@article {pmid40841174,
year = {2025},
author = {Chandra, G and Hossen, MH and Scholz, S and Dilthey, AT and Gibney, D and Jain, C},
title = {Pangenome-based genome inference using integer programming.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280567.125},
pmid = {40841174},
issn = {1549-5469},
abstract = {Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of haplotype-resolved pangenome graphs in addressing these challenges. Building on these developments, we propose a rigorous alignment-free genotyping method. Our optimization framework identifies a path through the pangenome graph that maximizes the matches between the path and substrings of sequencing reads (e.g., k-mers) while minimizing recombination events (haplotype switches) along the path. We prove that this problem is NP-Hard and develop efficient integer-programming solutions. We benchmarked the algorithm using downsampled short-read datasets from homozygous human cell lines with coverage ranging from 0.1× to 10×. Our algorithm accurately estimates complete major histocompatibility complex (MHC) haplotype sequences with small edit distances from the ground-truth sequences, providing a significant advantage over existing methods on low-coverage inputs. While this algorithm is designed for haploid genomes, we discuss directions for extending it to diploid genotyping.},
}

@article {pmid40835889,
year = {2025},
author = {Zhang, H and Liu, N and Wang, Y and Zheng, X and Li, W and Liu, Z and Liu, J and Wang, Y and Xing, L and Li, T and Yun, Y and Zhou, Q and Wang, M and Qin, Y and Yan, J and Gong, Z and He, Q and Du, H},
title = {Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40835889},
issn = {1546-1718},
abstract = {Common oat, belonging to the genus Avena with 30 recognized species, is a nutritionally important cereal crop and high-quality forage worldwide. Here, we construct a genus-level super-pangenome of Avena comprising 35 high-quality genomes from 14 cultivated oat accessions and 21 wild species. The fully resolved phylogenomic analysis unveils the origin and evolutionary scenario of Avena species, and the super-pangenome analysis identifies 26.62% and 59.93% specific genes and haplotypes in wild species. We delineate the landscape of structural variations (SVs) and the transcriptome profile based 1,401 RNA-sequencing (RNA-seq) samples from diverse abiotic stress treatments in oat. We highlight the crucial role of SVs in modulating gene expression and shaping adaptation to diverse stresses. Further combining SV-based genome-wide association studies (GWASs), we characterize 13 candidate genes associated with drought resistance such as AsARF7, validated by transgenic oat lines. Our study provides unprecedented genomic resources to facilitate genomic, evolution and molecular breeding research in oat.},
}

@article {pmid40835741,
year = {2025},
author = {Han, C and Lu, S and Hu, P and Chang, J and Zou, D and Li, F and Li, Y and Lu, Q and Ren, H},
title = {Machine learning based on pangenome-wide association studies reveals the impact of host source on the zoonotic potential of closely related bacterial pathogens.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1253},
pmid = {40835741},
issn = {2399-3642},
support = {CSTB2023NSCQ-MSX0515//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; },
mesh = {Animals ; *Machine Learning ; Humans ; *Genome-Wide Association Study ; *Brucella/genetics/pathogenicity/classification ; *Genome, Bacterial ; *Zoonoses/microbiology ; *Brucellosis/microbiology/transmission ; Swine ; Cattle ; Whole Genome Sequencing ; Sheep ; },
abstract = {Variations in host species significantly impact bacterial growth traits and antibiotic resistance, making it essential to consider host origin when evaluating the zoonotic potential of pathogens. This study focuses on multiple Brucella species, which share highly similar genetic material, to explore the relationship between host origin and zoonotic potential by integrating pan-genome-wide association studies (pan-GWAS) with machine learning (ML). Our results present an open pangenome of Brucella spp. derived from the whole-genome sequencing (WGS) data of 991 strains and identify 268 genes potentially associated with the zoonotic potential of Brucella. Integrating these genes into an ML model based on the support vector machine (SVM) algorithm allows us to predict the zoonotic potential of various Brucella strains with high accuracy. Our findings reveal that zoonotic potential varies by host origin: Brucella melitensis strains isolated from humans exhibit higher zoonotic potential than those isolated from cattle, goats, and sheep, while Brucella suis biovar 2 strains isolated from domestic pigs display higher zoonotic potential than those isolated from wild boars. Our study proposes a method for predicting and quantifying the zoonotic potential of closely related bacterial pathogens from different host origins, providing valuable insights for risk assessment and public health strategy.},
}

Animals
*Machine Learning
Humans
*Genome-Wide Association Study
*Brucella/genetics/pathogenicity/classification
*Genome, Bacterial
*Zoonoses/microbiology
*Brucellosis/microbiology/transmission
Swine
Cattle
Whole Genome Sequencing
Sheep

@article {pmid40830656,
year = {2025},
author = {Igolkina, AA and Vorbrugg, S and Rabanal, FA and Liu, HJ and Ashkenazy, H and Kornienko, AE and Fitz, J and Collenberg, M and Kubica, C and Mollá Morales, A and Jaegle, B and Wrightsman, T and Voloshin, V and Bezlepsky, AD and Llaca, V and Nizhynska, V and Reichardt, I and Bezrukov, I and Lanz, C and Bemm, F and Flood, PJ and Nemomissa, S and Hancock, A and Guo, YL and Kersey, P and Weigel, D and Nordborg, M},
title = {A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40830656},
issn = {1546-1718},
support = {EPICLINES//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 847548//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 1001GenomesPlus//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BB/S004661/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Making sense of whole-genome polymorphism data is challenging, but it is essential for overcoming the biases in SNP data. Here we analyze 27 genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation is mostly due to tandem repeat regions that are difficult to assemble. However, while the rest of the genome varies little in length, it is full of structural variants, mostly due to transposon insertions. Because of this, the pangenome coordinate system grows rapidly with sample size and ultimately becomes 70% larger than the size of any single genome, even for n = 27. Finally, we show how short-read data are biased by read mapping. SNP calling is biased by the choice of reference genome, and both transcriptome and methylome profiling results are affected by mapping reads to a reference genome rather than to the genome of the assayed individual.},
}

@article {pmid40829589,
year = {2025},
author = {Sibbald, SJ and Lawton, M and Maclean, C and Roger, AJ and Archibald, JM},
title = {Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.055},
pmid = {40829589},
issn = {1879-0445},
abstract = {In prokaryotes, lateral gene transfer (LGT) is a key mechanism leading to intraspecies variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens-a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Ac. anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase pairs [Mbp]), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain-level genetic variation in Ac. anophagefferens, with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. A total of 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5%-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.},
}

@article {pmid40828965,
year = {2025},
author = {Dai, S and Zhao, P and Li, W and Peng, L and Jiang, E and Du, Y and Zhang, W and Dai, X and Yang, L and Li, Z and Xu, L and Lan, X and Lyu, W and Yang, L and Fang, L and Liu, GE and Zhou, Y},
title = {Global pangenome analysis highlights the critical role of structural variants in cattle improvement and identifies a unique event as a novel enhancer in IGFBP7[+] cells.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf205},
pmid = {40828965},
issn = {1537-1719},
abstract = {Based on a pangenome graph platform, we simultaneously analyzed the impacts of SNPs and SVs in the population structure and phenotypic formation of global cattle using 2,409 individuals from 82 breeds. We demonstrated that SVs, like SNPs, effectively explain the population structure of global cattle. Genomic regions under strong selection, identified using both SNPs and SVs, consistently revealed footprints associated with human-mediated selection of economic traits in European improved cattle or natural selection of geographical adaptations. Notably, we detected that ∼40.14% of SVs were not tagged (LD, r2 < 0.6) by nearby SNPs. These "orphan" SVs may uncover new genetic signals and represent recent mutations associated with specific selection pressures or local environmental adaptation. Selected SVs tagged by SNPs also play causal or dominant roles in regions under selection. For example, our single-cell RNA sequencing has demonstrated that a notable SNP-tagged SV functions as an enhancer of the IGFBP7 gene, regulating fat deposition through IGFBP7+ cells. In conclusion, these SV-related mechanisms likely have caused some differences in economic traits and local adaptability across global cattle populations. Our integrated approaches highlight the unique and indispensable roles of SVs in shaping genetic diversity, offering novel insights into adaptation, selection, and strategies for improving cattle populations.},
}

@article {pmid40827877,
year = {2025},
author = {Kenney, SM and M'ikanatha, NM and Ganda, E},
title = {Genomic evolution of Salmonella Dublin in cattle and humans in the United States.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0068925},
doi = {10.1128/aem.00689-25},
pmid = {40827877},
issn = {1098-5336},
abstract = {Increasingly, antimicrobial-resistant (AMR) Salmonella Dublin is a threat to human and animal health, therefore requiring a One Health approach to comprehensively understand pathogen evolution. Moreover, S. Dublin dissemination throughout the United States and the food supply chain is a concern for food safety and security. Here, we leveraged multi-agency biosurveillance data and genomic sequencing of S. Dublin strains to provide a robust analysis of its evolution across human, animal, and environmental reservoirs. This study advances our understanding of AMR S. Dublin, elucidates factors driving AMR emergence, and informs interventions to protect public health. In total, 2,150 strains collected between 2002 and 2023 throughout the United States from clinical bovine (N = 581), clinical human (N = 664), and environmental (N = 905) sources were identified. After uniform quality control, raw reads were assembled de novo followed by genome annotation and characterization of plasmids, antimicrobial resistance genes, and virulence factors. Strain relatedness was evaluated using a core genome maximum-likelihood phylogeny and pairwise core genome single-nucleotide polymorphism (SNP) differences. We identified the highest prevalence of drug-specific antimicrobial resistance genes and multidrug resistance plasmid, IncA/C2 (P < 0.001), in bovine clinical strains, which also had the greatest genetic diversity. Despite source-dependent differences in antimicrobial resistance gene frequency and types, 72% of S. Dublin strains in our study differed with at least one other strain by 20 or fewer SNPs. This high degree of genomic similarity highlights the potential for cross-transmission between humans, animals, and the environment and underscores the importance of considering strain source when assessing and monitoring antimicrobial resistance.IMPORTANCESalmonella Dublin is a zoonotic, sometimes foodborne, pathogen that causes severe illness in cattle and humans. Our study takes a One Health approach to understanding genetic differences in strains within and between different reservoirs in the United States. We identified differences in antimicrobial resistance potential and genome content between clinical bovine, clinical human, and environmental strains. Nonetheless, the U.S. population of S. Dublin is highly related and diverges minimally over time and geography. These findings highlight the importance of the One Health framework when combating zoonotic antimicrobial-resistant pathogens like Salmonella Dublin.},
}

@article {pmid40811403,
year = {2025},
author = {Alanko, JN and Biagi, E and Puglisi, SJ},
title = {Finimizers: Variable-Length Bounded-Frequency Minimizers for $k$-mer Sets.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {2},
pages = {899-910},
doi = {10.1109/TCBBIO.2025.3545285},
pmid = {40811403},
issn = {2998-4165},
abstract = {The minimizer of a $k$-mer is the smallest $m$-mer inside the $k$-mer according to some total order $< $ of the $m$-mers. Minimizers are often used as keys in hash tables in indexing tasks in metagenomics and pangenomics. The main weakness of minimizer-based indexing is the possibility of very frequently occurring minimizers, which can slow query times down significantly. Popular minimizer alignment tools employ various and often wild heuristics as workarounds, typically by ignoring frequent minimizers or blacklisting commonly occurring patterns, to the detriment of other metrics (e.g., alignment recall, space usage, or code complexity). In this paper, we introduce frequency-bounded minimizers, which we call finimizers, for indexing sets of $k$-mers. The idea is to use an order relation $< $ for minimizer comparison that depends on the frequency of the minimizers within the indexed $k$-mers. With finimizers, the length $m$ of the $m$-mers is not fixed, but is allowed to vary depending on the context, so that the length can increase to bring the frequency down below a user-specified threshold $t$. Setting a maximum frequency solves the issue of very frequent minimizers and gives us a worst-case guarantee for the query time. We show how to implement a particular finimizer scheme efficiently using the Spectral Burrows-Wheeler transform ($SBWT$) (Alanko et al. Proc. SIAM ACDA, 2023) augmented with longest common suffix information. In experiments, we explore in detail the special case in which we set $t = 1$. This choice simplifies the index structure and makes the scheme completely parameter-free apart from the choice of $k$. A prototype implementation of this scheme exhibits $k$-mer localization times close to, and often faster than, state-of-the-art minimizer-based schemes.},
}

@article {pmid40802147,
year = {2025},
author = {Pushkarna, S and Kumar, A and Arora, K and Malhotra, P and Suneja, P and Dang, AS},
title = {Exploring the potential of Lactobacillus rhamnosus as gluten-digesting bacteria.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {40802147},
issn = {1863-4362},
support = {DST/INSPIRE Fellowship/2019/IF190883//INSPIRE ("Innovation in Science Pursuit for Inspired Research") Fellowship, Department of Science & Technology, under the Ministry of Science and Technology, Government of India, New Delhi/ ; },
abstract = {BACKGROUND: Celiac disease (CeD), a multifactorial disorder, develops when gluten, the toxic environmental inducer, interacts with CeD susceptibility genetic markers, resulting in a chronic enteropathy. Several extra-intestinal complications may also arise in cases of delayed management. There persists a growing demand to develop non-dietary adjuvant therapeutic options that can help relieve symptoms and improve patients' quality of life.

AIM: The present study conducted a bioinformatic approach to look into the potential of using Lactobacillus rhamnosus, a well-established probiotic, as gluten-digesting bacteria and provide the basis for future therapeutic developments.

METHODS: Complete genome assemblies of forty-nine L. rhamnosus strains were subjected to annotation using RAST and a pan genome analysis with BPGA. Genes for peptidases were identified using BlastKOALA and Prokka, followed by domain analysis using the NCBI-CD search tool to screen for gluten-digesting activity.

RESULTS: Genome annotation of all the strains under study highlighted the presence of sixty-one peptidases in L. rhamnosus. Domain analysis further revealed that nine of these peptidases, including aminopeptidase N, neutral endopeptidase, oligoendopeptidase F, dipeptidyl-peptidase 5, proline iminopeptidase, Xaa-Pro dipeptidyl-peptidase, aminopeptidase C, aminopeptidase E, and PII-type proteinase, shared domains with already established gluten-digesting enzymes, suggesting their potential role in degrading toxic gliadin peptides.

