus s.s., Sauropus, and Synostemon are obscure and that extensive cytonuclear discordance exists, we recommend accepting a broad circumscription of Phyllanthus.},
}

*Phylogeny
*Genome, Plastid
Evolution, Molecular
*Phyllanthus/genetics/classification
RNA, Transfer/genetics
*Plastids/genetics
RNA, Ribosomal/genetics

@article {pmid41219063,
year = {2025},
author = {Hulevata, I and M Porteiro, F and Giacomello, E and Catarino, D},
title = {On the occurrence of the snakefish Trachinocephalus myops (Aulopiformes: Synodontidae) in the Azores archipelago.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70266},
pmid = {41219063},
issn = {1095-8649},
support = {UIDB/05634/2025//Fundação para a Ciência e a Tecnologia/ ; UIDP/05634/2025//Fundação para a Ciência e a Tecnologia/ ; UIDP/05634/2020//Fundação para a Ciência e a Tecnologia/ ; M1.1.A/FUNC.UI&D/003/2021-2024//Azores Government/ ; M1.1.A/REEQ.CIENTÍFICO UI&D/2021/010//Azores Government/ ; },
abstract = {The snakefish Trachinocephalus myops is an Atlantic species distributed in tropical and temperate coastal waters on sandy substrates. This study reports the validated record of an adult T. myops in the Azores archipelago caught by a fisherman at Faial Island. Meristic, morphometric characters and molecular analyses supported species identity. The possibilities of recurrent misidentification or recent colonization of the species in the region and its biogeographic affinities are discussed. T. myops is hereby included as a native species in the Azores.},
}

@article {pmid41218139,
year = {2025},
author = {He, L and Dang, K and Sun, Q and Wang, W and Li, W and Zhang, W and Ye, K and Wang, H and Li, Z and Guo, Y and Li, Z and Yao, C and Li, P and Huang, Y and Zhao, X},
title = {High-Resolution Multiplexed Sequencing of Single-Cell Full-length Transcriptome Via Combinational Barcoded Tn5 Transposon Insertion.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e16013},
doi = {10.1002/advs.202516013},
pmid = {41218139},
issn = {2198-3844},
support = {82361138570//National Natural Science Foundation of China/ ; 81827901//National Natural Science Foundation of China/ ; 32371393//National Natural Science Foundation of China/ ; 2022YFC2702701//National Key R&D Program of China/ ; },
abstract = {The technological advancements in single-cell transcriptome analysis make significant progress in both depth and breadth. However, balancing the cell analysis throughput with full-length transcript coverage remains a persistent challenge. Here, CBTi-seq (Combinational Barcoded Tn5 Transposon Insertion sequencing) is reported, leveraging Tn5 transposase-mediated molecular assembly of combinatorial barcodes and unique molecular identifiers (UMIs) to enable high-resolution multiplexed sequencing of the full-length transcriptome in single cells. This approach achieves molecular resolution by end-to-end sequencing, enabling unambiguous reconstruction of splice variants and structural variations with base-pair precision. The design of orthogonal combination barcode Tn5 reduces DNA barcode diversity while enhancing multiplexing flexibility, and Tn5-delivered UMIs insertion eliminates read bias, providing accurately quantifies transcript abundance through the tagging of each fragment. The method is compatible with both single-cell and spatially resolved tissue microenvironment. Compared with commercial terminal library and other full-length sequencing methods, CBTi-seq achieves superior sensitivity and resolution while significantly reducing costs and work time (≈5 h). Moreover, cell-type-specific alternative splicing patterns are robustly identified in both gene-edited cells and human testicular cells, leveraging this high-resolution capability to further reveal modality dynamic events and isoform switching independent of gene expression changes during spermatogenesis with the potential to reproductive development and diagnostic treatment.},
}