CONCLUSION: The current in silico analysis indicates that this well-known probiotic species, in addition to showcasing a plethora of beneficial properties, may also hold great potential in terms of reducing gluten toxicity. With further studies, L. rhamnosus can prove to be a promising candidate in CeD treatment and management.},
}

@article {pmid40753951,
year = {2025},
author = {Wei, CR and Basharat, Z and Adhikari, P},
title = {Implications of virtual screening for South African natural compounds against Plesiomonas shigelloides, a pathogen with zoonotic potential.},
journal = {Computers in biology and medicine},
volume = {196},
number = {Pt B},
pages = {110882},
doi = {10.1016/j.compbiomed.2025.110882},
pmid = {40753951},
issn = {1879-0534},
abstract = {Plesiomonas shigelloides is an emerging pathogen associated with gastroenteritis and poses a growing public health concern, especially in regions with limited access to advanced medical treatments. The purpose of this study was to explore the therapeutic potential of South African natural product compounds against P. shigelloides by targeting the essential enzyme Pyridoxine 5'-phosphate synthase or PPS (encoded by PdxJ). P. shigelloides proteomes (n = 26) were processed using the Bacterial Pan Genome Analysis (BPGA) pipeline to identify conserved targets. Targeting conserved protein ensures the potential for broad-spectrum efficacy. PPS was chosen as drug target and its structure was predicted using AlphaFold, enabling high-confidence modeling. Subsequently, docking was performed using AutoDock Vina, focusing on a library of South African compounds (n > 1000). The three inhibitors demonstrating strong binding affinities to the PPS were Scutiaquinone A, Mesquitol-(4α→5)-3,3',4',7,8-pentahydroxyflavonone, and Riccardin C. To further validate the stability and efficacy of these interactions, molecular dynamics (MD) simulations were carried out for 100 ns. The simulations revealed stable interactions between the inhibitors and PPS, suggesting potential inhibition of the PPS enzyme. Mesquitol derivative was found to be the safest and recommended for further experimental validation. This study highlights the promising potential of South African natural compounds in combating P. shigelloides infections, paving the way for the development of novel therapeutic strategies.},
}

@article {pmid38421269,
year = {2024},
author = {Deery, J and Carmody, M and Flavin, R and Tomanek, M and O'Keeffe, M and McGlacken, GP and Reen, FJ},
title = {Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa.},
journal = {Microbial genomics},
volume = {10},
number = {2},
pages = {},
pmid = {38421269},
issn = {2057-5858},
mesh = {Humans ; Pseudomonas aeruginosa/genetics ; Genomics ; *Pseudomonas Infections ; Pseudomonas ; *Cystic Fibrosis/genetics ; },
abstract = {Pseudomonas aeruginosa, a harmful nosocomial pathogen associated with cystic fibrosis and burn wounds, encodes for a large number of LysR-type transcriptional regulator proteins. To understand how and why LTTR proteins evolved with such frequency and to establish whether any relationships exist within the distribution we set out to identify the patterns underpinning LTTR distribution in P. aeruginosa and to uncover cluster-based relationships within the pangenome. Comparative genomic studies revealed that in the JGI IMG database alone ~86 000 LTTRs are present across the sequenced genomes (n=699). They are widely distributed across the species, with core LTTRs present in >93 % of the genomes and accessory LTTRs present in <7 %. Analysis showed that subsets of core LTTRs can be classified as either variable (typically specific to P. aeruginosa) or conserved (and found to be distributed in other Pseudomonas species). Extending the analysis to the more extensive Pseudomonas database, PA14 rooted analysis confirmed the diversification patterns and revealed PqsR, the receptor for the Pseudomonas quinolone signal (PQS) and 2-heptyl-4-quinolone (HHQ) quorum-sensing signals, to be amongst the most variable in the dataset. Successful complementation of the PAO1 pqsR [-] mutant using representative variant pqsR sequences suggests a degree of structural promiscuity within the most variable of LTTRs, several of which play a prominent role in signalling and communication. These findings provide a new insight into the diversification of LTTR proteins within the P. aeruginosa species and suggests a functional significance to the cluster, conservation and distribution patterns identified.},
}

Humans
Pseudomonas aeruginosa/genetics
Genomics
*Pseudomonas Infections
Pseudomonas
*Cystic Fibrosis/genetics

@article {pmid37804413,
year = {2023},
author = {Bouznada, K and Belaouni, HA and Meklat, A},
title = {Genome-based reclassification of Kitasatospora niigatensis as a later heterotypic synonym of Kitasatospora cineracea Tajima et al. (2001).},
journal = {Antonie van Leeuwenhoek},
volume = {116},
number = {12},
pages = {1327-1335},
pmid = {37804413},
issn = {1572-9699},
mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; Streptomycetaceae ; },
abstract = {The present study used genome-based approaches to investigate the taxonomic relationship between Kitasatospora cineracea DSM 44780[T] and Kitasatospora niigatensis DSM 44781[T], two species that were previously described by Tajima et al. (Int J Syst Evol Microbiol 51:1765-1771, 2001). The digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values between the genomes of the two type strains were 90.3, 98.7, and 99.1%, respectively. These values exceeded the established thresholds of 70% (dDDH) and 95-96% (ANI and AAI) for bacterial species delineation, suggesting that K. cineracea and K. niigatensis should share the same taxonomic position. Furthermore, our analysis using the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and the Maximum Likelihood core-genes tree inferred using FastTree2 consistently demonstrated that K. cineracea DSM 44780[T] and K. niigatensis DSM 44781[T] are closely related, as indicated by the clustering of these strains in the core-genes phylogenomic tree. Based on these findings, we propose that K. niigatensis should be considered a later heterotypic synonym of K. cineracea.},
}

Bacterial Typing Techniques
DNA, Bacterial/genetics
Nucleic Acid Hybridization
Phylogeny
RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
Streptomycetaceae

@article {pmid24733489,
year = {2014},
author = {Islam, MA and Waller, AS and Hug, LA and Provart, NJ and Edwards, EA and Mahadevan, R},
title = {New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes.},
journal = {PloS one},
volume = {9},
number = {4},
pages = {e94808},
pmid = {24733489},
issn = {1932-6203},
mesh = {Bacterial Proteins/genetics/metabolism ; Chloroflexi/*genetics/*metabolism ; Cluster Analysis ; Electron Transport ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Hydrolases/metabolism ; Metabolic Networks and Pathways/*genetics ; Molecular Sequence Annotation ; Operon/genetics ; Principal Component Analysis ; Proteomics ; Reproducibility of Results ; *Systems Biology ; Transcriptome/*genetics ; },
abstract = {Organohalide respiration, mediated by Dehalococcoides mccartyi, is a useful bioremediation process that transforms ground water pollutants and known human carcinogens such as trichloroethene and vinyl chloride into benign ethenes. Successful application of this process depends on the fundamental understanding of the respiration and metabolism of D. mccartyi. Reductive dehalogenases, encoded by rdhA genes of these anaerobic bacteria, exclusively catalyze organohalide respiration and drive metabolism. To better elucidate D. mccartyi metabolism and physiology, we analyzed available transcriptomic data for a pure isolate (Dehalococcoides mccartyi strain 195) and a mixed microbial consortium (KB-1) using the previously developed pan-genome-scale reconstructed metabolic network of D. mccartyi. The transcriptomic data, together with available proteomic data helped confirm transcription and expression of the majority genes in D. mccartyi genomes. A composite genome of two highly similar D. mccartyi strains (KB-1 Dhc) from the KB-1 metagenome sequence was constructed, and operon prediction was conducted for this composite genome and other single genomes. This operon analysis, together with the quality threshold clustering analysis of transcriptomic data helped generate experimentally testable hypotheses regarding the function of a number of hypothetical proteins and the poorly understood mechanism of energy conservation in D. mccartyi. We also identified functionally enriched important clusters (13 for strain 195 and 11 for KB-1 Dhc) of co-expressed metabolic genes using information from the reconstructed metabolic network. This analysis highlighted some metabolic genes and processes, including lipid metabolism, energy metabolism, and transport that potentially play important roles in organohalide respiration. Overall, this study shows the importance of an organism's metabolic reconstruction in analyzing various "omics" data to obtain improved understanding of the metabolism and physiology of the organism.},
}

Bacterial Proteins/genetics/metabolism
Chloroflexi/*genetics/*metabolism
Cluster Analysis
Electron Transport
Gene Expression Regulation, Bacterial
Genes, Bacterial
Hydrolases/metabolism
Metabolic Networks and Pathways/*genetics
Molecular Sequence Annotation
Operon/genetics
Principal Component Analysis
Proteomics
Reproducibility of Results
*Systems Biology
Transcriptome/*genetics

@article {pmid40826220,
year = {2025},
author = {Näpflin, N and Schubert, C and Malfertheiner, L and Hardt, WD and von Mering, C},
title = {Gene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1241},
pmid = {40826220},
issn = {2399-3642},
support = {310030_192567//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_192569//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_192569//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 10.001.588//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; SCHU 3606/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Enterobacteriaceae is a diverse bacterial family that commonly colonizes the gastrointestinal tracts of humans and animals, influences host health, and also includes members adapted to colonize the phyllosphere as well as insect hosts. We lack systematic knowledge regarding the core metabolic strategy shared among Enterobacteriaceae. To address this gap, we have analyzed the pan-genome of nearly 20,000 genomes, including Citrobacter, Escherichia, Klebsiella, and Salmonella. We found that genes necessary for monosaccharide-fuelled mixed acid fermentation and (micro-)aerobic respiration are part of the Enterobacteriaceae core genome, whereas most genes involved in anaerobic respiration and carbohydrate utilization are associated to the accessory genome. Most Enterobacteriaceae possess genes enabling the utilization of D-glucose, its epimers, D-glucose-containing disaccharides, and chemically modified derivatives of D-glucose - highlighting the evolutionary adaptation of this family to efficiently exploit this simple sugar. Understanding Enterobacteriaceae's core metabolic strategy helps clarify the distinction of niche-defining nutrient sources, which can be genus-, species- or strain-specific. This study highlights the core metabolic strategy of Enterobacteriaceae, supporting the development of targeted interventions in microbiome research and infectious disease control.},
}

@article {pmid40825048,
year = {2025},
author = {Rosani, U and Gerdol, M and Krupovic, M},
title = {The highly dynamic pangenome of basal chordates is enriched in defence and immunity genes and is inherited following the Mendelian law.},
journal = {PLoS genetics},
volume = {21},
number = {8},
pages = {e1011833},
doi = {10.1371/journal.pgen.1011833},
pmid = {40825048},
issn = {1553-7404},
abstract = {Pangenome analyses, which encompass the full genetic repertoire of a species, offer valuable insights into intraspecific diversity and phylogeographic gene patterns. While the taxonomic breadth and functional significance of animal pangenomes remain to be fully uncovered, recent findings (such as reports of open, bacterial-like pangenomes in bivalves) highlight the need to better understand the molecular mechanisms driving inter-haplotype structural variation. Genes affected by presence-absence variation (PAV), along with non-reference sequences (NRSs), represent evolutionary footprints that may shape genome architecture and plasticity, ultimately influencing the adaptability and long-term fitness of species. To investigate the pangenomic architecture of basal chordates, we analyzed available whole-genome resequencing data from Branchiostoma belcheri and B. floridae, examined the impact of structural genomic variation, and assessed the inheritance patterns of dispensable genes across generations. The pangenomes of both species include over a thousand of genes affected by PAV and exhibiting trans-generational Mendelian transmission from parents to offspring. We further demonstrate that 35 dispensable genes in B. belcheri are of exogenous origin, likely resulting from the integration of a malacoherpesvirus genome, thereby extending the known host range of Malacoherpesviridae from invertebrates to chordates. PAV preferentially targeted gene families involved in defense, immunity, and cell signaling, including GTPases of immunity-associated proteins (GIMAPs), caspases, toll-like receptors, and pattern recognition receptors containing apextrin C-terminal (APEC) domains. The dynamic nature of immunity genes in cephalochordates parallels patterns seen in open bacterial pangenomes, suggesting that fundamental principles of genome evolution and innovation across life domains are shaped by host-pathogen interactions.},
}

@article {pmid40823826,
year = {2025},
author = {Sadler, MC and Wietz, M and Mino, S and Morris, RM},
title = {Genomic diversity and adaptation in Arctic marine bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0155525},
doi = {10.1128/mbio.01555-25},
pmid = {40823826},
issn = {2150-7511},
abstract = {Arctic marine bacteria experience seasonal changes in temperature, salinity, light, and sea ice cover. Time-series and metagenomic studies have identified spatiotemporal patterns in Arctic microbial communities, but a lack of complete genomes has limited efforts to identify the extent of genomic diversity in Arctic populations. We cultured and sequenced the complete genomes of 34 Arctic marine bacteria to identify patterns of gene gain, loss, and rearrangement that structure genomes and underlie adaptations to Arctic conditions. We found that the most abundant lineage in the Arctic (SAR11) is comprised of diverse species and subspecies, each encoding 50-150 unique genes. Half of the 16 SAR11 genomes harbor a genomic island with the potential to enhance survival in the Arctic by utilizing the osmoprotectant and potential methyl donor glycine betaine. We also cultured and sequenced four species representing an uncultured family of Pseudomonadales, four subspecies of Pseudothioglobus (SUP05), a genus of high GC Puniceispirillales (SAR116), and a family of low GC SAR116. Time-series 16S rRNA amplicon data indicate that this culture collection represents up to 60% of the marine bacterial community in Arctic waters. Their genomes provide insights into the evolutionary processes that underlie bacterial diversity and adaptation to Arctic waters.IMPORTANCEGenetic diversity has limited efforts to assemble and compare whole genomes from natural populations of marine bacteria. We developed a cultivation-based population genomics approach to culture and sequence the complete genomes of bacteria from the Arctic Ocean. Cultures and closed genomes obtained in this study represent previously uncultured families, genera, and species from the most abundant lineages of bacteria in the Arctic. We report patterns of gene gain, loss, rearrangement, and adaptation in the dominant lineage (SAR11), as well as the size, composition, and structure of genomes from several other groups of marine bacteria. This work demonstrates the potential for cultivation-based high-throughput genomics to enhance understanding of the processes underlying genomic diversity and adaptation.},
}

@article {pmid40822568,
year = {2024},
author = {Henry, JA},
title = {Population health management genomic new-born screens and multi-omics intercepts.},
journal = {Frontiers in artificial intelligence},
volume = {7},
number = {},
pages = {1496942},
pmid = {40822568},
issn = {2624-8212},
abstract = {INTRODUCTION: The Population Health Management (PHM) Genomic Newborn Screens (GNBS) and Multi-Omics Intercepts for Human Phenotype Ontology (HPO) using Federated Data Platforms (FDP) represent a groundbreaking innovation in global health. This reform, supported by the UK's Genomic Medical Services (GMS) through "The Generation Study," aims to significantly reduce infant mortality by identifying and managing over 200 rare diseases from birth, paving the way for personalised health planning.

METHODS: Using an ecosystem approach, this study evaluates a diverse pangenome to predict health outcomes or confirm diagnoses prior to symptomatic manifestations. GNBS standardises care by integrating diagnostic techniques such as blood spot analysis and full blood cell diagnostics to stratify risk. The approach enhances the understanding of rare diseases in primary care medicine, with biomedical and haematology diagnoses re-evaluated. Scientific proof of concept and fit-for-purpose technology align multi-omics in pre-eXams (X = Gen AI).

RECOMMENDATIONS: The Digital Regulation Service (DRS) assembles an agile group of experts to enhance medical science through human phenotype ontology (HPO) for precise disease segmentation, scheduling accurate eXam intercepts where needed. This team strategically plans regulation services for digital HPO eXam assurance and implements Higher Expert Medical Science Safety (HEMSS) frameworks. The DRS is responsible for overseeing gene, oligonucleotide, and recombinant protein intercepts; commissioning blood pathology HPO eXam intercepts; and monitoring preliminary eXams with advanced imaging techniques.

DISCUSSION: In pursuit of excellence in PHM of HPO, HEMSS with Agile Group Development leverages the Genomic Newborn Screens (GNBS) and multi-omics to create personalised health plans integrated with NHS England Genomics and AI-driven DRS. The discourse extends to examining GNBS predictors and intercepts, focusing on their impact on public health and patient safety. Discussions encompass structured HPO knowledge addressing newborn health, ethical considerations, family privacy, and the benefits and limitations of pre-eXam screenings and life eXam intercepts. These debates involve stakeholders in adopting HPO-enhanced clinical pathways through Alliances for Health Systems Networking-Genomic Enterprise Partnerships (AHSN-GEP).