@article {pmid41218017,
year = {2025},
author = {Patterson, EC and Morrison-Lanjouw, S and Jobling, MA and Wetton, JH},
title = {Rapid on-site universal vertebrate species identification via multi-barcode nanopore sequencing.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336383},
pmid = {41218017},
issn = {1932-6203},
abstract = {The growing illegal wildlife trade (IWT) threatens biodiversity and is a conduit for zoonotic disease, yet its risk of detection is low. Once processed, trafficked species are difficult to identify morphologically, and currently require DNA-based approaches that are time-consuming, costly, and lab-based. There is thus a need for a rapid, cheap, on-site method for species identification. We describe VeRIF-ID (Vertebrate Rapid In-Field Identification via DNA), a method that employs simultaneous on-site nanopore sequencing of four different mitochondrial DNA barcodes. Primers were designed to produce short amplicons to aid analysis of damaged DNA, and to be effective over a broad taxonomic range of vertebrates from lamprey to chimpanzee. Validation demonstrated species-level identification in 91% of 83 tested species, and genus/tribe-level identification of the remaining species (which are also problematic with existing approaches). DNA extraction, PCR and library preparation steps were simplified and optimised so that sampling to species identification takes <3 h for a single sample. Species components are identifiable non-quantitatively in prepared mixtures of muscle tissue from up to five species, and laboratory tests of Traditional East Asian Medicine samples reveal DNA from species including critically endangered saiga antelope and black rhinoceros. In conjunction with a portable Bento Lab device the necessary equipment and reagents are easily portable, and we apply the method to analyse seized bushmeat and fish samples within an airport customs zone, identifying mammal and fish species in 15 samples within 6 h. The initial equipment costs for VeRIF-ID are ~ $8K, and the cost per sample of ~$10-48 (depending on set-up), considerably cheaper than current conventional lab-based approaches. The method requires only basic hands-on skills. Ongoing trials with potential end-users will focus on establishing forensic reporting criteria prior to casework implementation. Future development of user-friendly bioinformatic interfaces will aim to fully democratise species identification.},
}

@article {pmid41216496,
year = {2025},
author = {Zhou, LN and Wu, SZ and Ma, Q and Jia, XW and Li, P and Jin, XJ and Zhang, YH},
title = {Phylogenomic Analyses and DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72399},
pmid = {41216496},
issn = {2045-7758},
abstract = {Moraceae, with its seven tribes, 45 genera, and approximately 1200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for 46 other species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 158,459 to 162,594 bp in length. Comparative plastome analyses revealed 10 highly variable regions (ndhF-rpl32, rps4-trnT, rps15-ycf1, trnC-petN, ycf1). A total of 5350 dispersed and tandem repeats along with 4751 simple sequence repeats (SSRs) were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes ndhK, ndhD, rps2, and rps12 displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as clpP, ndhC, ndhI, etc. Additionally, 13 optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity toward the end of the Cretaceous period. Overall, the resolution of Moraceae tribal-level phylogeny provides a foundational framework for revising taxonomic classifications. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.},
}

@article {pmid41210971,
year = {2025},
author = {Wu, JW and Yang, M and Chen, CC and Au, G and Wang, S and Xu, Y and Chern, GW and Huang, CH},
title = {Robust calibration and quantification of FRET signals using multiplexed biosensor barcoding.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113743},
pmid = {41210971},
issn = {2589-0042},
abstract = {Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) underpins many genetically encoded fluorescent biosensors for monitoring biochemical activities in live cells. However, the FRET ratio (acceptor-to-donor signal ratio), commonly used as a proxy for FRET efficiency, is highly sensitive to imaging parameters, complicating data interpretation. Using FP-based barcodes, we introduced calibration standards into subsets of cells for normalization of fluorescence signals. Theoretical analysis indicated the need for both high- and low-FRET standards for calibration under different excitation intensities. We validated this prediction using engineered "FRET-ON" and "FRET-OFF" standards, demonstrating that calibrated FRET ratios are independent of imaging conditions. Including donor-only and acceptor-only cells enabled simultaneous determination of FRET efficiency for multiple biosensors. Calibration also restored expected reciprocal changes in donor and acceptor signals, often obscured by imaging fluctuations and photobleaching. Together, our studies introduce a simple strategy for robust, multiplexed FRET biosensor imaging, facilitating cross-experimental and long-term studies.},
}