CONCLUSION: "The Generation Study" represents a paradigm in digital child health management using an HPO-X-Gen-AI framework, transitioning from trusted research to evidence-based discovery. This approach sets a standard for personalised healthcare practices, incorporating ontology risk stratification and future-ready analytics as outlined in the NHS Constitution. The discourse on higher expert medical science safety governance will continue in the forthcoming manuscript, "PHM Fit Lifecycles in Future Analytics," which will further explore developing localised health solutions for "Our Future Health."},
}

@article {pmid40819063,
year = {2025},
author = {Qian, Y and Zhou, Z and Ouyang, T and Li, D and Li, R and Gan, P and Qiao, R and Tan, Y and Qian, M and Liu, L and Li, J and Lu, K and Luo, J and Chen, LL and Song, JM},
title = {Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7634},
pmid = {40819063},
issn = {2041-1723},
abstract = {Transposable elements (TEs) introduce genetic and epigenetic variability, contributing to gene expression patterns that drive adaptive evolution in plants. Here, we investigate TE architecture and its effect on cold tolerance in rice. By analyzing a pangenome graph and the resequencing data of 165 rice accessions, we identify 30,316 transposable element insertion polymorphism (TIP) sites, highlighting significant diversity among polymorphic TEs (pTEs). We observe that pTEs exhibit increased H3K27me3 enrichment, suggesting a potential role in epigenetic differentiation under cold stress and in the transcriptional regulation of the cold response. We identify 26,914 TEs responsive to cold stress from transcriptome data, indicating their potential significance in regulatory networks for this response. Our TIP-GWAS analysis reveal two cold tolerance genes OsCACT and OsPTR. The biological functions of these genes are confirmed using knockout and overexpression lines. Our web tool (https://cbi.gxu.edu.cn/RICEPTEDB/) makes all pTEs available to researchers for further analysis. These findings provide valuable targets for breeding cold-tolerant rice varieties, indicating the potential importance of pTEs in crop enhancement.},
}

@article {pmid40818300,
year = {2025},
author = {Li, Y and Huang, Z and Zhu, X and Liu, C and Cao, S and Li, Y},
title = {Serotyping, molecular typing, and vaccine protein screening for Riemerella anatipestifer: Overcoming challenges in prevention and treatment.},
journal = {Veterinary microbiology},
volume = {309},
number = {},
pages = {110663},
doi = {10.1016/j.vetmic.2025.110663},
pmid = {40818300},
issn = {1873-2542},
abstract = {Riemerella anatipestifer (R. anatipestifer) affects the duck farming industry worldwide, causing substantial economic losses. The current disease prevention and treatment strategies primarily include vaccines and antibiotics. However, the large number of serotypes and increasing resistance to R. anatipestifer make it challenging to prevent and treat the infection. This study carried out the serotyping and molecular typing of 51 R. anatipestifer strains and predicted vaccine proteins based on pan-genome analysis and cross-immune protection potential. For serotype identification, the rabbits were immunized with antigens, and 9 serotyped sera were prepared, the data revealed 6 serotypes with two unformed strains. The results for the self-made serotypes were consistent with those obtained from the externally submitted strains. Moreover, the pan-genome analysis was performed on 51 R. anatipestifer strains, and an open pan-genome set of 5094 genes was constructed. In addition, the COG annotation classification indicated that the core and non-core genomes were significantly different in gene functions. A total of 1116 core genomes that could serve as better cross-protective vaccine proteins were analyzed and revealed 5 genes of interest. In addition, the oprM-1 protein, a highly reactive protein, was expressed and purified, and the immunoreactivity with five antisera (anti-serotypes 1, 2, 5, 11, and 18) was demonstrated by Western blotting. This study fills the gaps in the existing typing systems for R. anatipestifer by combining serotyping, MLST typing, and pan-genome analysis. Furthermore, it provides valuable insights into the epidemiology, evolution, and pathogenesis of R. anatipestifer and paves the way for developing effective cross-protective vaccines.},
}

@article {pmid40817095,
year = {2025},
author = {Hatmaker, EA and Barber, AE and Drott, MT and Sauters, TJC and Gumilang, A and Alastruey-Izquierdo, A and Garcia-Hermoso, D and Eagan, JL and Keller, NP and Kontoyiannis, DP and Kurzai, O and Rokas, A},
title = {Population structure in a fungal human pathogen is potentially linked to pathogenicity.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7594},
pmid = {40817095},
issn = {2041-1723},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; DEB-2110404//National Science Foundation (NSF)/ ; N/A//Burroughs Wellcome Fund (BWF)/ ; F31 EY033235/EY/NEI NIH HHS/United States ; Germany's Excellence Strategy - EXC 20151 - Project-ID 390813860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; N/A//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {Aspergillus flavus is a clinically and agriculturally important saprotrophic fungus responsible for severe human infections and extensive crop losses. Here, we analyze genomic data from 300 (117 clinical and 183 environmental) A. flavus isolates from 13 countries, including 82 clinical isolates sequenced in this study, to examine population and pan-genome structure and their relationship to pathogenicity. We use single nucleotide polymorphisms to build a phylogeny, analyze admixture, and perform discriminant analysis of principal components. We identify five A. flavus populations, including a new population, D, corresponding to distinct clades in the genome-wide phylogeny. Strikingly, > 75% of clinical isolates were in population D and <5% in population B. We also use orthogroup clustering to identify core and accessory genes within the pan-genome. Accessory genes, including genes within biosynthetic gene clusters, were significantly more common in some populations but rare in others. Our functional annotations show that population D is enriched for genes associated with carbohydrate metabolism, lipid metabolism and certain types of hydrolase activity, whereas a non-clinical population is depleted in genes related to zinc ion binding. In contrast to previous results from the major human pathogen Aspergillus fumigatus, isolation of A. flavus from human specimens is associated with population structure, providing a promising system for future investigations into the contributions of population-specific genetic differences to human infection.},
}

@article {pmid40812179,
year = {2025},
author = {Teasdale, LC and Murray, KD and Collenberg, M and Contreras-Garrido, A and Schlegel, T and van Ess, L and Jüttner, J and Lanz, C and Deusch, O and Fitz, J and Mencia, R and van Velthoven, R and Drost, HG and Weigel, D and Shirsekar, G},
title = {Pangenomic context reveals the extent of intraspecific plant NLR evolution.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1291-1305.e9},
doi = {10.1016/j.chom.2025.07.011},
pmid = {40812179},
issn = {1934-6069},
abstract = {Nucleotide-binding leucine-rich repeat (NLR) proteins are major components of the plant immune system, recognizing pathogen effectors and triggering defense responses. Because of the diversity of pathogen effector repertoires, NLRs have extraordinary sequence, structural, and regulatory variability. Although processes contributing to NLR diversity have been identified, the precise evolution of NLRs in their genomic context and along the multiple axes of diversity has been difficult to trace. We integrate genome-specific full-length transcript, homology, and transposable element information to annotate 3,789 NLRs in 17 diverse Arabidopsis thaliana accessions. We define 121 pangenomic NLR neighborhoods, which vary greatly in size, content, and complexity. NLRs are diverse across many axes, and multiple metrics are required to fully capture NLR variation. Based on these findings, we propose that diversity in diversity generation is fundamental to maintaining a functionally "adaptive" immune system in plants and that mechanistic studies should consider multiple axes of immune system diversity.},
}

@article {pmid40810913,
year = {2025},
author = {Li, M and Wu, Y and Li, H and Zhang, Z and Qin, R and Wen, J and Xu, Y and Bao, C and Wang, D},
title = {Comparative pan-genome analysis of Huperzia and Phlegmariurus and transcriptomics reveals thermal adaptation in Huperzia.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {168},
pmid = {40810913},
issn = {1438-7948},
support = {NBSXZX2025-023//Germplasm Resource Protection Project of Yuyao Seedling Management Station/ ; 2021C02043//Key Research and Development Program of Zhejiang Province/ ; },
abstract = {Huperzia and Phlegmariurus are ancient genera within the Lycopodiaceae family with significant medicinal value and ecological adaptability, yet the evolutionary dynamics and genetic diversity of their chloroplast genomes remain poorly characterized. Specifically, critical aspects such as intergeneric differences, phylogenetic relationships, and adaptive evolution within their chloroplast genomes remain insufficiently explored. This study analyzed the chloroplast genomes of 66 species from these two genera through comparative genomics to elucidate their structural dynamics and adaptive mechanisms. Results revealed that Huperzia chloroplast genomes (153-155 kb, GC content 36.25-36.39%) are significantly larger than those of Phlegmariurus (148-151 kb, GC content 33.78-34.26%), with pronounced differences in IR boundary dynamics, repetitive sequence distribution, nucleotide diversity, and codon usage bias. Phylogenetic and population structure analyses confirmed the monophyly of both genera and demonstrated significantly higher genetic diversity in Phlegmariurus, likely linked to adaptive radiation driven by humid tropical environments. Transcriptomic data revealed a temporally coordinated chloroplast response to heat stress in Huperzia serrata. Photosynthetic core genes (such as psaB and rrna16) were downregulated, leading to sustained functional impairment. In contrast, early stress-response genes (such as rbcL and trnI-GAU) peaked at 4 h to enhance carbon fixation and transport. Mid-phase repair genes (such as ndhG and rps8) exhibited inverted U-shaped expression patterns to activate electron transport and protein synthesis, whereas late-stage overexpression of atpI restored energy homeostasis. This coordinated regulatory mechanism illustrates a survival strategy of "photosynthetic inhibition-stress compensation-energy reorganization" for thermal adaptation. Future studies should integrate nuclear genome and epigenetic modification data to further unravel the synergistic nucleo-cytoplasmic interactions underlying environmental adaptation.},
}

@article {pmid40809109,
year = {2025},
author = {Ahmad, B and Su, Y and Hao, Y and Razzaq, T and Arshad, R and Zhang, Y and Zhang, Y and Wang, X and Huang, G and Su, X and Hou, T and Li, C and Yang, X and Li, C and Chu, Z and Wang, Q and Zhang, Y and Jin, Z and Xu, Q and Xu, X and Peng, Y and Bi, G and Chen, C and Chen, Y and Xiao, H and Huang, J and Zhou, Y and Tian, X},
title = {Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.},
journal = {Horticulture research},
volume = {12},
number = {9},
pages = {uhaf166},
pmid = {40809109},
issn = {2662-6810},
abstract = {Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention. This study compared population genomic analyses using four different reference genomes of mango (Mangifera indica), including the two haploid assemblies of haplotype-resolved telomere-to-telomere (T2T) genome assembly, a pangenome, and an older version of the reference genome available on NCBI. The choice of reference genome dramatically impacted the mapping efficiency and resulted in notable differences in calling the genetic variants, particularly structural variations (SVs). Phylogenetic analysis was more sensitive to the reference genome compared to genetic differentiation. Population genomic analyses of artificial selection in domestication and SV hotspot regions varied across reference genomes. Notably, the gene enrichment analyses showed significant differences in the top enriched biological processes depending on the reference genome used. Overall, the mango pangenome outperformed the other reference genomes across various metrics, followed by T2T reference genomes, as they captured greater diversity and effectively reduced reference bias. Our findings highlight the role of the mango pangenome in reducing reference bias and underscore the critical role of reference genome selection, suggesting that it is one of the most important factors in population genomic studies.},
}

@article {pmid40799803,
year = {2025},
author = {Li, H},
title = {Finding easy regions for short-read variant calling from pangenome data.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {40799803},
issn = {2331-8422},
abstract = {BACKGROUND: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider non-reference samples or are biased towards existing short-read data or aligners.

RESULTS: Here, using hundreds of high-quality human assemblies, we derived a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. These regions cover 88.2% of GRCh38, 92.2% of coding regions and 96.3% of ClinVar pathogenic variants. They achieve a good balance between coverage and easiness and can be generated for other human assemblies or species with multiple well assembled genomes.

CONCLUSION: This resource provides a convient and powerful way to filter spurious variant calls for clinical or research human samples.},
}

@article {pmid40799530,
year = {2025},
author = {Salehi Nowbandegani, P and Zhang, S and Hu, H and Li, H and O'Connor, LJ},
title = {Defining and cataloging variants in pangenome graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.04.668502},
pmid = {40799530},
issn = {2692-8205},
abstract = {Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to 'reference bias'. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a 'genetic variant.' We introduce a definition of pangenome variants and a method, pantree , to identify them. Our approach involves a pangenome reference tree which includes all nodes (sequences) of the pangenome graph, but only a subset of its edges; non-reference edges are variant edges . Our variants are biallelic and have well-defined positions. Analyzing the Minigraph-Cactus draft human pangenome reference graph, we identified 29.6 million genetic variants. Most variants (99.2%) are small, and most small variants (73.9%) are SNPs. 3.5 million variants (11.7%) have a reference allele which is not on GRCh38; these variants are difficult to detect without a pangenome reference, or with existing pangenome-based approaches. They tend to be embedded within tangled, multiallelic regions. We analyze two medically relevant regions, around the HLA-A and RHD genes, identifying thousands of small variants embedded within several large insertions, deletions, and inversions. We release an open-source software tool together with a VCF variant catalogue.},
}

@article {pmid40796877,
year = {2025},
author = {Depuydt, L and Renders, L and Van de Vyver, S and Veys, L and Gagie, T and Fostier, J},
title = {b-move: faster lossless approximate pattern matching in a run-length compressed index.},
journal = {Algorithms for molecular biology : AMB},
volume = {20},
number = {1},
pages = {15},
pmid = {40796877},
issn = {1748-7188},
support = {1117322N//Fonds Wetenschappelijk Onderzoek/ ; RGPIN-07185-2020//Natural Sciences and Engineering Research Council of Canada/ ; 1SE7822N//Fonds Wetenschappelijk Onderzoek/ ; R01HG011392/NH/NIH HHS/United States ; R01 HG011392/HG/NHGRI NIH HHS/United States ; },
abstract = {BACKGROUND: Due to the increasing availability of high-quality genome sequences, pan-genomes are gradually replacing single consensus reference genomes in many bioinformatics pipelines to better capture genetic diversity. Traditional bioinformatics tools using the FM-index face memory limitations with such large genome collections. Recent advancements in run-length compressed indices like Gagie et al.'s r-index and Nishimoto and Tabei's move structure, alleviate memory constraints but focus primarily on backward search for MEM-finding. Arakawa et al.'s br-index initiates complete approximate pattern matching using bidirectional search in run-length compressed space, but with significant computational overhead due to complex memory access patterns.

RESULTS: We introduce b-move, a novel bidirectional extension of the move structure, enabling fast, cache-efficient, lossless approximate pattern matching in run-length compressed space. It achieves bidirectional character extensions up to 7 times faster than the br-index, closing the performance gap with FM-index-based alternatives. For locating occurrences, b-move performs ϕ and ϕ - 1 operations up to 7 times faster than the br-index. At the same time, it maintains the favorable memory characteristics of the br-index, for example, all available complete E. coli genomes on NCBI's RefSeq collection can be compiled into a b-move index that fits into the RAM of a typical laptop.

CONCLUSIONS: b-move proves practical and scalable for pan-genome indexing and querying. We provide a C++ implementation of b-move, supporting efficient lossless approximate pattern matching including locate functionality, available at https://github.com/biointec/b-move under the AGPL-3.0 license.},
}

@article {pmid40796583,
year = {2025},
author = {Kulmanov, M and Ashouri, S and Liu, Y and Abdelhakim, M and Alsolme, E and Nagasaki, M and Ohkawa, Y and Suzuki, Y and Tawfiq, R and Tokunaga, K and Katayama, T and Abedalthagafi, MS and Hoehndorf, R and Kawai, Y},
title = {Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1316},
pmid = {40796583},
issn = {2052-4463},
support = {REI/1/5659-01-01//King Abdullah University of Science and Technology (KAUST)/ ; 5932//King Abdullah University of Science and Technology (KAUST)/ ; JPMJND2302//MEXT | JST | National Bioscience Database Center (NBDC)/ ; JP18H05527//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP24H02323//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JP21wm0425009//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0210111//Japan Agency for Medical Research and Development (AMED)/ ; JP22tm0424222//Japan Agency for Medical Research and Development (AMED)/ ; JP23ek0109675//Japan Agency for Medical Research and Development (AMED)/ ; JP23ek0109672//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0210138//Japan Agency for Medical Research and Development (AMED)/ ; JP23ek0210194//Japan Agency for Medical Research and Development (AMED)/ ; JP24gm2010001//Japan Agency for Medical Research and Development (AMED)/ ; JP21H02681//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.},
}

@article {pmid40796304,
year = {2025},
author = {Qing, Y and Liao, Z and An, D and Zeng, Y and Zhu, Q and Zhang, X},
title = {Comparative genomics reveals the genetic diversity and plasticity of Clostridium tertium.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf201},
pmid = {40796304},
issn = {1365-2672},
abstract = {AIMS: Clostridium tertium, increasingly recognized as the emerging human pathogen frequently isolated from environmental and clinical specimens, remains genetically underexplored despite its clinical relevance. This study aims to explore the genetic characteristics of C. tertium by genomic analysis.

METHODS AND RESULTS: This study presented a comprehensive genomic investigation of 45 C. tertium strains from the GenBank database. Genome sizes (3.27-4.55 Mbp) and coding gene counts varied markedly across strains. Phylogenetic analyses based on 16S rRNA gene and core genome uncovered distinct intra-species lineages, including evolutionarily divergent clusters likely shaped by niche specialization. Pan-genomic analysis confirmed an open genome, with accessory and strain-specific genes enriched in functions related to environmental adaptation and regulation. Functional annotation further identified diverse virulence factor genes (e.g. clpP, nagK) and antibiotic resistance genes (e.g. vatB, tetA(P)) co-occurring with mobile genetic elements (MGEs), suggesting that horizontal gene transfer (HGT) may be a key driver of genome plasticity in C. tertium. Notably, one-third of the strains carried CRISPR-Cas systems, indicating the defense potential against exogenous genetic elements.