@article {pmid41210617,
year = {2025},
author = {Neo, I and Loh, RK and Cho, TJY and Puniamoorthy, N and Yeo, DCJ and Tan, MK},
title = {First DNA barcodes and morphometric analysis of Singaporean Tetrigidae (Orthoptera, Caelifera) support color variations as intraspecific polymorphism through integrative taxonomy.},
journal = {ZooKeys},
volume = {1257},
number = {},
pages = {305-326},
pmid = {41210617},
issn = {1313-2989},
abstract = {Integrative taxonomy refers to the practice of incorporating multiple lines of evidence, including morphology and genetics, to delineate species. While both morphology and genetic markers, such as the Cytochrome c oxidase subunit I (COI), have been widely applied in insect taxonomy, their use remains limited in the taxonomic studies of pygmy grasshoppers (Orthoptera: Tetrigidae). Currently, DNA barcodes for tetrigids, especially from Southeast Asia, remain scarce. This limitation is especially pressing given the extensive color variation documented in pygmy grasshoppers, which has rarely been systematically tested to determine whether such variation represents intraspecific polymorphisms or species differences. Historically, color polymorphism has even led to erroneous species delimitation. In this study, we examined taxa from Singapore previously reported to exhibit color variation and applied an integrative taxonomic framework to investigate whether these morphs represent intraspecific polymorphism or species-level differences. Our analyses combined morphometrics of 22 characters with principal component analyses, and DNA barcoding using short gene fragments of COI and small ribosomal RNA subunit III (12S). We focused on four taxa: two morphospecies of Coptotettix, Loxilobus insidiosus (Bolívar, 1887), and Thoradonta nodulosa (Stål, 1861). DNA barcoding revealed that color morphs are genetically similar, and morphometric analysis likewise showed no distinct clustering. Together, these results indicate that different color morphs indeed represent intraspecific polymorphisms. More importantly, we demonstrate that combining molecular data with morphological evidence offers an effective, integrative framework for resolving taxonomic challenges within tetrigids and highlights the value of integrative approaches for clarifying species boundaries in morphologically variable taxa.},
}

@article {pmid41210614,
year = {2025},
author = {Theron, GL and Ellis, AG and Midgley, JM},
title = {A revision of a spring-active clade of Prosoeca Schiner, 1867 (Diptera, Nemestrinidae), keystone pollinators from the Greater Cape Floristic Region in South Africa, with descriptions of three new species.},
journal = {ZooKeys},
volume = {1257},
number = {},
pages = {249-284},
pmid = {41210614},
issn = {1313-2989},
abstract = {Prosoeca Schiner, 1867 is the most diverse genus of Nemestrinidae in Africa and is endemic to southern Africa. The 37 described species in this genus are all thought to be important pollinators for the plants that they visit. A recent phylogenetic study has shown that the diversity of this group is far larger than is formally recognised. Using of the phylogeny published by Theron et al. (2020), the monophyletic clade of six species from the Succulent Karoo that are on the wing during the spring flowering season are revised. The known species are redescribed and three new species are described: Prosoeca ora sp. nov., P. aquilo sp. nov., and P. parva sp. nov. A lectotype is designated for Prosoeca peringueyi Lichtwardt, 1920. DNA barcodes have been generated for five species to aid molecular identification of species.},
}

@article {pmid41210188,
year = {2025},
author = {Lv, X and Zhang, X and Azad, R and Zaman, M},
title = {Biosystematics of Angulitermes dehraensis in the Northwestern Indomalayan region by integrating morphometrics and distributional data with DNA barcoding.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1695789},
pmid = {41210188},
issn = {2673-8600},
abstract = {Termites are eusocial and economically important insects which are found in the world's tropical regions as a harmful or beneficial organism. They play a dual role, both as pests damaging crops and urban structure and as an ecological engineer sustaining the ecosystem. Pakistan is part of the Indomalayan realm hosting diverse flora and fauna including termites; however, the status (diversity, distribution, feeding hosts, pest and non-pest) of the genus Angulitermes in the northwestern region (Khyber Pakhtunkhwa, Pakistan) has been largely neglected. Termite cultures were collected from diverse ecosystems, cleaned, and preserved in alcohol-filled vials for subsequent morphometric identification and DNA barcoding. Coordinates with relevant ecological data were also recorded. Soldiers were used for capturing refined images and morphometric identification through available literature, which resulted as an Angulitermes dehraensis and a new locality record. A revised and updated world's species list for the genus was made along with the distribution map of this study via ArcGIS. The identified representative soldier's leg was processed for mtDNA extraction followed by amplification and sequencing. The received sequence was subjected to BLASTn search, and only top 15 sequences via BLASTn search and then via manual search for taxon Angulitermes were retrieved from GenBank. Aligned and trimmed sequences were processed for phylogenetic tree (neighbor-joining and maximum-likelihood) construction and validation of understudy species sequence analogy. A novel sequence was submitted to GenBank for accession number (PX423737). Based on the available and recorded feeding host substrate data, it is a pest species which needs management.},
}