CONCLUSIONS: C. tertium exhibited extensive genetic diversity and genome plasticity, probably driven by MGE-mediated HGT, defense mechanisms of CRISPR-Cas systems, and functional adaptation related to virulence and resistance. These traits may underlie its ability to colonize diverse environments and acquire pathogenicity and resistance.},
}

@article {pmid40794526,
year = {2025},
author = {Anderson, OH and Chong, JPJ and Thomas, GH},
title = {Comparative genomics of Clostridium butyricum reveals a conserved genome architecture and novel virulence-related gene clusters.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
pmid = {40794526},
issn = {2057-5858},
mesh = {*Clostridium butyricum/genetics/pathogenicity/classification ; *Genome, Bacterial ; Virulence/genetics ; *Multigene Family ; *Genomics ; Humans ; Phylogeny ; },
abstract = {Bacteria from the species Clostridium butyricum encompass a diverse range of phenotypes. While some strains are used as probiotics, others have been isolated from cases of botulism and necrotizing enterocolitis (NEC) in preterm neonates. We identify a unique genomic feature of this species, namely a highly conserved extrachromosomal element of ~0.8 Mb. This replicon satisfies the three principal criteria used to define a chromid, which include the possession of core genes that are encoded on the main chromosome in other species. Although C. butyricum is the type species of Clostridium, we find that the possession of a chromid is not a typical feature of members of this genus and represents a unique genomic fingerprint of the species C. butyricum. Furthermore, we show that pathogenic C. butyricum strains from the sequenced examples are not monophyletic, which suggests that virulence has evolved multiple times from related non-pathogenic ancestors. However, we were able to identify common genes which are found exclusively in these pathogenic strains. In addition to the botulinum neurotoxin genes, these include a novel set of genes involved in the biosynthesis of a capsular polysaccharide (CPS), and genes that confer the ability to utilize the mucin-derived sugar l-fucose, which may provide a competitive advantage for growth in the colon. Moreover, by identifying NEC strain-associated virulence factors, we are able to further the understanding of these particularly harmful strains.},
}

*Clostridium butyricum/genetics/pathogenicity/classification
*Genome, Bacterial
Virulence/genetics
*Multigene Family
*Genomics
Humans
Phylogeny

@article {pmid40790212,
year = {2025},
author = {Zou, Y and Zhu, W and Hou, Y and Sloan, DB and Wu, Z},
title = {The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {240},
pmid = {40790212},
issn = {1474-760X},
support = {110243160001007//the Chinese Academy of Agricultural Sciences Elite Youth Program/ ; 32170238//National Natural Science Foundation of China/ ; 2023A1515111029//Basic and Applied Basic Research Foundation of Guangdong Province/ ; R35 GM148134/GM/NIGMS NIH HHS/United States ; 32400191//National Natural Science Foundation of China/ ; 2021QN02N792//the Guangdong Pearl River Talent Program/ ; R35GM148134/NH/NIH HHS/United States ; RCYX20200714114538196//the Science, Technology and Innovation Commission of Shenzhen Municipality/ ; },
mesh = {*Arabidopsis/genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; *Genome, Plant ; },
abstract = {BACKGROUND: In plants, comparative analyses of organellar genomes are often based on draft assemblies. Large-scale investigations into the complex structural rearrangements of mitochondrial genomes remain scarce.

RESULTS: Here, we perform a comprehensive analysis of the dominant conformations and dynamic heteroplasmic variants of organellar genomes in the model plant Arabidopsis thaliana, utilizing high-quality long-read assemblies validated at high resolution from 149 samples. We find that mitochondrial and plastid genomes share common types of structural and small-scale variants driven by similar DNA sequence features. However, rearrangements mediated by repetitive sequences in mitochondrial genomes evolve so rapidly that they are often decoupled from other types of variants. Rare complex events involving elongation and fusion of existing repeats are also observed, contributing to the unalignable regions commonly found at the interspecies level. Additionally, we demonstrate that disrupting and rescuing organellar DNA maintenance could drive the rapid evolution of dominant mitochondrial genome conformations.

CONCLUSIONS: Our study provides an unprecedentedly detailed view of the dynamics of organellar genomes at pan-genome scale in Arabidopsis thaliana, paving the way to unlock the full potential of organellar genetic resources.},
}

*Arabidopsis/genetics
*Evolution, Molecular
*Genome, Mitochondrial
*Genome, Plastid
*Genome, Plant

@article {pmid40789919,
year = {2025},
author = {Engelhorn, J and Snodgrass, SJ and Kok, A and Seetharam, AS and Schneider, M and Kiwit, T and Singh, A and Banf, M and Doan, DTH and Khaipho-Burch, M and Runcie, DE and Sánchez-Camargo, VA and Bader, R and Vladimir Torres-Rodriguez, J and Sun, G and Stam, M and Fiorani, F and Beier, S and Schnable, JC and Bass, HW and Hufford, MB and Stich, B and Frommer, WB and Ross-Ibarra, J and Hartwig, T},
title = {Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40789919},
issn = {1546-1718},
support = {101081770//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 390686111//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 458854361//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390686111//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390686111//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ANR-22-CPJ2-0110-01//Agence Nationale de la Recherche (French National Research Agency)/ ; 1744592//National Science Foundation (NSF)/ ; 1822330//National Science Foundation (NSF)/ ; DE-SC0020355//U.S. Department of Energy (DOE)/ ; DE-SC0020355//U.S. Department of Energy (DOE)/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture (United States Department of Agriculture)/ ; },
abstract = {Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1, ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.},
}

@article {pmid40787854,
year = {2025},
author = {Tellatin, D and Cornet, L and Snauwaert, V and Compère, P and Ongena, M and Quinton, L and Stulanovic, N and Monteiro, SR and Rigolet, A and Burguet, P and Van Damme, P and Carro, L and Rigali, S},
title = {Melissospora conviva gen. nov., sp. nov., a novel actinobacterial genus isolated from beehive through cross-feeding interactions.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {8},
pages = {},
doi = {10.1099/ijsem.0.006868},
pmid = {40787854},
issn = {1466-5034},
mesh = {*Phylogeny ; Bees/microbiology ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Animals ; Bacterial Typing Techniques ; Genome, Bacterial ; Whole Genome Sequencing ; *Micromonosporaceae/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; },
abstract = {Most micro-organisms remain unculturable under standard laboratory conditions, limiting our understanding of microbial diversity and ecological interactions. One major cause of this uncultivability is the loss of access to essential cross-fed metabolites when bacteria are removed from their natural communities. During a bioprospecting campaign targeting actinomycetes of an Apis mellifera beehive, we identified five isolates (DT32, DT45[T], DT55, DT59 and DT194) that required co-cultivation for growth recovery, suggesting a dependence on microbial interactions in their native habitat. Whole-genome sequencing and phylogenetic analysis positioned these isolates within a distinct lineage of Micromonosporaceae, separate from the five officially recognized clades of the Micromonospora genus. A combination of microscopic, chemotaxonomic and physiological characterizations further supported their uniqueness. Notably, they exhibited high auxotrophy, being unable to use all carbon sources tested, likely due to genome reduction (4.6 Mbp) compared to other Micromonosporaceae. Pangenomic comparisons with their closest Micromonospora relatives revealed gene losses in key metabolic pathways, including the glyoxylate bypass and the Entner-Doudoroff pathway, which may explain their metabolic reliance. These findings reveal a highly specialized, ecologically adapted lineage with deep evolutionary divergence and further support microbial interdependence isolation strategies to explore the microbial dark matter. We propose Melissospora conviva as a novel genus and species within the Actinomycetota phylum, with isolate DT45[T] as the representative type species and type strain, which has been deposited in public collections under the accession numbers DSM 117791 and LMG 33580.},
}

*Phylogeny
Bees/microbiology
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Animals
Bacterial Typing Techniques
Genome, Bacterial
Whole Genome Sequencing
*Micromonosporaceae/classification/genetics/isolation & purification
Sequence Analysis, DNA

@article {pmid40784926,
year = {2025},
author = {Yerka, MK and Liu, Z and Bean, S and Nigam, D and Hayes, C and Druetto, D and Krishnamoorthy, G and Meiwes, S and Cucit, G and Patil, GB and Jiao, Y},
title = {An updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench].},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {40784926},
issn = {2190-3883},
support = {2019-67014-29174//National Institute of Food and Agriculture/ ; NEV00763//National Institute of Food and Agriculture/ ; 3096-21000-024-000-D//Agricultural Research Service/ ; },
abstract = {Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600; commonly known as Waxy (Wx)] result in a low amylose:amylopectin starch ratio. Recessive waxy (wx) alleles improve starch digestibility in ethanol production, human foods and beverages, and animal feed. However, breeding waxy sorghum is challenging due to reliance on traditional PCR markers for genotyping, which are not amenable to next-generation sequencing (NGS). Most commercial breeding programs use high-throughput genotyping and genomic selection in large, segregating populations prior to flowering. This study provides the first published NGS markers for the two most commonly used waxy (wx) alleles of sorghum and is the first to fully sequence the large insertion that is causal of the wx[a] allele. In the absence of a pangenome including wx[a] genotypes, we constructed an in silico B.Tx623 wx[a] genome assembly from the B.Tx623 reference genome (v3.1.1) including the insertion, a ~ 5-kb-long terminal repeat (LTR) retrotransposon of the copia superfamily. The in silico wx[a] assembly improved read mapping at Sobic.010G022600 in wx[a] individuals, identified 78 new uniquely mapped reads, and made it possible to distinguish different Waxy genotypes using short-read sequencing data. Functional PACE-PCR markers, suitable for marker-assisted selection and multiplexed, low-to-mid-density genomic selection, were developed for Wx, wx[a], and wx[b] alleles. The PACE markers were validated in segregating populations of three public and private breeding programs. These new molecular breeding resources comprise a toolkit that will improve the efficiency of developing commercial waxy sorghum hybrids using genomics-assisted approaches.},
}

@article {pmid40784629,
year = {2025},
author = {Weers, T and Feng, Y and Peters, RJ},
title = {Uncrossing the 'X': Characterization of alternative alleles for KSLX in Oryza.},
journal = {Phytochemistry},
volume = {240},
number = {},
pages = {114634},
doi = {10.1016/j.phytochem.2025.114634},
pmid = {40784629},
issn = {1873-3700},
abstract = {The widely cultivated Asian rice (Oryza sativa) produces a variety of physiologically relevant diterpenoid products, which range in effect from the phytohormone gibberellin, derived from ent-kaurene, to phytoalexins such as the momilactones, derived from syn-pimara-7,15-diene. Previous reports have shown functional variation in the kaurene synthase-like (KSL) genes responsible for synthesizing diterpene precursors to more specialized metabolites, leading to the creation of distinct diterpenoids from allelomorphic genes. Here is reported the product of two previously discovered but uncharacterized alleles of the unusual KSLX, representing a cross between (fusion of) the tandem pair KSL8-KSL9p found in most cultivars. The previously characterized allele (KSLXo) was reported to act on syn-copalyl pyrophosphate (syn-CPP) to produce syn-abieta-7,12-diene, precursor to the phytoalexin oryzalactone. However, at least one other functionally distinct allele was reported from the O. sativa pan-genome (KSLXn), along with another phylogenetically distinct allele found in Oryza barthii (KSLXb), but these were not further characterized. Here both KSLXn and KSLXb were found to selectively react with syn-CPP and produce syn-pimara-9(11),15-diene, a novel diterpene in rice. Additionally, evolution of this locus was investigated, with KSLXb hypothesized to be a functional KSL9. The striking complexity of this locus, which includes distinct composition (KSL8-KSL9(p) or KSLX) as well as allelomorphism of both KSL8 and KSLX, suggests it is subject to balancing selection, consistent with the competing pressures exerted on phytoalexin biosynthesis. Regardless, the studies reported here clarify this additional example of allelomorphic variation in the rice KSL family, providing insight into the rice pan-genomic diterpenoid arsenal.},
}

@article {pmid40783340,
year = {2025},
author = {Gross, JE and Fullmer, J and McCleland, G and Caceres, SM and Poch, KR and Hasan, NA and Jia, F and Epperson, LE and Lipner, EM and Vang, CK and Honda, JR and Strand, MJ and de Moura, VCN and Daley, CL and Strong, M and Nick, JA},
title = {Genomic and epidemiologic investigation of Mycobacterium abscessus isolates in a cystic fibrosis center to determine potential routes of transmission.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.07.003},
pmid = {40783340},
issn = {1873-5010},
abstract = {BACKGROUND: Cystic Fibrosis (CF) Centers worldwide have reported healthcare-associated outbreaks of nontuberculous mycobacteria (NTM). We report a retrospective investigation of shared Mycobacterium abscessus strains among people with cystic fibrosis (pwCF) receiving care at Dell Children's/Ascension combined Pediatric and Adult CF Program (DCMC).

METHODS: Whole genome sequencing (WGS) was used to identify genetically similar isolates among 167 NTM isolates from 57 pwCF. Epidemiological investigation, respiratory and environmental isolate comparisons, and watershed mapping were performed.

RESULTS: WGS analysis revealed four M. abscessus clusters, two ssp. abscessus and two ssp. massiliense. One subject was infected with two distinct clustered M. abscessus (ssp. abscessus and ssp. massiliense). Epidemiologic investigation demonstrated opportunities for healthcare-associated transmission within all clusters. Two ssp. massiliense subject pairs had healthcare overlaps and high genomic relatedness, including one cohabitating sibling pair. M. abscessus recovered from DCMC revealed genetic similarity to a respiratory isolate from one patient who was never exposed to the hospital environment.

CONCLUSIONS: We identified shared M. abscessus strains via genomic analysis among pwCF at DCMC. None of the clustered patient isolates matched hospital environmental isolates at the genomic level. One hospital environmental isolate had genomic similarity to a respiratory isolate of M. abscessus, but the epidemiologic investigation revealed no evidence of subject exposure to the hospital setting. One ssp. massiliense subject pair had the same level of pangenome relatedness as the sibling pair and epidemiological investigation revealed overlap in the clinic, supporting healthcare-associated person-to-person transmission among the pair within a cluster. One pwCF had polyclonal clustered infections, suggesting multiple environmental sources of acquisition outside the healthcare environment.},
}

@article {pmid40781705,
year = {2025},
author = {Wu, H and Chen, S and Wang, J and Zong, Y and Yang, L and Tong, C and Li, H},
title = {Pangenome analysis of Liriodendron reveals presence/absence variations associated with growth traits.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1039},
pmid = {40781705},
issn = {1471-2229},
support = {32371910//National Natural Science Foundation of China/ ; 2022YFD2200104//National Key Research and Development Program of China/ ; },
mesh = {*Liriodendron/genetics/growth & development ; Genome-Wide Association Study ; *Genome, Plant ; *Genetic Variation ; Polymorphism, Single Nucleotide ; Genes, Plant ; Hybrid Vigor/genetics ; Genotype ; Phenotype ; },
abstract = {Beyond single nucleotide polymorphisms (SNPs), gene presence/absence variation (PAV) plays a crucial role in elucidating species' genetic diversity, uncovering the genetic basis of key traits, and advancing molecular marker-assisted breeding in plants. In this study, we constructed a pangenome of Liriodendron based on 24 accessions. Comparative analysis with the reference genome revealed 116 Mb of non-reference sequences and obtained 32,773 genes, including 3,558 novel genes. We subsequently employed resequencing data from 247 Liriodendron genotypes to identify PAVs, comprising 13,779 core genes and 18,179 dispensable genes. To further assess PAV applicability, a genome-wide association study (GWAS) was conducted to link gene PAVs with growth traits in hybrid Liriodendron, and identified 14 candidate genes associated with these growth traits above. Additionally, gene PAVs appeared to predominantly contribute to heterosis in growth traits, displaying a dominant expression pattern when comparing leaf, shoot, and phloem tissues of strong and weak heterotic combinations. Additionally, two key candidate genes, Litul.02G164100 and Litul.01G057400, exhibit high parental expression patterns consistent with hybrid vigor in strong heterotic combinations of leaf and shoot tissues. Altogether, this study expands the Liriodendron genomic dataset, identifies candidate genes linked to growth traits, and provides insights into their heterotic mechanisms in hybrid Liriodendron.},
}

*Liriodendron/genetics/growth & development
Genome-Wide Association Study
*Genome, Plant
*Genetic Variation
Polymorphism, Single Nucleotide
Genes, Plant
Hybrid Vigor/genetics
Genotype
Phenotype

@article {pmid40781446,
year = {2025},
author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK},
title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {305},
pmid = {40781446},
issn = {1573-0972},
support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; },
mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; },
abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.},
}

*Desulfovibrio/genetics/metabolism/classification
*Genome, Bacterial
*Sulfates/metabolism
Phylogeny
Multigene Family
Gene Regulatory Networks
Genes, Bacterial
Gene Ontology