@article {pmid41209357,
year = {2025},
author = {Fraga Dornellas, L and Mata, VA and Mendes, S and Leitão, R and Bartz, M and Nascimento, E and Costa, J and Sousa, JP and Cunha, L},
title = {Establishing DNA-Based Strategies for Soil Biodiversity Assessment: Insights From Carabid Beetles.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72461},
pmid = {41209357},
issn = {2045-7758},
abstract = {Molecular-based methods offer valuable opportunities for assessing soil biodiversity in different ecosystems. However, their reliability and large-scale applicability depend on developing, optimizing protocols and establishing high quality, curated local reference databases. This study aimed to evaluate key steps in soil macroinvertebrate metabarcoding workflow, including the sample decontamination process and the efficiency of taxa recovery. Specifically, we sought to: (1) determine the impact of sample decontamination, (2) validate species-level recovery efficiency of the metabarcoding pipeline spiked with a curated mock community of morphologically identified and barcoded carabid beetles, and (3) compare traditional morphological identification and metabarcoding for specimens' taxonomic assignment and recovery. Our results showed that the commonly used decontamination process did not significantly impact OTU richness, suggesting it is not essential for this fauna. Compared to morphology, to metabarcoding provided a more comprehensive taxonomic overview at higher level taxa. However, validation with the mock community revealed discrepancies in species-level recovery, underscoring that its accuracy is highly contingent on the quality of the reference database. DNA metabarcoding is a currently used and promising technique for macroinvertebrate assessment regarding time, efficiency, and costs, yet reaching greater depth in taxonomic resolution. Yet, its species-level accuracy remains dependent on comprehensive and well-curated barcode reference databases. We recommend an integrative approach, combining molecular data with targeted validation, for the most robust outcomes. For this reason, we recommend the use of integrative methodologies for robust and rapid biodiversity assessments. We found that the common decontamination step is not crucial for soil macrofauna metabarcoding accuracy. Consequently, its removal streamlines sample processing.},
}

@article {pmid41208904,
year = {2025},
author = {Pykälä, J and Myllys, L},
title = {Unexpected species richness of the lichen genus Protoblastenia (Lecanorales, Psoraceae) in Finland.},
journal = {MycoKeys},
volume = {124},
number = {},
pages = {193-226},
pmid = {41208904},
issn = {1314-4049},
abstract = {The taxonomy of Protoblastenia in Finland was studied, based on morphology and molecular data (nuITS rDNA sequences). Twenty species were recognised, with sixteen species being newly described here: P. arupii sp. nov., P. borealis sp. nov., P. compressa sp. nov., P. dolomitica sp. nov., P. ekmanii sp. nov., P. fennoarctica sp. nov., P. minuta sp. nov., P. oulankaensis sp. nov., P. pseudocompressa sp. nov., P. pseudoterricola sp. nov., P. remota sp. nov., P. rikkinenii sp. nov., P. saanaensis sp. nov., P. timdalii sp. nov., P. violacea sp. nov. and P. westbergii sp. nov. All species are confined to calcareous rocks, except P. terricola which also grows on calcareous soil. The calcareous fells in Enontekiö in NW Finland were identified as hot spots of Protoblastenia diversity. Nine newly-described species (P. arupii, P. fennoarctica, P. minuta, P. pseudoterricola, P. rikkinenii, P. saanaensis, P. timdalii, P. violacea and P. westbergii) are restricted to this area in Finland. Several of the species are semi-cryptic. On average, they may have minor morphological differences, but many specimens cannot be identified, based on morphology only. Protoblastenia rikkinenii is reported from Norway and P. oulankaensis from Italy, based on GenBank sequences. Full descriptions and a preliminary key of Protoblastenia in Finland are provided.},
}