@article {pmid40778144,
year = {2025},
author = {Sui, Y and Lin, J and Noyes, MD and Kwon, Y and Wong, I and Koundinya, N and Harvey, WT and Wu, M and Hoekzema, K and Munson, KM and Garcia, GH and Knuth, J and Wertz, J and Wang, T and Hennick, K and Karunakaran, D and Polo Prieto, RA and Meyer-Schuman, R and Cherry, F and Pehlivan, D and Suter, B and Gustafson, JA and Miller, DE and , and Berk-Rauch, H and Nowakowski, TJ and Chakravarti, A and Zoghbi, HY and Eichler, EE},
title = {Pangenome discovery of missing autism variants.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.21.25331932},
pmid = {40778144},
abstract = {Autism spectrum disorders (ASDs) are genetically and phenotypically heterogeneous and the majority of cases still remain genetically unresolved. To better understand large-effect pathogenic variation, we generated long-read sequencing data to construct phased and near-complete genome assemblies (average contig N50=43 Mbp, QV=56) for 189 individuals from 51 families with unsolved cases of autism. We applied read- and assembly-based strategies to facilitate comprehensive characterization of de novo mutations (DNMs), structural variants (SVs), and DNA methylation profiles. Merging common SVs obtained from long-read pangenome controls, we efficiently filtered >97% of common SVs exclusive to 87 offspring. We find no evidence of increased autosomal SV burden for probands when compared to unaffected siblings yet note a trend for an increase of SV burden on the X chromosome among affected females. We establish a workflow to prioritize potential pathogenic variants by integrating autism risk genes and putative noncoding regulatory elements defined from ATAC-seq and CUT&Tag data from the developing cortex. In total, we identified three pathogenic variants in TBL1XR1 , MECP2 , and SYNGAP1 , as well as nine candidate de novo and biparental homozygous SVs, most of which were missed by short-read sequencing. Our work highlights the potential of phased genomes to discover complex more pathogenic mutations and the power of the pangenome to restrict the focus on an increasingly smaller number of SVs for clinical evaluation.},
}

@article {pmid40776455,
year = {2025},
author = {Rohde, A and Albertsen, MC and Boden, SA and Bansept-Basler, P and Boeven, PHG and Cavanagh, C and Dixon, LE and Frohberg, C and Griffe, L and Lage, J and Maeder, L and Millán-Blánquez, M and Olson, PD and Röhrig, L and Schnurbusch, T and Uauy, C and Whitford, R},
title = {New genomic resources to boost research in reproductive biology to enable cost-effective hybrid seed production.},
journal = {The plant genome},
volume = {18},
number = {3},
pages = {e70092},
pmid = {40776455},
issn = {1940-3372},
support = {DP210103744//Australian Research Council/ ; FT210100810//Australian Research Council/ ; IM230100042//Australian Research Council/ ; FKZ 031B1300A//Bundesministerium für Bildung und Forschung/ ; FKZ 2818401A18//Bundesministerium für Ernährung und Landwirtschaft/ ; },
mesh = {Flowers/genetics ; *Genome, Plant ; Genomics ; Hybridization, Genetic ; Plant Breeding ; Pollen/genetics ; Pollination/genetics ; Reproduction/genetics ; *Seeds/genetics/growth & development ; *Triticum/genetics/growth & development/physiology ; },
abstract = {The commercial realization of hybrid wheat (Triticum aestivum L.) is a major technological challenge to sustainably increase food production for our growing population in a changing climate. Despite recent advances in cytoplasmic- and nuclear-based pollination control systems, the inefficient outcrossing of wheat's autogamous florets remains a barrier to hybrid seed production. There is a pressing need to investigate wheat floral biology and enhance the likelihood of ovaries being fertilized by airborne pollen so breeders can select and utilize male and female parents for resilient, scalable, and cost-effective hybrid seed production. Advances in understanding the wheat genomes and pangenome will aid research into the underlying floral organ development and fertility with the aim to stabilize pollination and fertilization under a changing climate. The purpose of this position paper is to highlight priority areas of research to support hybrid wheat development, including (1) structural aspects of florets that affect stigma presentation, longevity, and receptivity to airborne pollen, (2) pollen release dynamics (e.g., anther extrusion and dehiscence), and (3) the effect of heat, drought, irradiation, and humidity on these reproductive traits. A combined approach of increased understanding built on the genomic resources and advanced trait evaluation will deliver to robust measures for key floral characteristics, such that diverse germplasm can be fully exploited to realize the yield improvements and yield stability offered by hybrids.},
}

Flowers/genetics
*Genome, Plant
Genomics
Hybridization, Genetic
Plant Breeding
Pollen/genetics
Pollination/genetics
Reproduction/genetics
*Seeds/genetics/growth & development
*Triticum/genetics/growth & development/physiology

@article {pmid40774991,
year = {2025},
author = {Tabashiri, R and Mahmoodian, S and Pakdel, MH and Shariati, V and Meimandipour, A and Zamani, J},
title = {Comprehensive in vitro and whole-genome characterization of probiotic properties in Pediococcus acidilactici P10 isolated from Iranian broiler chicken.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28953},
pmid = {40774991},
issn = {2045-2322},
mesh = {*Pediococcus acidilactici/genetics/isolation & purification ; Genome, Bacterial ; *Probiotics ; Iran ; *Chickens/microbiology ; Whole Genome Sequencing ; Genetic Association Studies ; Functional Food ; Animals ; Bacteriocins/genetics ; },
abstract = {This study presents a comprehensive characterization of Pediococcus acidilactici strain P10, a novel probiotic isolated from native broiler chickens, integrating in vitro analyses with whole-genome sequencing. P10 demonstrates promising probiotic attributes, supported by both phenotypic and genomic evidence. The strain was non-hemolytic and exhibited high survival rates under simulated gastrointestinal conditions (95-99% in acidic pH, 55% in bile salts), with genomic analysis confirming the presence of associated stress resistance genes. Importantly, P10 displayed potent broad-spectrum antimicrobial activity against key pathogens, underpinned by the identification of multiple putative bacteriocin-encoding genes. Furthermore, the strain showed strong adherence to intestinal epithelial cells, with corresponding adhesion genes identified in its genome. Beyond these phenotypic-genotypic correlations, P10's whole-genome sequencing revealed significant novel findings. The 1.84 Mb genome confirmed P10 as P. acidilactici and, most notably, identified a complete, functional Type II-A CRISPR-Cas system. This system, with 17 phage-matching spacers, represents a robust antiviral defense mechanism, a key and distinct feature for probiotic application. Additionally, pan-genomic analysis highlighted 59 genes unique to P10 not found in other P. acidilactici strains, suggesting novel metabolic and adaptive capabilities previously uncharacterized within the species. In summary, Pediococcus acidilactici strain P10 is a highly promising probiotic, combining confirmed resilience and antimicrobial action with unique genomic advantages such as its specialized CRISPR-Cas system and novel genetic elements, making it a valuable candidate for applications in animal health and functional foods.},
}

*Pediococcus acidilactici/genetics/isolation & purification
Genome, Bacterial
*Probiotics
Iran
*Chickens/microbiology
Whole Genome Sequencing
Genetic Association Studies
Functional Food
Animals
Bacteriocins/genetics

@article {pmid40770875,
year = {2025},
author = {Du, ZZ and He, JB and Xiao, PX and Hu, J and Yang, N and Jiao, WB},
title = {Varigraph: an accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.08.001},
pmid = {40770875},
issn = {1752-9867},
abstract = {Accurate variant genotyping is crucial for genomics-assisted breeding. Graph pangenome references can address single-reference bias, thereby enhancing the performance of variant genotyping and empowering downstream applications in population genetics and quantitative genetics. However, existing pangenome-based genotyping methods struggle with large or complex pangenome graphs, particularly in polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages the comparison of unique and repetitive k-mers between variant sites and short reads for genotyping both small and large variants. We evaluated Varigraph on a diverse set of representative plant genomes as well as human genomes. Varigraph outperforms current state-of-the-art linear and graph-based genotypers across non-human genomes while maintaining comparable genotyping performance in human genomes. By employing efficient data structures including Counting Bloom Filter and bitmap storage, as well as GPU models, Varigraph achieves improved precision and robustness in repetitive regions while managing computational costs for large datasets. Its wide applicability extends to highly repetitive or large genomes, such as those of maize and wheat. Significantly, Varigraph can handle extensive pangenome graphs, as demonstrated by its performance on a dataset containing 252 rice genomes, where it achieved a precision exceeding 0.9 for both small and large variants. Notably, Varigraph is capable of effectively utilizing pangenome graphs for genotyping autopolyploids, enabling precise determination of allele dosage. This work provides a robust and accurate solution for genotyping plant genomes and will advance plant genomic studies and genomics-assisted breeding.},
}

@article {pmid40770196,
year = {2025},
author = {Cao, S and Sawettalake, N and Shen, L},
title = {Lactuca super-pangenome provides insights into lettuce genome evolution and domestication.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7257},
pmid = {40770196},
issn = {2041-1723},
support = {NRF-CRP22-2019-0001//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; },
mesh = {*Lactuca/genetics/classification ; *Genome, Plant/genetics ; *Domestication ; *Evolution, Molecular ; DNA Copy Number Variations ; DNA Methylation ; Genomics/methods ; Gene Expression Regulation, Plant ; },
abstract = {Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. These assemblies exhibit diverse genome sizes ranging from 2.1 Gb to 5.5 Gb with abundant repetitive sequences, and expansion of repetitive sequences, associated with low DNA methylation levels, likely contributes to the genome size variations. Furthermore, by constructing a graph-based lettuce pangenome reference, we explore the landscape, genomic, and epigenetic features of structural variations, and reveal their contributions to gene expression and domestication. We also identify copy number variations in FLOWERING LOCUS C in association with delayed flowering in cultivated lettuce. Overall, this comprehensive Lactuca super-pangenome assembly will expedite functional genomics studies and breeding efforts of this globally important crop.},
}

*Lactuca/genetics/classification
*Genome, Plant/genetics
*Domestication
*Evolution, Molecular
DNA Copy Number Variations
DNA Methylation
Genomics/methods
Gene Expression Regulation, Plant

@article {pmid40766081,
year = {2025},
author = {Elakkya, M and González-Salazar, LA and López-Reyes, K and Rebelo-Romão, I and Sousa, A and Gödde, V and Niehaus, K and Thenappan, DP and Vilchez, JI and Paul, S and Licona-Cassani, C},
title = {Comparative genomics and metabolomics reveal phytohormone production, nutrient acquisition, and osmotic stress tolerance in Azotobacter chroococcum W5.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626016},
pmid = {40766081},
issn = {1664-302X},
abstract = {INTRODUCTION: Concerns about ecological degradation and reduced biodiversity have intensified the search for sustainable solutions in agriculture. The use of plant growth-promoting bacteria (PGPB) offers a promising alternative to enhance soil quality and crop yield while reducing the consumption of chemical fertilizers.

METHODS: Here, we characterize the plant growth-promoting potential of Azotobacter chroococcum W5 through comparative genomics, in vitro experiments, and metabolomic analyses.

RESULTS: Comparative genomic analysis revealed plant growth-promoting traits, including phytohormone biosynthesis, nutrient acquisition, stress adaptation, and colonization in the A. chroococcum W5 strain. Experimental assays confirmed the production of auxin, gibberellic acid, phosphate solubilization, moderate nitrogen fixation, and growth on ACC. Wheat seed inoculation significantly enhanced germination metrics, seedling vigor, and altered carbohydrate metabolism in the seed endosperm. Under salt and osmotic stress, A. chroococcum W5 metabolomic profiling revealed adaptive responses, including elevated levels of osmoprotectants (proline, glycerol) and oxidative stress markers such as 2-hydroxyglutarate, while putrescine and glycine decreased.

DISCUSSION: Our results show that the A. chroococcum W5 strain has great potential for the development of novel formulations. More importantly, our results highlight the potential of using plant growth-promoting microorganisms for innovative, sustainable solutions in agriculture.},
}

@article {pmid40765478,
year = {2025},
author = {Stevens-Green, R and Chénard, C and Mordret, S and MacKinnon, J and Robicheau, BM and LaRoche, J},
title = {Organellar Genomes of Three Globally Important Nanoplanktonic Diatoms Refine Their Taxon-Specific Distribution and Succession Patterns in the Northwest Atlantic.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {5},
pages = {e70033},
pmid = {40765478},
issn = {1550-7408},
support = {A1-019982//NRC-ACRD Internal Project/ ; OCN-500//NRC Ocean Program Grant and Contribution/ ; (RGPIN/04060-2021)//NSERC Discovery Grant awarded to JLR/ ; //CFREF (NWA BCP) awarded to JLR/ ; },
mesh = {*Diatoms/genetics/classification ; Atlantic Ocean ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Chloroplast ; *Phytoplankton/genetics/classification ; DNA Barcoding, Taxonomic ; },
abstract = {Nanoplanktonic diatoms (2-20 μm) are a significant yet historically understudied component of marine ecosystems. We investigated three recently isolated nanoplanktonic diatoms from the Northwest Atlantic Ocean (NWA): Minidiscus spinulatus, Mediolabrus comicus, and Minidiscus trioculatus. Using Oxford Nanopore sequencing, we assembled and annotated their complete chloroplast and mitochondrial genomes. Pangenome analyses revealed that Minidiscus species consistently clustered more closely with select Thalassiosira species, whereas M. comicus formed a sister clade with Skeletonema. Circularized chloroplast genomes allowed us to characterize the full-length 16S ribosomal RNAs for each isolate, thereby leading to higher resolution of these taxa in preexisting 16S metabarcoding data. During our study, M. spinulatus was primarily restricted to the Bedford Basin. In contrast, both M. trioculatus and M. comicus had larger geographic ranges extending to the Labrador Sea, and in the case of M. comicus, to the Canadian Arctic Gateway. Weekly metabarcoding from the coastal Bedford Basin, N.S., Canada (2014-2022), revealed a seasonal succession of nanoplanktonic taxa, with Minidiscus trioculatus dominating in the early months, followed by M. comicus and M. spinulatus. Our results highlight the critical value of phytoplankton isolations and organelle genomics for expanding our understanding of the diversity and biogeography of nanoplanktonic diatoms.},
}

*Diatoms/genetics/classification
Atlantic Ocean
*Genome, Mitochondrial
Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Chloroplast
*Phytoplankton/genetics/classification
DNA Barcoding, Taxonomic

@article {pmid40763020,
year = {2025},
author = {Wang, H and Nielsen, J and Zhou, YJ and Lu, H},
title = {Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2502044122},
doi = {10.1073/pnas.2502044122},
pmid = {40763020},
issn = {1091-6490},
support = {22378263//MOST | National Natural Science Foundation of China (NSFC)/ ; 22425807//MOST | National Natural Science Foundation of China (NSFC)/ ; 22208211//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFA0913000//National Key R&D Program of China/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; Genomics/methods ; *Genome, Fungal ; Metabolic Networks and Pathways/genetics ; *Adaptation, Physiological/genetics ; Transcriptome ; Gene Expression Regulation, Fungal ; Humans ; Ecosystem ; Metabolic Reprogramming ; },
abstract = {The famous model organism Saccharomyces cerevisiae is widely present in a variety of natural and human-associated habitats. Despite extensive studies of this organism, the metabolic mechanisms driving its adaptation to varying niches remain elusive. We here gathered genomic resources from 1,807 S. cerevisiae strains and assembled them into a high-quality pangenome, facilitating the comprehensive characterization of genetic diversity across isolates. Utilizing the pangenome, 1,807 strain-specific genome-scale metabolic models (ssGEMs) were generated, which performed well in quantitative predictions of cellular phenotypes, thus helping to examine the metabolic disparities among all S. cerevisiae strains. Integrative analyses of fluxomics and transcriptomics with ssGEMs showcased ubiquitous transcriptional regulation of metabolic flux in specific pathways (i.e., amino acid synthesis) at a population level. Additionally, the gene/reaction inactivation analysis through the ssGEMs refined by transcriptomics showed that S. cerevisiae strains from various ecological niches had undergone reductive evolution at both the genomic and metabolic network levels when compared to wild isolates. Finally, the compiled analysis of the pangenome, transcriptome, and metabolic fluxome revealed remarkable metabolic differences among S. cerevisiae strains originating from distinct oxygen-limited niches, including human gut and cheese environments, and identified convergent metabolic evolution, such as downregulation of oxidative phosphorylation pathways. Together, these results illustrate how yeast adapts to distinct niches modulated by genomic and metabolic reprogramming, and provide computational resources for translating yeast genotype to fitness in future studies.},
}

*Saccharomyces cerevisiae/genetics/metabolism
Genomics/methods
*Genome, Fungal
Metabolic Networks and Pathways/genetics
*Adaptation, Physiological/genetics
Transcriptome
Gene Expression Regulation, Fungal
Humans
Ecosystem
Metabolic Reprogramming

@article {pmid40762505,
year = {2025},
author = {Liu, Y and Wang, X and Wu, L and Shi, Z and Zhu, M and Ye, L and Xu, P},
title = {Prediction of antimicrobial resistance in Staphylococcus aureus with a machine learning classifier based on WGS data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0006525},
doi = {10.1128/spectrum.00065-25},
pmid = {40762505},
issn = {2165-0497},
abstract = {UNLABELLED: The phenomenon of antimicrobial resistance (AMR) often results in treatment failure and restrictions on precision medicine, emphasizing the need for molecular diagnosis of drug resistance. The current use of machine learning (ML) techniques based on whole genome sequencing (WGS) data offers a more precise prediction of phenotypes. We incorporated WGS data from 3979 Staphylococcus aureus strains in our study. We modeled 10 common antibiotics using three types of features: gene, single nucleotide polymorphism (SNP), and k-mer to identify the best model and to determine which feature values most significantly contributed to the model's performance. The area under the curve (AUC) values of 40 mL models for 10 antibiotics ranged from 0.8345 to 0.9995. We noted that the performance indices such as the AUC of the gene model (0.9311-0.9992) and the integrated model (0.9313-0.9995) were markedly better than the SNP model (0.8345-0.9933) and the k-mer model (0.9024-0.9969). The best model AUC values for six antibiotics-cefoxitin, tetracycline, methicillin, gentamicin, erythromycin, and clindamycin-were over 0.99; nine antibiotic models had AUC values over 0.96, and all could effectively predict AMR phenotypes. Additionally, we discovered that certain non-AMR genes, such as the X998_03220 gene, significantly contributed to drug resistance prediction and overlapped in various antibiotic-related models simultaneously. Our study developed ML models that can reliably predict AMR phenotypes for commonly used antibiotics in S. aureus. We also identified potential molecular markers that can contribute to precision medicine implementation and healthcare cost reduction.

IMPORTANCE: In our study, we developed a machine learning (ML) model that reliably predicts the antimicrobial resistance (AMR) phenotypes of Staphylococcus aureus to commonly used antibiotics. This model not only predicts AMR phenotypes but also identifies potential molecular markers, which could facilitate the implementation of precision medicine and contribute to reducing healthcare costs. The integration of diverse biomarker types is crucial for enhancing model performance; however, their effectiveness may vary depending on the specific antibiotic in question. Furthermore, our pan-genome-based characterization has revealed novel potential molecular markers associated with AMR, thereby enhancing our comprehension of the underlying molecular mechanisms of AMR in S. aureus. The expedited implementation of early and targeted antimicrobial therapies for S. aureus infections is essential for advancing precision medicine and can potentially lead to significant healthcare cost savings.},
}

@article {pmid40762257,
year = {2025},
author = {Homsombat, T and Yoshii, K and Fukada, Y and Koiwai, K and Hirono, I and Kondo, H},
title = {Comparative Genomics of Edwardsiella piscicida in the Japanese Flounder (Paralichthys olivaceus): Discovery and Implications of a Novel Genomic Island.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70035},
doi = {10.1111/jfd.70035},
pmid = {40762257},
issn = {1365-2761},
support = {JPMJSA1806//Science and Technology Research Partnership for Sustainable Development/ ; },
abstract = {Edwardsiella piscicida is a significant pathogen that poses a particular threat to Japanese flounder (Paralichthys olivaceus) aquaculture in Japan and other countries. The damage is caused by the pathogen's ability to evade host immune defences and establish intracellular infections, intensified by its genomic plasticity and capacity for horizontal gene transfer. To investigate evolutionary adaptations between one older (2019) and four recent (2023) E. piscicida strains from the same geographical locations, we performed comparative genomic analysis of five isolates using high-quality hybrid genome assemblies and compared them with 27 Edwardsiella reference genomes. Pangenome analysis identified distinct novel genomic islands (GIs) specific to the 2023 strains. These GIs (~100 kb in size) shared 85 gene clusters encoding multiple antibiotic resistance genes, phage defence systems, mobilisation genes, and mercury resistance. In addition, they encoded integrases, transposases, and conjugative transfer genes, suggesting they function as integrative and conjugative elements (ICEs), a type of mobile genetic element. Phenotypic characterisation showed the 2023 strains carrying novel GI increased antibiotic resistance, but no significant difference in virulence in Japanese flounder infection trials. These findings highlight the recent genomic diversification of E. piscicida in aquaculture and the importance of monitoring emerging GIs driving antibiotic resistance and environmental persistence.},
}

@article {pmid40756639,
year = {2025},
author = {Zhao, L and Hu, Y and Ji, QY and Gong, LX and Lu, MJ and Yu, XN and Jin, ZS and Zhou, M and Dai, XL and Xiao, SY and Jiang, Y and Wen, YQ},
title = {Chromosome-level reference genome of Vitis piasezkii var. pagnucii provides insights into a new locus of resistance to grapevine powdery mildew.},
journal = {Horticulture research},
volume = {12},
number = {9},
pages = {uhaf146},
pmid = {40756639},
issn = {2662-6810},
abstract = {Grapevine powdery mildew (GPM), caused by Erysiphe necator, poses a significant threat to all green grapevine tissues, leading to substantial economic losses in viticulture. Traditional grapevine cultivars derived from Vitis vinifera are highly susceptible to GPM, whereas the wild Chinese accession Baishui-40 (BS-40) of V. piasezkii var. pagnucii exhibits robust resistance. To illuminate the genetic basis of resistance, we sequenced and assembled the chromosome-level genome of 'BS-40', achieving a total mapped length of 578.6 Mb distributed across nineteen chromosomes. A comprehensive annotation identified 897 nucleotide-binding leucine-rich repeat (NLR) genes in the 'BS-40' genome, which exhibited high sequence similarity across Vitis genomes. 284 of these NLR genes were differentially expressed upon GPM infection. A hybrid population of 'BS-40' and V. vinifera was constructed and 195 progenies were whole-genome re-sequenced. A new GPM-resistant locus, designated Ren17, located within the 0.74-1.23 Mb region on chromosome 1 was identified using genome-wide association study, population selection, and QTL analysis. Recombinant events indicated that an NLR gene cluster between 1 045 489 and 1 089 719 bp on chromosome 1 is possibly the key contributor to GPM resistance in 'BS-40'. Based on an SNP within this region, a dCAPS marker was developed that can predict the GPM resistance in 'BS-40'-derived materials with 99.4% accuracy in the progenies of 'BS-40' and V. vinifera. This chromosome-level genome assembly of V. piasezkii var. pagnucii provides a valuable resource not only for grapevine evolution, genetic analysis, and pan-genome studies but also a new locus Ren17 as a promising target for GPM-resistant breeding in grapevine.},
}

@article {pmid40752099,
year = {2025},
author = {Huang, C and Ding, C and Tang, J and Sun, W and Zhang, Y and Chen, Y and Huang, M and Li, H and Wang, X and Yu, J and Wang, Y and Hao, X},
title = {Evolutionary and functional characterization of tea plant DELLA proteins.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt A},
pages = {110317},
doi = {10.1016/j.plaphy.2025.110317},
pmid = {40752099},
issn = {1873-2690},
abstract = {DELLA proteins function as key negative regulators in gibberellin signaling, driving numerous molecular mechanisms that impact plant morphogenesis and ontogeny. In this study, eight representative DELLA proteins were identified based on pan-genome analysis of Camellia sinensis var. assamica (CSA) and Camellia sinensis var. sinensis (CSS). Phylogenetically, these DELLA proteins were subdivided into five groups, and their evolutionary trajectories were systematically investigated. Five DELLA proteins identified in Longjing43, including a newly discovered CsDELLA5, were found to be crucial for growth and exhibited distinct expression patterns in different tissues of tea plant during seasonal transitions. The five proteins were mainly located in the nucleus, CsDELLA2 exhibited a spotted distribution in the cytoplasm. CsDELLAs also showed varied protein structure, hormone responses and expression patterns in bud sprouting. Notably, the presence of GAs significantly enhanced the interaction between CsDELLA2/4/5 and CsGID1a/b. Inhibition of the expression of CsDELLA2 and CsDELLA4 significantly increase the bud sprouting rate indicating a negative function in regulation of bud break. This study offers valuable insights into the roles of DELLA proteins in tea plants and provides a theoretical foundation for DELLA protein research in other species.},
}

@article {pmid40750043,
year = {2025},
author = {Elias, R and Phelan, JE and Lito, L and Caneiras, C and Marques, C and Pinto, M and Cavaco-Silva, P and Ferreira, H and Pomba, C and Da Silva, GJ and Saavedra, MJ and Coelho, R and Lourinho, R and Gonçalves, L and Hinthong, W and Rosa, MJ and Melo-Cristino, J and Campino, S and Portugal, I and Duarte, A and Clark, TG and Perdigão, J},
title = {Genome-Wide Analysis and Longitudinal Study of Klebsiella pneumoniae in Portugal: Tracing the Evolution and Spread of Carbapenem Resistance.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107583},
doi = {10.1016/j.ijantimicag.2025.107583},
pmid = {40750043},
issn = {1872-7913},
abstract = {BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) has high incidence in Portugal, causing severe and often fatal infections.

OBJECTIVES: Characterize the evolutionary history and epidemiology of CRKP in Portugal over a 40-year period.

METHODS: WGS was performed using the Illumina platform. In silico multilocus sequence typing, surface antigen characterization, and resistance gene detection were subsequently carried out. Core and pan-genome analyses were conducted using Roary. Genomic clusters (GCs) were identified based on a 21-SNP threshold. To estimate the divergence times of the most prevalent sequence types (ST) in the dataset, Bayesian evolutionary analysis was performed using BEAST.

RESULTS: Nineteen GCs harboring carbapenemases were identified. The blaKPC-3 gene was the most prevalent carbapenemase, linked to strains circulating in both hospital and community settings, with dissemination patterns at regional, interregional, and international levels. ST15 was the most established sequence type in Portugal, with nine distinct GCs identified in both clinical and environmental samples. Towards the end of 2010s, ST147 and ST13 were responsible for significant outbreaks associated with blaKPC-3.

CONCLUSIONS: This study underscores the value of genomic-based surveillance in understanding the evolution of high-risk clones coupled with the spread of AMR determinants. The data obtained highlights a shift in ST predominance across the country from an ST15-dominated period and strongly associated with ESBL dissemination, to the emergence of ST147 and ST13 CRKP clones, the latter associated with international transmission. This work further stresses the importance of cross-border surveillance efforts to monitor the emergence and dissemination of CRKP strains and inform risk assessment and prevention.},
}

@article {pmid40749792,
year = {2025},
author = {Li, W and Sun, J and Wu, Q and Kwok, LY and Dong, G and Sun, Z},
title = {Global genomics of Lactococcus lactis: horizontal gene transfer and intergenic variation drive multiple domestication and dairy adaptation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.053},
pmid = {40749792},
issn = {2090-1224},
abstract = {INTRODUCTION: Lactococcus lactis is a crucial lactic acid bacterium of great economically significance for cheese product. The species exhibits wildly distribution and significant genetic diversity, yet the underlying drivers of its differentiation remain elusive.

OBJECTIVES: Lactococcus lactis, exhibits complex genetic diversity, yet the mechanisms driving its differentiation and niche adaptation remain poorly understood.

METHODS: This study assembled a genome dataset of 1008 isolates of Lactococcus lactis from six major habitats across five continents. And combined with public database data, used population genomics and function genomics to analysis the population structure and adaptation.

RESULTS: To elucidate its population structure and domestication history, 1008 genomes from six diverse habitats across five continents were analyzed, revealing two major genetic branches subdivided into ten distinct lineages. Phylogenomic and ancestral analyses support a multiple domestication model, with the ancestral plant-associated lineage (L6) diversified into dairy-adapted lineages (L8-L10) through extensive horizontal gene transfer, primarily facilitated by mobile genetic elements. Notably, intergenic regions (IGRs) critically influence phenotypic diversity and genetic structure, underscoring the functional significance of non-coding sequences in microbial adaptation. Pan-genome analysis highlights extensive accessory gene and IGR diversity, with habitat-specific enrichments: dairy lineages are enriched in mobile genetic elements and carbohydrate-active enzymes, while plant isolates show reduced genetic exchange. A machine learning framework integrating single nucleotide polymorphisms, genes, and IGRs accurately predicts isolate-specific fermentation traits, enabling efficient industrial strain selection.

CONCLUSION: These findings redefine non-coding regions as key drivers of microbial domestication and provide a genomic framework to optimize Lactococcus lactis for dairy fermentation and biotechnology, bridging ecological adaptation with applied innovation.},
}

@article {pmid40748957,
year = {2025},
author = {Cui, W and Fendley, JM and Srikant, S and Shraiman, BI},
title = {A minimal model of panimmunity maintenance by horizontal gene transfer in the ecological dynamics of bacteria and phages.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2417628122},
pmid = {40748957},
issn = {1091-6490},
support = {PHY:1748958//National Science Foundation (NSF)/ ; NSF PHY:1707973//National Science Foundation (NSF)/ ; 2919.02//Gordon and Betty Moore Foundation (GBMF)/ ; KTIP//Simons Foundation (SF)/ ; PHY:2210612//National Science Foundation (NSF)/ ; Life Sciences Research Foundation//Howard Hughes Medical Institute (HHMI)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteriophages/genetics/immunology ; *Bacteria/genetics/immunology/virology ; },
abstract = {Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counterdefense mechanisms of specific phages. These defense/counterdefense systems are a major element of microbial genetic diversity and have been demonstrated to propagate between strains by horizontal gene transfer (HGT). It has been proposed that the totality of defense systems found in microbial communities collectively form a distributed "pan-immune" system with individual elements moving between strains via ubiquitous HGT. Here, we formulate a Lotka-Volterra type model of a bacteria/phage community interacting via a combinatorial variety of defense/counterdefense systems and show that HGT enables stable maintenance of diverse defense/counterdefense genes in the microbial pan-genome even when individual microbial strains inevitably undergo extinction. This stability requires the HGT rate to be sufficiently high to ensure that some descendant of a "dying" strain survives, thanks to the immunity acquired through HGT from the community at large, thus establishing a new strain. This mechanism of persistence for the pan-immune gene pool is fundamentally similar to the "island migration" model of ecological diversity, with genes moving between genomes instead of species migrating between islands.},
}

*Gene Transfer, Horizontal
*Bacteriophages/genetics/immunology
*Bacteria/genetics/immunology/virology

@article {pmid40748669,
year = {2025},
author = {Cui, S and Ma, W and Peng, H and Ye, Y and Qing, Y and Wei, G and Wang, J and Zhang, X},
title = {Genome-wide mining reveals the genetic plasticity of antibiotic resistance/virulence factor genes in Enterobacter hormaechei subsp. xiangfangensis.},
journal = {Journal of applied microbiology},
volume = {136},
number = {8},
pages = {},
doi = {10.1093/jambio/lxaf196},
pmid = {40748669},
issn = {1365-2672},
support = {2025JJ50123//Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 32200676//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; },
abstract = {AIMS: This study aims to systematically characterize the genetic basis and intra-species differentiation of antibiotic resistance/virulence factor genes (ARGs/VFGs) in Enterobacter hormaechei subsp. xiangfangensis.

METHODS AND RESULTS: A high-quality metagenome-assembled genome of E. hormaechei subsp. xiangfangensis bin99 (97.22% completeness, 1.63% contamination) was acquired. Phylogenomic and average nucleotide identity (≥95%) analyses confirmed its taxonomic assignment. Pan-genomic analysis revealed an open configuration (Heap's exponent B = 0.34) with a large accessory genome (approximate 2965 genes) and a stabilized core genome (1139 genes). Critically, a strong positive correlation (r = 0.86, P < 2.2e-16) was observed between mobile genetic elements (MGEs) and accessory gene abundance, probably suggesting horizontal gene transfer (HGT) as a potential driver of genome diversity. Functional annotation highlighted distinct roles: core genes enriched in essential metabolism, while accessory/strain-specific genes were linked to adaptation. Screening identified significant inter-strain variation in ARGs (n = 31) and VFGs (n = 35). Bin99 itself harbored 19 ARGs (e.g. multidrug: soxS, ramA, oqxB) and 40 VFGs (e.g. flagella, T6SS). Importantly, MGE abundance showed a significant positive correlation with ARGs (r = 0.67, P < 2.2e-16) but a negative correlation with VFGs (r = -0.29, P < 3.7e-9), suggesting that ARGs were frequently linked to MGEs facilitating HGT-mediated spread, while VFGs might rely less on this route.