@article {pmid41204963,
year = {2025},
author = {Diani Gohar, S and Soorni, A},
title = {Plastome diversity and phylogenomic analysis of Satureja (Lamiaceae): uncovering evolutionary patterns and diagnostic markers.},
journal = {Planta},
volume = {262},
number = {6},
pages = {149},
pmid = {41204963},
issn = {1432-2048},
mesh = {Phylogeny ; *Genome, Chloroplast/genetics ; *Satureja/genetics/classification ; Evolution, Molecular ; Genetic Markers ; Genetic Variation ; },
abstract = {The chloroplast genomes of Satureja are highly conserved but contain hypervariable loci like ndhF and ycf1. These loci provide powerful molecular tools for precise species identification, phylogenetic resolution, and future conservation efforts in this important genus. The genus Satureja (Lamiaceae) comprises a valuable number of aromatic herbs and shrubs with significant ecological, medicinal, and economic value, particularly in the Mediterranean and Southwest Asia. Satureja species are renowned for their therapeutic essential oils, yet their chloroplast (cp) genomic resources remain vastly understudied, with only S. montana complete cp genome available. To address this gap, we sequenced and analyzed the complete cp genomes of three taxonomically and ecologically distinct Satureja species (S. hortensis, S. khuzestanica, and S. montana subsp. variegata) and a new individual of S. montana, using Illumina sequencing and comparative genomic approaches. The assembled cp genomes exhibited a conserved quadripartite structure, with sizes ranging narrowly from 151,777 to 151,924 bp, featuring typical large (LSC) and small (SSC) single-copy regions flanked by inverted repeats (IRs). Genome annotation revealed 128-130 genes, including core photosynthetic and ribosomal genes, with notable interspecific variation in tRNA copy numbers. Comparative analyses identified hypervariable loci (ndhF, ycf1, petN) as promising DNA barcodes for species discrimination, while codon use bias strongly favored A/T-ending codons. Simple sequence repeats (SSRs) were predominantly mononucleotide (A/T), and long repetitive sequences showed species-specific length polymorphisms. Phylogenetic reconstruction using the whole cp genomes strongly supported the monophyly of Satureja and resolved infrageneric relationships with high bootstrap confidence (> 90%), placing these species in a distinct clade sister to Thymus and Mentha. Our study provides the first comprehensive cp genomic resource for Satureja, elucidating evolutionary patterns, identifying molecular markers for taxonomy, and establishing a foundation for future conservation and biotechnological applications in this economically important genus.},
}

Phylogeny
*Genome, Chloroplast/genetics
*Satureja/genetics/classification
Evolution, Molecular
Genetic Markers
Genetic Variation

@article {pmid41204855,
year = {2025},
author = {Viruel, J and Sweeney, CJ and Day, R and White, K and Dawson, W and Myer, B and Floyd, K and Corcoran, M and Kelting, C and Poncet, S and Forest, F and Clubbe, C and Newton, RJ},
title = {Phylogenomic Barcoding of Soil Seed Bank-Persistent and Wind-Dispersed Non-Native Plant Species in South Georgia.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70068},
doi = {10.1111/1755-0998.70068},
pmid = {41204855},
issn = {1755-0998},
support = {DPLUS080//Darwin Initiative/ ; RYC2023-042611-I//MCIU/AEI/10.13039/501100011033 and FSE+/ ; },
abstract = {Climate change and invasive species are leading drivers of biodiversity loss, with island ecosystems being especially vulnerable. South Georgia, a remote sub-Antarctic island, is 170 km long with approximately 30,000 ha of vegetated coastal areas, as snow and ice dominate the inland regions. Human activities on the island have historically introduced non-native species, resulting in 41 introduced vascular plant species compared with only 24 native ones. To address this imbalance, the South Georgia Non-Native Plant Management Strategy was implemented (2016-2020) to control non-native plant populations. We assessed emergent seedlings from South Georgia soil samples and wind-dispersed seeds to determine which species persist in the soil seed bank and contribute to dispersal. Using a molecular barcoding approach, we evaluated traditional markers (rbcL and matK) and optimized a high-throughput Angiosperms353 sequencing pipeline for accurate seedling identification. We generated a reference library covering all native and non-native species and applied this to 1,498 emergent seedlings and 737 trapped seeds. Molecular barcoding identified 21 species, including 10 non-natives and 11 natives. Strikingly, 84% of emergent seedlings were non-native, with Class III invasive species (Cerastium fontanum, Poa annua, Taraxacum officinale) dominating across most sites and in all wind traps. By contrast, Class I and II species occurred rarely and only at a few sites, indicating that management efforts have substantially reduced their spread, though viable seeds persist in the soil. These findings highlight both the continued threat from persistent seed banks of dominant invaders and the value of molecular barcoding for long-term monitoring. Our approach provides a framework for biosecurity and restoration management in South Georgia and other vulnerable ecosystems under climate change pressures.},
}

@article {pmid41204321,
year = {2025},
author = {Wang, Y and Xie, Y and Jin, J and Li, J and Lai, X and Qiu, X and Tong, Y and Zhang, Z},
title = {New insights into the phylogenetic and biogeographic analysis of Elaeocarpus (Elaeocarpaceae) in China, and further consolidated 'Acronodia' as a distinct group.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1524},
pmid = {41204321},
issn = {1471-2229},
support = {190781//Key Science and Technology Research Project in Jiangxi Province Department of Education/ ; 31110103911//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; China ; *Genome, Chloroplast/genetics ; Phylogeography ; DNA, Chloroplast/genetics ; },
abstract = {BACKGROUND: Elaeocarpus is the most species-rich genus in Elaeocarpaceae (Oxalidales), comprising 39 species of trees that grow in tropical and subtropical forests in China, 14 of which are endemic. Few studies to focus on the phylogeny of Elaeocarpus in China. Limited available evidence indicates a close phylogenetic relationship between Sect. Ganitrus and Sect. Dicera, while the question of whether the 'Acronodia' group warrants taxonomic separation from Sect. Monocera remains unresolved. The status of group 'Acronodia' in Elaeocarpus is uncertain because the combination of molecular fragments available to construct the phylogenetic tree has not been evaluated.

RESULTS: In this study, we compared chloroplast genome sequences on the basis of the alignment of 4 chloroplast genome sequences with the mVISTA and KaKs_Calculator tools. The results revealed that the phylogeny has good bootstrap value for ycf1, ITS and trnS-atpA and that 27 Elaeocarpus species (40 samples), including 3 species that are distributed naturally outside China, are grouped into 2 major clades: one comprising Sect. Ganitrus and Sect. Dicera, and the other consisting of Sect. Monocera and the 'Acronodia' group. Furthermore, the results of the phylogenetic analysis with the BEAST tool suggest that Elaeocarpus originated from Southwest China during the early Eocene (40 Ma) and started to diversify south of the Yangtze River during the early Miocene (15 Ma).

CONCLUSION: Overall, this study highlights the taxonomic utility of chloroplast genomes in Elaeocarpus, and the time and regions of origin will facilitate future studies on conservation.},
}

*Phylogeny
China
*Genome, Chloroplast/genetics
Phylogeography
DNA, Chloroplast/genetics

@article {pmid41203862,
year = {2025},
author = {Dagher, M and Ongo, G and Robichaud, N and Kong, J and Rho, W and Teahulos, I and Tavakoli, A and Bovaird, S and Merjaneh, S and Tan, A and Edwardson, K and Scheepers, C and Ng, A and Hajjar, A and Sow, B and Vrouvides, M and Lee, A and DeCorwin-Martin, P and Rasool, S and Huang, J and Erps, T and Coffin, S and Rashidi, NM and Han, Y and Chandrasekaran, SN and Miller, L and Kost-Alimova, M and Skepner, A and Singh, S and Carpenter, AE and Munzar, JD and Juncker, D},
title = {nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41203862},
issn = {1548-7105},
abstract = {Existing high-plex protein measurement tools compromise on quantification, precision and cost efficiency. Here, to address this, we present nELISA, a platform that combines a DNA-mediated, bead-based sandwich immunoassay with advanced multicolor bead barcoding. Antibody pairs are preassembled on target-specific, barcoded beads, which ensures spatial separation between noncognate assays. Detection antibodies are tethered via flexible single-stranded DNA to enable efficient ternary sandwich formation. Detection is achieved through toehold-mediated strand displacement, where fluorescently labeled DNA oligos simultaneously untether and label detection antibodies. nELISA delivers sub-picogram-per-milliliter sensitivity across seven orders of magnitude. Using a 191-plex inflammation panel, we profiled cytokine responses in 7,392 peripheral blood mononuclear cell samples, generating ~1.4 million protein measurements and revealing over 440 robust cytokine responses, including previously unreported effects. nELISA thus provides a simple, scalable and cost-efficient solution for large-scale, high-fidelity phenotypic screening.},
}