CONCLUSIONS: The findings provide genome-wide evidence for distinct genetic plasticity underlying ARG and VFG evolution in E. hormaechei subsp. xiangfangensis, highlighting implications for resistance and virulence dissemination.},
}

@article {pmid40748397,
year = {2025},
author = {Velo, J and Caipang, CM and Noblezada, A and Banabatac, LI and Tan, NP and Ferriols, VME},
title = {Whole genome sequence of Arthrobacter sp. from Iloilo City landfill soil unveils potential plastic biodegradation genes.},
journal = {Biodegradation},
volume = {36},
number = {4},
pages = {72},
pmid = {40748397},
issn = {1572-9729},
mesh = {Biodegradation, Environmental ; *Arthrobacter/genetics/metabolism/isolation & purification ; *Soil Microbiology ; Phylogeny ; *Plastics/metabolism ; Whole Genome Sequencing ; *Genome, Bacterial ; Waste Disposal Facilities ; Polyethylene/metabolism ; Polypropylenes/metabolism ; },
abstract = {Plastics are synthetic materials that have transformed society in a lot of ways, yet widespread use of these materials has caused a staggering amount of pollution in the environment. Among these plastics, polypropylene and low-density polyethylene are two of the most used plastics for packaging globally. Currently, only two enzymes were characterized for low density polyethylene degradation while no specific enzymes have been confirmed to degrade polypropylene. In this study, one bacterial isolate from landfill soil was assessed for potential polypropylene and low-density polyethylene degradation abilities using gravimetric methods by measuring the initial and final weight of plastic films. Results showed that after 60 days of incubation, a total decrease of 8.04% was observed for polypropylene plastics and 3.13% for low density polyethylene plastics. Whole genome sequencing using Illumina Nextseq™ 1000 generated a total number of 3,746,011 assembled base pairs for Isolate 1 using SPAdes. Phylogenetic tree construction using the Bacterial Pan-Genome Analysis (BPGA) tool revealed close relation of the isolate to Arthrobacter sp. Analysis of the annotated whole genome sequence against the Plastic database revealed 11 putative protein coding genes that encode enzymes with potential to break down plastics.},
}

Biodegradation, Environmental
*Arthrobacter/genetics/metabolism/isolation & purification
*Soil Microbiology
Phylogeny
*Plastics/metabolism
Whole Genome Sequencing
*Genome, Bacterial
Waste Disposal Facilities
Polyethylene/metabolism
Polypropylenes/metabolism

@article {pmid40746326,
year = {2025},
author = {Qiu, Y and Guo, P and Tian, H and Zhou, Y and Wen, H and Liang, H},
title = {The restriction impacts of the Type III restriction-modification system on the transmission dynamics of antimicrobial resistance genes in Campylobacter jejuni.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496275},
pmid = {40746326},
issn = {1664-302X},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes among Campylobacter jejuni (C. jejuni) is a serious problem, and the effects of the restriction-modification (R-M) system on the transmission dynamics of these genes in C. jejuni remain poorly understood.

MATERIALS AND METHODS: Complete genome sequences of C. jejuni strains were extracted from the BV-BRC database until March 25, 2024. The phylogenetic and the resistance analysis were used to analyze the distribution of resistance genes in C. jejuni. The impacts of the R-M systems on the AMR genes transmission between C. jejuni strains and the possible mechanisms were explored through recombination, pangenome and mobile genetic elements analysis.

RESULTS: C. jejuni strains carrying the Type III R-M system have a significantly lower number of antimicrobial resistance (AMR) genes compared to strains without this system (p < 0.0001), with covariance value being -0.0526. The recombination analysis also shows that the median number of the number of AMR genes in the strains not possessing the Type III R-M system increases by 19.38% compared to strains carrying that system (p < 0.0001). We also find that the horizontal gene transfer frequency might have limited relationship with the Type III R-M system in C. jejuni through pangenome and mobile genetic elements analysis.

CONCLUSION: Our research indicates that the Type III R-M system might restrict the transmission of AMR genes potentially by affecting recombination in C. jejuni, which provides a theoretical basis for addressing the drug resistance problem.},
}

@article {pmid40745104,
year = {2025},
author = {Jha, UC and Naik, YD and Priya, M and Nayyar, H and Sofi, PA and Beena, R and Kudapa, H and Atta, K and Thudi, M and Prasad, PVV and Siddique, KHM},
title = {Chickpea (Cicer arietinum L.) battling against heat stress: plant breeding and genomics advances.},
journal = {Plant molecular biology},
volume = {115},
number = {4},
pages = {101},
doi = {10.1007/s11103-025-01628-z},
pmid = {40745104},
issn = {1573-5028},
mesh = {*Cicer/genetics/physiology ; *Plant Breeding ; *Genomics/methods ; *Heat-Shock Response/genetics ; Genome, Plant ; Genome-Wide Association Study ; },
abstract = {Global climate change, particularly the increasing frequency and intensity of heat stress, poses a significant threat to crop productivity. Chickpea (Cicer arietinum L.) employs various physiological, biochemical, and molecular mechanisms to cope with elevated temperatures, including maintaining leaf chlorophyll content to preserve the functional integrity of photosystem II (PSII) and enhancing canopy temperature depression to reduce overheating. These traits are crucial for sustaining photosynthetic efficiency, plant health, and yield stability under heat stress. Recent advances in multi-omics approaches-including genomics, transcriptomics, proteomics, and metabolomics-have enhanced our understanding of the genetic basis of heat stress tolerance in chickpea. These tools have facilitated the identification of key genes and molecular pathways involved in heat stress responses. Functional characterization of these genes has provided insights into their roles within the complex metabolic and signaling networks that underpin heat resilience. This review explores integrating conventional and modern breeding technologies with high-throughput phenotyping (HTP) platforms to accelerate genetic gains in chickpea under heat stress. HTP tools enable rapid, precise screening of heat-resilient traits, facilitating early selection of superior genotypes. We also highlight recent genomic advancements, including genome-wide association studies, whole-genome resequencing, and pangenome assemblies, which have uncovered novel structural variants, candidate genes, and haplotypes associated with heat tolerance. Leveraging these resources in conjunction with functional analyses offers new opportunities for breeding climate-resilient chickpea cultivars capable of delivering stable yields and quality under adverse conditions. These developments are crucial for safeguarding chickpea productivity and ensuring global food and nutrition security amid climate change.},
}

*Cicer/genetics/physiology
*Plant Breeding
*Genomics/methods
*Heat-Shock Response/genetics
Genome, Plant
Genome-Wide Association Study

@article {pmid40744123,
year = {2025},
author = {Wang, J and Chen, D and Hu, H and Ma, Y and Yang, T and Guo, J and Chen, K and Ye, C and Liu, J and Zhou, X and Liu, C and Zhao, J},
title = {Functional characterization of OsLT9 in regulating rice leaf thickness.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2025.07.010},
pmid = {40744123},
issn = {1673-8527},
abstract = {Leaf thickness in rice critically influences photosynthetic efficiency and yield, yet its genetic basis remains poorly understood, with few functional genes previously characterized. In this study, we employ a pangenome-wide association study (Pan-GWAS) on 302 diverse rice accessions from southern China, identifying 49 quantitative trait loci (QTLs) associated with leaf thickness. The most significant locus, qLT9, is fine-mapped to a 79 kb region on chromosome 9. Transcriptomic and genomic sequence analyses identify LOC_Os09g33480, which encodes a protein belonging to Multiple Organellar RNA Editing Factor (MORF) family, as the key candidate gene. Overexpression and complementation transgenic experiments confirm LOC_Os09g33480 (OsLT9) as the functional gene underlying qLT9, demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness. Notably, OsLT9 overexpression lines show not only thicker leaf, but also significantly enhanced photosynthetic efficiency and grain yield, establishing a link between leaf thickness modulation and yield enhancement. Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding, with modern cultivars favoring thick leaf haplotype of OsLT9. This study establishes OsLT9 as a key regulator controlling leaf thickness in rice, and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.},
}

@article {pmid40740683,
year = {2025},
author = {Rotaru, LI and Surleac, M},
title = {PeGAS: a versatile bioinformatics pipeline for antimicrobial resistance, virulence and pangenome analysis.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf165},
pmid = {40740683},
issn = {2635-0041},
abstract = {MOTIVATION: Antimicrobial resistance is increasingly recognized as one of the most significant global health threats, with profound implications for human, animal, and environmental health. Genome analysis represents a very useful tool that provides accurate and reproducible results allowing for the advancement of knowledge regarding antimicrobial resistance diagnosis, therapeutics, surveillance, transmission, and evolution. However, due to increasing complexity of bacterial genome analysis and computational power required for genomic approaches, there is a continuous need for comprehensive, user-friendly tools for data analysis. We developed Pangenome and Genomic Analysis Suite (PeGAS), to address some of these challenges by offering an all-in-one pipeline that performs a range of analyses.

RESULTS: PeGAS integrates key genomic analysis features of bacteria whole genome sequencing, including the prediction of antimicrobial resistance profiles, sorted by various categories of antibiotics, VF detection, and plasmid replicon assignment. The pipeline also performs pangenome analysis, multilocus sequence typing, genome assembly quality control (by reporting statistics such as GC content, contig length, the number of contigs, as well as variation from certain GC thresholds) providing a comprehensive genomic overview. PeGAS also offers the ability to restart seamlessly from any sporadic interruptions that might occur during long or resource-intensive runs.

PeGAS is available at: https://github.com/liviurotiul/PeGAS.},
}

@article {pmid40738999,
year = {2025},
author = {Wang, L and Jiang, X and Jiao, W and Mao, J and Ye, W and Cao, Y and Chen, Q and Song, Q},
title = {Pangenome analysis provides insights into legume evolution and breeding.},
journal = {Nature genetics},
volume = {57},
number = {8},
pages = {2052-2061},
pmid = {40738999},
issn = {1546-1718},
support = {32372126 and 32300494//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Fabaceae/genetics/classification ; *Genome, Plant ; *Plant Breeding ; *Evolution, Molecular ; DNA Transposable Elements/genetics ; Phylogeny ; Genes, Plant ; },
abstract = {Grain legumes hold great promise for advancing sustainable agriculture. Although the evolutionary history of legume species has been investigated, the conserved mechanisms that drive adaptive evolution and govern agronomic improvement remain elusive. Here we present high-quality genome assemblies for nine widely consumed pulses, including common bean, chickpea, pea, lentil, faba bean, pigeon pea, cowpea, mung bean and hyacinth bean. Pangenome analysis reveals the expansion of distinct gene sets in cool-season and warm-season legumes, highlighting the role of gene birth and duplication in the autoregulation of nodulation. Notably, hundreds of genes undergo convergent selection during the evolution of legumes, affecting agronomic traits such as seed weight. In addition, we demonstrate that tandem amplification of transposable elements in gene-depleted regions has a crucial role in driving genome enlargement and the formation of regulatory elements in cool-season legumes. Our results provide insights into the molecular mechanisms underlying the diversification of legumes and represent a valuable resource for facilitating legume breeding.},
}

*Fabaceae/genetics/classification
*Genome, Plant
*Plant Breeding
*Evolution, Molecular
DNA Transposable Elements/genetics
Phylogeny
Genes, Plant

@article {pmid40736903,
year = {2025},
author = {Papastolopoulou, C and Yang, Z and van Workum, DM and Wijfjes, RY and Smit, S},
title = {High-Quality Plant Genomes for and through Pangenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {293-316},
doi = {10.1007/978-1-0716-4702-8_14},
pmid = {40736903},
issn = {1940-6029},
mesh = {*Genome, Plant ; *Genomics/methods ; Molecular Sequence Annotation ; *Plants/genetics ; Genetic Variation ; Capsicum/genetics ; },
abstract = {The field of comparative genomics is shifting toward pangenomics, aiming to alleviate the reference bias observed in reference-based approaches. High-quality genomes are needed as input for pangenomics, as explained by the principle of "garbage in, garbage out". Errors in an assembly or annotation will lead to technical variation in a pangenome, while it is meant to reveal genuine biological variation only. Achieving the required assembly and annotation quality remains challenging, particularly in plants, given the complexity in genome size, ploidy level, and repeat content present in the plant kingdom.Nevertheless, the (technical) variation uncovered by pangenomics can, in turn, guide iterative refinements that yield high-quality genomes. The comparative approach is especially powerful to identify "abnormalities" in a set of genomes, which cannot be detected from traditional, stand-alone quality assessment. Two use cases, on roses and chili peppers, illustrate the role of pangenomics in this iterative process leading toward meaningful pangenome analyses. Thus, we argue that high-quality genomes can be achieved through pangenomics, facilitating the convergence on real genetic variation underlying complex traits and diseases, not only in plants but also in other organisms.},
}

*Genome, Plant
*Genomics/methods
Molecular Sequence Annotation
*Plants/genetics
Genetic Variation
Capsicum/genetics

@article {pmid40736902,
year = {2025},
author = {Gifford, H and Wilson, D and Rhodes, J and Farrer, RA},
title = {Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {263-291},
pmid = {40736902},
issn = {1940-6029},
mesh = {Humans ; *Candidiasis/microbiology/diagnosis ; *Candida auris/genetics/pathogenicity ; Animals ; Computational Biology/methods ; Host-Pathogen Interactions ; *Candida/genetics ; },
abstract = {Discovery science in Medical Mycology requires a range of tools, from optimized experimental models to near-patient clinical applications, with the common goal of reducing morbidity and mortality from fungal diseases. Assembly tools underpin bioinformatic discovery across this spectrum of research, setting the scene for genomic enquiry, and promising an unprecedented wave of breakthrough in mechanistic understanding of pathobiology that could unearth critical diagnostic and treatment advances. This chapter examines the investigation of Candida auris, an emerging human fungal pathogen, in the context of clinic detection and treatment of infection. In the laboratory, we cover the use of the Arabian Killifish (AK) as a non-model organism to understand transcriptional responses to both host and pathogen during infection.},
}

Humans
*Candidiasis/microbiology/diagnosis
*Candida auris/genetics/pathogenicity
Animals
Computational Biology/methods
Host-Pathogen Interactions
*Candida/genetics

@article {pmid40732189,
year = {2025},
author = {Mashzhan, A and Smekenov, I and Bakiyev, S and Utegenova, K and Samatkyzy, D and Daniyarov, A and Kairov, U and Sarbassov, D and Bissenbaev, A},
title = {Whole-Genome Sequencing of a Potentially Novel Aeromonas Species Isolated from Diseased Siberian Sturgeon (Acipenser baerii) Using Oxford Nanopore Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732189},
issn = {2076-2607},
support = {АP23487566//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakh-stan/ ; },
abstract = {Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation-differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966[T]) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}

@article {pmid40728297,
year = {2025},
author = {Guo, X and He, Z-G},
title = {Pangenome-scale annotation of mycobacteriophages for dissecting phage-host interactions based on a sequence clustering and structural homology analysis strategy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050825},
doi = {10.1128/msystems.00508-25},
pmid = {40728297},
issn = {2379-5077},
abstract = {With the increasing severity of bacterial drug resistance, there is a growing need for phages with well-defined genetic backgrounds to combat drug-resistant infections. Mycobacteriophages constitute the largest genome-sequenced phage group; however, the vast majority of these phage proteins have not yet been effectively annotated. In this study, we employed a structure-based similarity search approach to improve protein annotation. Through the application of this approach to 240,754 proteins from 2,169 mycobacteriophage genomes, we increased the protein annotation rate from 34% to 52.11%. Additionally, we identified a series of predicted counter-defense proteins, including anti-CRISPR proteins and antitoxins, and inferred the potential interaction network of phage-encoded proteins involved in replication, transcription, and translation with host-associated molecular machinery. This study addresses a substantial gap in the current knowledge of the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.IMPORTANCEMycobacteriophages constitute the largest group of phages with sequenced genomes. However, a significant portion of these phage proteins have not yet been effectively annotated, seriously hindering our understanding of the basic biological processes of phage-host interactions and their practical applications. This study utilized a structure-based similarity search approach to enhance phage protein annotation. This approach led to the identification of novel predicted protein folds, structural domain fusion phenomena, and putative new enzymes. Additionally, the study identified a series of phage-encoded proteins that may play a role in hijacking host-associated replication, transcription, and translation processes, providing insights into the molecular mechanisms underlying mycobacteriophage interactions with host machinery. This study addresses a critical knowledge gap regarding the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.},
}

@article {pmid40726548,
year = {2025},
author = {Li, Q and Fu, Y and Zhang, C and Zhang, G and Zhao, Y and Wang, Y and Dou, Y and Gao, L and Abdullah, S and Ma, X and Su, Y and Song, X},
title = {Deciphering the near-complete genome and conducting pan-genome analysis of Brassica oleracea.},
journal = {Horticulture research},
volume = {12},
number = {8},
pages = {uhaf189},
pmid = {40726548},
issn = {2662-6810},
}

@article {pmid40724005,
year = {2025},
author = {Tristancho-Baró, A and López-Calleja, AI and Milagro, A and Ariza, M and Viñeta, V and Fortuño, B and López, C and Latorre-Millán, M and Clusa, L and Badenas-Alzugaray, D and Martínez, R and Torres, C and Rezusta, A},
title = {Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40724005},
issn = {2079-6382},
abstract = {Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was blaNDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512. Genes associated with toxin-antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems-especially in those encoded by fec, fhu, and cir operons-play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies.},
}