@article {pmid41203832,
year = {2025},
author = {Lewis, SM and Berthelet, J and Whitehead, LW and Rajasekhar, P and El-Saafin, F and Bell, C and Naik, S and Merino, D and Wimmer, VC and Rogers, KL},
title = {LeGO-3D: 3D imaging of lung metastases and vascularisation using light sheet fluorescence microscopy.},
journal = {Npj imaging},
volume = {3},
number = {1},
pages = {58},
pmid = {41203832},
issn = {2948-197X},
support = {GNT2036844//National Health and Medical Research Council/ ; GNT2027459//National Health and Medical Research Council/ ; MCRF21011//Victorian Cancer agency/ ; IIRS0049//National Breast Cancer Foundation/ ; },
abstract = {Cancer metastasis involves a complex cascade of events, where cancer cells migrate from their site of origin to secondary sites via the lymphatic and circulatory system. During this process, some cancer subclones will successfully 'seed' at distant organs to generate lethal metastases. Here, we optimised a method for tracking cancer cells in metastatic breast cancer tumours and investigated their complex interplay with the lung vasculature using lentiviral-based optical barcoding (LeGO). Given the regional heterogeneity in lung tissue microenvironments as well as lobar asymmetry, we used light sheet microscopy to perform three-dimensional (3D) imaging of wholemount lung lobes. The results revealed that polychromatic metastases occurred less frequently than monochromatic metastases and were more likely to be located nearer to blood vessels in both spontaneous (i.e. mammary fat pad injections) and experimental (i.e. tail vein injections) mouse assays of metastasis. This 3D imaging and analytic pipeline can provide unique insights about metastatic heterogeneity and dynamics, and represents a new avenue for studying therapeutic response across large volumes of lung tissue.},
}

@article {pmid41202131,
year = {2025},
author = {Liu, Y and Ban, Y and Gao, D},
title = {Oligo-CALL: A next-generation barcoding platform for studying resistance to targeted therapy.},
journal = {Science advances},
volume = {11},
number = {45},
pages = {eadw9990},
doi = {10.1126/sciadv.adw9990},
pmid = {41202131},
issn = {2375-2548},
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; Cell Line, Tumor ; CRISPR-Cas Systems ; *Lung Neoplasms/genetics/drug therapy/pathology ; Single-Cell Analysis ; Molecular Targeted Therapy ; Proto-Oncogene Proteins p21(ras)/genetics/antagonists & inhibitors ; },
abstract = {Understanding therapy resistance requires deconvolving heterogeneous cell populations and tracking clonal trajectories. While CRISPR-based cellular barcoding is powerful for lineage tracing, many platforms suffer from low efficiency and limited compatibility with single-cell transcriptomics. We developed Oligo-CALL (Oligonucleotide-inducible CRISPR transcriptional activator-Assisted Lineage Labeling), an advanced barcoding system enabling precise lineage tracing, live clone isolation, and seamless integration with single-cell RNA sequencing. Applied to lung cancer cells treated with a KRAS[G12C] inhibitor, Oligo-CALL identified clones consistently enriched posttreatment, supporting a model of predestined resistance. Oligo-CALL achieved >95% efficiency in linking lineage identity to transcriptomes, uncovering diverse clone-specific pathways with underlying resistance. Paired analysis of barcode-matched clones from naïve and resistant populations revealed transient and fixed resistance phenotypes. Notably, DNA repair pathways are recurrently altered in resistant clones, and inhibition of poly(adenosine 5'-diphosphate-ribose) polymerase synergizes with KRAS G12C inhibition to overcome resistance. Together, Oligo-CALL provides a versatile platform for dissecting lineage evolution and molecular dynamics of targeted therapy resistance.},
}

Humans
*Drug Resistance, Neoplasm/genetics
Cell Line, Tumor
CRISPR-Cas Systems
*Lung Neoplasms/genetics/drug therapy/pathology
Single-Cell Analysis
Molecular Targeted Therapy
Proto-Oncogene Proteins p21(ras)/genetics/antagonists & inhibitors

@article {pmid41198699,
year = {2025},
author = {Lin, R and Xu, Y and Yang, S and Chen, S and Wang, Z and Wang, K and Gao, Z and Zhao, YS},
title = {Regioselective on-surface crystallization of one-dimensional organic barcode-like heterostructures of MOFs with fluorescent stripe patterns.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9810},
pmid = {41198699},
issn = {2041-1723},
support = {2022YFA1204403//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Heterostructures, integrating different semiconducting materials in a single structure, are key components for various modern electrical and optoelectronic devices. However, it is difficult to maintain the sequential epitaxial nucleation due to the passivation of crystal seeds, thus resulting in limited spatial segments in heterostructures. Here, we report an interface-recognition assembly strategy assisted by Plateau-Rayleigh instability (PRI) to spontaneously form one-dimensional (1D) heterostructures featuring abundant fluorescent stripe patterns. Guided by 1D metal-organic frameworks (MOFs) templates with exposed electron-donating sites, the de-wetting process promotes the effective regioselective crystallization of solute molecules with electron-withdrawing feature on template surface, thus forming 1D barcode-like heterostructures. The spatial locations and number of the stripes are effectively controlled by PRI and template parameters, while their emission colors are primarily governed by the charge-transfer (CT) interactions between solutes. On this basis, we have achieved full-color and heterogeneous stripe patterns by tuning the CT strengths and controlling the stripe nucleation sequences, thus creating abundant 1D barcode-like heterostructures. Through integrating the photoisomers into stripes, these heterostructures exhibit time-dependent graphical patterns and enable construction of 2D photonic barcodes. Our work offers a supramolecular approach for patterning of well-aligned organic heterostructures and rational design of optoelectronic devices that have potential in anti-counterfeiting applications.},
}

@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}

@article {pmid41193241,
year = {2025},
author = {Kawabata, H and Miura, O},
title = {Excess of non-synonymous mutations and structural variations in mitogenomes of freshwater snails in the genus Semisulcospira.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2025.2583076},
pmid = {41193241},
issn = {2470-1408},
abstract = {Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent 'enigmatic' lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.},
}

@article {pmid41193180,
year = {2025},
author = {Hormiga, G and Lavery, AH and Arnedo, MA},
title = {The spider genus Stictonanus Millidge, 1991 in the Juan Fernandez Archipelago (Araneae, Linyphiidae): systematics and biogeography.},
journal = {Invertebrate systematics},
volume = {39},
number = {11},
pages = {},
doi = {10.1071/IS25046},
pmid = {41193180},
issn = {1447-2600},
mesh = {Animals ; *Spiders/classification/anatomy & histology/genetics ; *Phylogeny ; Phylogeography ; Male ; },
abstract = {We studied the systematics of the Juan Fernandez linyphiid species originally classified in the genus Juanfernandezia Koçak & Kemal, 2008. In an earlier study, we had hypothesized that the two Juanfernandezia species, each endemic to a single island, form a clade that was sister to the southern South American genus Notholepthyphantes Millidge, 1985. We have carried out a multi-locus phylogenetic analysis to infer the relationships of Juanfernandezia based on an extended taxon sampling. Our study shows that Juanfernandezia is sister to the South American genus Stictonanus Millidge, 1991, which until recently remained poorly known. The striking similarity of the somatic and genitalic morphology of these two genera suggest that the clade is better classified as a single genus, with Stictonanus being the oldest available generic name for this lineage. Stictonanus, circumscribed now to include five species, is sister to a lineage composed of two small genera, Notholepthyphantes and Falklandoglenes Usher, 1986. Stictonanus fernandezi (Berland, 1924) comb. nov. and Stictonanus paolae Hormiga & Arnedo, sp. nov., both from the Juan Fernandez Islands, are described and illustrated. The type species of the genus, Stictonanus paucus Millidge, 1991, and the second continental species, S. exiguus Millidge, 1991, are here redescribed and illustrated (the male of S. exiguus is described here for the first time). We further infer a time calibrated tree to discuss the biogeographic history of Stictonanus. ZooBank: urn:lsid:zoobank.org:pub:C6D833D0-0422-401C-B010-B12618B1633C.},
}

Animals
*Spiders/classification/anatomy & histology/genetics
*Phylogeny
Phylogeography
Male

@article {pmid41192368,
year = {2025},
author = {Lin, YT and Lin, YH and Shiu, YW and Han, YS},
title = {Morphological and molecular evidence reveal the Sarotherodon melanotheron invasion off Taiwan, East Asia.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118898},
doi = {10.1016/j.marpolbul.2025.118898},
pmid = {41192368},
issn = {1879-3363},
abstract = {The blackchin tilapia, Sarotherodon melanotheron Rüppell, 1852, is a highly euryhaline cichlid native to West and Central Africa. Due to its broad salinity tolerance and rapid reproduction, it has become a high-risk invasive species in brackish and coastal ecosystems worldwide. This study reports the first and northernmost confirmed record of wild blackchin tilapia population in East Asia, based on 13 specimens collected from coastal waters of Kaohsiung City, Southern Taiwan. Morphological and meristic data, together with cytochrome c oxidase subunit I (COI) gene sequencing, confirmed species identity and consistency with native and invasive populations elsewhere. The occurrence of mature individuals and a substantial wild population confirms the establishment of invasion population in Taiwanese coastal environment. Given its wide salinity tolerance and omnivorous diet, this species poses potential ecological and economic threats to native ecosystems and aquaculture. This finding also represents the northernmost record of blackchin tilapia in the western Pacific.},
}