@article {pmid40722552,
year = {2025},
author = {Moustakli, E and Christopoulos, P and Potiris, A and Zikopoulos, A and Mavrogianni, D and Karampas, G and Kathopoulis, N and Anagnostaki, I and Domali, E and Tzallas, AT and Drakakis, P and Stavros, S},
title = {Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {40722552},
issn = {2075-4418},
abstract = {Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption.},
}

@article {pmid40721945,
year = {2025},
author = {Zhang, X and Chen, X and Wu, X and Liu, Y and Wei, Y},
title = {Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27420},
pmid = {40721945},
issn = {2045-2322},
support = {42073077//the National Natural Science Foundation of China/ ; },
mesh = {*Micromonospora/genetics/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; },
abstract = {In this study, we aimed to clarify the taxonomic positions of Micromonospora veneta DSM 109713[T] and Micromonospora coerulea JCM 3175[T] using whole-genome phylogenetic analysis, pangenomic analysis and chemotaxonomic characteristics. The 16S rRNA gene sequences of veneta DSM 109713[T] and M. coerulea JCM 3175[T] were highly similar (99.2%), and in the phylogenetic trees constructed using whole genome sequences and 16S rRNA gene sequences, M. veneta DSM 109713[T] and M. coerulea JCM 3175[T] clustered together and formed a clade. The values of average amino acid (AAI), ANI-BLAST (ANIb) and ANI-MUMmer (ANIm), and digital DNA-DNA hybridization (dDDH) between M. veneta DSM 109713[T] and M. coerulea JCM 3175[T] were 97.57%, 97.81%, 98.40%, 85.0%, respectively, which are all greater than the thresholds used for species delimitation (AAI: 95.5%, ANI: 95-96%, and dDDH: 70%). Most phenotypic and chemotaxonomic features between the two species were similar, with only a few differences. Based on the combined evidence from genomic and phenotypic comparison, we propose Micromonospora veneta as a later heterotypic synonym of Micromonospora coerulea.},
}

*Micromonospora/genetics/classification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Bacterial

@article {pmid40721805,
year = {2025},
author = {Wen, H and Yang, J and Zhao, X and Wang, X and Lei, J and Li, Y and Du, W and Li, D and Xu, Y and Lonardi, S and Pan, W},
title = {TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {227},
pmid = {40721805},
issn = {1474-760X},
support = {32100501//National Natural Science Foundation of China/ ; ZDRW202503//the Agricultural Science and Technology Innovation Program/ ; Y2025QC36//the Youth Innovation Program of the Chinese Academy of Agricultural Sciences/ ; CAAS-CSIAF-202301//The Agricultural Science and Technology Innovation Program/ ; },
mesh = {Humans ; *Tandem Repeat Sequences ; *Algorithms ; Solanum lycopersicum/genetics ; Centromere/genetics ; *Sequence Analysis, DNA/methods ; Software ; Telomere/genetics ; },
abstract = {The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.},
}

Humans
*Tandem Repeat Sequences
*Algorithms
Solanum lycopersicum/genetics
Centromere/genetics
*Sequence Analysis, DNA/methods
Software
Telomere/genetics

@article {pmid40721218,
year = {2025},
author = {Hu, M and Wan, P and Chen, C and Tang, S and Chen, J and Wang, L and Chakraborty, M and Zhou, Y and Chen, J and Gaut, BS and Emerson, JJ and Liao, Y},
title = {Accurate, scalable structural variant genotyping in complex genomes at population scales.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf180},
pmid = {40721218},
issn = {1537-1719},
abstract = {Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.},
}

@article {pmid40716970,
year = {2025},
author = {Rodriguez-Valera, F and Molina-Pardines, C},
title = {On the biological meaning of the population pangenome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.07.004},
pmid = {40716970},
issn = {1878-4380},
abstract = {The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool within a single population, defined as cells of the same species coexisting in the same time and place. This single-population pangenome reflects the minimal flexible gene repertoire required in a specific environmental context. Recent long-read metagenomic studies of marine prokaryotes show that local population pangenomes remain large, often comprising thousands of genes. Specifically, cells belonging to the same species of the streamlined alfaproteobacterium Pelagibacter, coming from the same sampling site and even sample, contain more than a thousand genes. Many of these genes are related variants that collectively expand the population's metabolic potential, akin to paralogs within a single large genome. We propose for them the name 'metaparalogs' together with the idea that these data reflect cooperative, population-level strategies, where the flexible genome operates as a public good (sensu Samuelson), enhancing both adaptability and ecological resilience. A role for extracellular vesicles in facilitating resource sharing is also suggested.},
}

@article {pmid40719802,
year = {2025},
author = {Ajdig, M and Mbarki, A and Chouati, T and Rached, B and Gardoul, M and Filali-Maltouf, A and Talbi, C and Fahime, EE and Melloul, M},
title = {Comprehensive genomic and pan-genomic analysis of the drought-tolerant Bacillus halotolerans strain OM-41 isolated from Olive rhizosphere, reveals potential plant growth-promoting and biocontrol traits.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {276},
pmid = {40719802},
issn = {1573-0972},
mesh = {*Rhizosphere ; Phylogeny ; Droughts ; *Olea/microbiology/growth & development ; *Bacillus/genetics/isolation & purification/classification/physiology ; Genome, Bacterial ; Genomics ; Soil Microbiology ; Indoleacetic Acids/metabolism ; Stress, Physiological ; Biological Control Agents ; Plant Development ; Whole Genome Sequencing ; Siderophores/metabolism ; Plant Growth Regulators/metabolism ; },
abstract = {Abiotic and biotic stresses increasingly threaten plant health and productivity, causing substantial yield losses in vital crops. In this study, 99 rhizobacteria isolated from Moroccan olive rhizospheres, OM-41 was selected as the most potent strain, exhibiting exceptional drought tolerance (thriving at Aw 0.859), thermotolerance (up to 55 °C), and halotolerance (15% NaCl), alongside plant growth-promoting (PGP) traits such as phosphate solubilization, indole-acetic acid (IAA), gibberellic acid, siderophore production, and hydrolytic enzyme secretion. The strain suppressed V. dahliae via diffusible and volatile antifungal compounds, achieving 76% and 69% inhibition rates, respectively. Whole-genome sequencing revealed a 4.2 Mbp genome (43.5% GC content) with 4362 protein-coding genes. Phylogenetic analyses confirmed its classification as B. halotolerans. Genomic annotation identified 11 secondary metabolite clusters and stress-related genes, including those linked to phosphate solubilization (phy, pho, pst family), IAA synthesis (dhaS, trp operon), siderophores (dhb cluster), nitrogen fixation (nif, suf, urt genes), ammonia production (gudB, nasD/E), biofilm formation (tasA, bsl genes), antifungal volatiles (alsD, ilv operon), hydrolytic enzymes (e.g., amyE, eglS), and vitamin biosynthesis (thiamine/riboflavin operons). Pangenome analysis of 79 B. halotolerans strains highlighted an open pangenome with 12,679 total genes (2270 core, 2382 accessory and 8027 unique); OM-41 harbored 98 unique genes. These findings underscore potential of OM-41 as a biofertilizer and biocontrol agent, leveraging antibiosis, resource competition, and plant defense induction to mitigate pathogens and abiotic stresses. Up to our knowledge, this is the first work that evaluates the pangenome features of B. halotolerans, offering insights into its genomic plasticity and adaptive traits. The strain's multifunctional PGP capabilities and stress resilience position it as a promising solution for sustainable agriculture in challenging environments.},
}

*Rhizosphere
Phylogeny
Droughts
*Olea/microbiology/growth & development
*Bacillus/genetics/isolation & purification/classification/physiology
Genome, Bacterial
Genomics
Soil Microbiology
Indoleacetic Acids/metabolism
Stress, Physiological
Biological Control Agents
Plant Development
Whole Genome Sequencing
Siderophores/metabolism
Plant Growth Regulators/metabolism

@article {pmid40709915,
year = {2025},
author = {Qin, C and Lypaczewski, P and Sayeed, MA and Cuénod, A and Brinkley, L and Creasy-Marrazzo, A and Cato, ET and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, Y and Kamat, MN and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Vibrio cholerae lineage and pangenome diversity vary geographically across Bangladesh over 1 year.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001437},
pmid = {40709915},
issn = {2057-5858},
mesh = {Bangladesh/epidemiology ; *Vibrio cholerae/genetics/classification/drug effects/isolation & purification ; *Cholera/epidemiology/microbiology ; Humans ; *Genome, Bacterial ; Phylogeny ; Genetic Variation ; Disease Outbreaks ; Whole Genome Sequencing ; },
abstract = {Cholera is an acute diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in V. cholerae isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018-2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the V. cholerae pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.},
}

Bangladesh/epidemiology
*Vibrio cholerae/genetics/classification/drug effects/isolation & purification
*Cholera/epidemiology/microbiology
Humans
*Genome, Bacterial
Phylogeny
Genetic Variation
Disease Outbreaks
Whole Genome Sequencing

@article {pmid40707445,
year = {2025},
author = {Nassir, N and Almarri, MA and Kumail, M and Mohamed, N and Balan, B and Hanif, S and AlObathani, M and Jamalalail, B and Elsokary, H and Kondaramage, D and Shiyas, S and Kosaji, N and Satsangi, D and Abdelmotagali, MHS and Abou Tayoun, A and Ahmed, OZS and Youssef, DF and Suwaidi, HA and Albanna, A and S Du Plessis, S and Khansaheb, HH and Alsheikh-Ali, A and Uddin, M},
title = {A draft UAE-based Arab pangenome reference.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6747},
pmid = {40707445},
issn = {2041-1723},
mesh = {Humans ; United Arab Emirates ; *Arabs/genetics ; *Genome, Human/genetics ; Genetic Variation ; Haplotypes ; Genetics, Population ; Gene Duplication ; },
abstract = {Pangenomes provide a robust and comprehensive portrayal of genetic diversity in humans, but Arab populations remain underrepresented. We present a preliminary UAE-based Arab Pangenome Reference (UPR) utilizing 53 individuals of diverse Arab ethnicities residing in the United Arab Emirates. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads. This approach yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of previously uncharacterized euchromatic sequences absent from existing human pangenomes, the T2T-CHM13 and GRCh38 reference human genomes, and other public datasets. Moreover, we identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome, not present in linear and pangenome references and public datasets. We detected 883 gene duplications, including the TATA-binding protein gene TAF11L5, which was uniquely duplicated across all Arab populations and that included 15.06% of genes associated with recessive diseases. By exploring the mitochondrial pangenome, we identified 1,436 bp of previously unreported sequences. Our study provides a valuable resource for future genetic research and genomic medicine initiatives in Arab population and other population with similar genetic backgrounds.},
}

Humans
United Arab Emirates
*Arabs/genetics
*Genome, Human/genetics
Genetic Variation
Haplotypes
Genetics, Population
Gene Duplication

@article {pmid40704999,
year = {2025},
author = {Ono, M and Yamaguchi, M and Motooka, D and Hirose, Y and Higashi, K and Sumitomo, T and Miyoshi-Akiyama, T and Okuno, R and Yamaguchi, T and Kawahara, R and Otsuka, H and Nakanishi, N and Kazawa, Y and Nakagawa, C and Yamaguchi, R and Sakai, H and Matsumoto, Y and Ikebe, T and Kawabata, S},
title = {Identifying genetic variations in emm89 Streptococcus pyogenes associated with severe invasive infections.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40704999},
issn = {2050-084X},
support = {20KK0210//Japan Society for the Promotion of Science/ ; 22H03262//Japan Society for the Promotion of Science/ ; 22K19618//Japan Society for the Promotion of Science/ ; 22K19619//Japan Society for the Promotion of Science/ ; 23H03073//Japan Society for the Promotion of Science/ ; 23K19687//Japan Society for the Promotion of Science/ ; 24K19854//Japan Society for the Promotion of Science/ ; 2022B05//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; 2025B01//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; 2025B13//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; JPMJSP2138//Japan Science and Technology Agency SPRING/ ; JP17fk0108044//AMED/ ; JP20fk0108130//AMED/ ; JP20wm0325001//AMED/ ; JP243fa727001h//AMED/ ; EX22701//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh230035//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh240003//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh250016//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; },
mesh = {*Streptococcus pyogenes/genetics/pathogenicity ; Humans ; *Streptococcal Infections/microbiology/pathology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Genetic Variation ; Virulence/genetics ; INDEL Mutation ; },
abstract = {Streptococcus pyogenes causes mild human infections as well as life-threatening invasive diseases. Since the mutations known to enhance virulence to date account for only half of the severe invasive infections, additional mechanisms/mutations need to be identified. Here, we conducted a genome-wide association study of emm89 S. pyogenes strains to comprehensively identify pathology-related bacterial genetic factors (single-nucleotide polymorphisms [SNPs], indels, genes, or k-mers). Japanese (n = 311) and global (n = 666) cohort studies of strains isolated from invasive or non-invasive infections revealed 17 and 1075 SNPs/indels and 2 and 169 genes, respectively, that displayed associations with invasiveness. We validated one of them, a non-invasiveness-related point mutation, fhuB T218C, by structure predictions and introducing it into a severe invasive strain and confirmed that the mutant showed slower growth in human blood. Thus, we report novel mechanisms that convert emm89 S. pyogenes to an invasive phenotype and a platform for establishing novel treatments and prevention strategies.},
}

*Streptococcus pyogenes/genetics/pathogenicity
Humans
*Streptococcal Infections/microbiology/pathology
Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Genetic Variation
Virulence/genetics
INDEL Mutation

@article {pmid40704797,
year = {2025},
author = {Yu, Z and Wang, R},
title = {Genomic-enabled classification of three Mycobacteroides abscessus subspecies and an effective subspecies-specific identification method.},
journal = {Journal of clinical microbiology},
volume = {63},
number = {8},
pages = {e0069725},
pmid = {40704797},
issn = {1098-660X},
support = {37013//National Institute for Communicable Disease Control and Prevention/ ; },
abstract = {Mycobacteroides abscessus (Mab) is a clinically significant non-tuberculous mycobacterium. It comprises three distinct subspecies being considered to have different macrolide susceptibilities, transmission patterns, and treatment outcomes. In this study, systematic analysis was conducted on 2,006 Mab genomes deposited in the National Center for Biotechnology Information genome database, and the taxonomic classification of their subspecies was revised accordingly. The findings revealed that: (i) in terms of three distinct subspecies classification, the analysis based on core genes and average nucleotide identity (ANI) values was completely consistent; (ii) ANI was a reliable criterion for Mab species and subspecies classification, with defined thresholds of 95% ANI for species-level and 98% ANI for subspecies-level differentiations; and (iii) the integrity of the erm(41) gene or the similarity of the rpoB gene was an unreliable characteristic for Mab subspecies, and the assertions that subspecies massiliense lack inducible resistance to macrolides also cannot be sustained. Moreover, through a subspecies re-classification of genomes and pangenome analysis, Mab subspecies-specific genes were successfully identified, and a novel single-gene test with enhanced clinical applicability was developed. Additionally, the impact of reference genome selection on taxonomic classification highlighted the importance of adopting a standardized set of reference genomes in species/subspecies identification to significantly enhance the comparability across different studies.IMPORTANCEMycobacteroides abscessus (Mab) is a clinically challenging non-tuberculous mycobacteria species. The accurate identification of subspecies is of utmost importance for clinical diagnosis and treatment, as well as for research on pathogenicity, drug resistance, and other related aspects. This study provided a clear average nucleotide identity threshold for Mab subspecies classification, as well as revised options of the three Mab subspecies, new and accurate Mab subspecies-special biomarker, and a detection technique with practical clinical application.},
}

@article {pmid40703244,
year = {2025},
author = {Chen, S and Agah, G and Blom, J and Walker, ED},
title = {Molecular characterization, comparative genome analysis and resistance determinants of three clinical Elizabethkingia miricola strains isolated from Michigan.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582121},
pmid = {40703244},
issn = {1664-302X},
abstract = {INTRODUCTION: Elizabethkingia miricola is a gram-negative bacterium that causes life-threatening infections in vulnerable populations. Unlike other species in the Elizabethkingia genus, E. miricola also leads to meningitis-like diseases in aquatic invertebrates such as frogs, raising concerns about its zoonotic transmission potential. Management of its infection is complicated by unclear transmission pathways and multi-drug resistance.

METHODS: In this study, we analyzed three clinical strains (E. miricola Mich-1, Mich-2, and Mich-3) isolated from patients in Michigan using morphology observations, biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF/MS), and genome sequencing.

RESULTS: Average Nucleotide Identity (ANI) analysis revealed that the Michigan strains were nearly identical and shared 96.52% identity with the type strain E. miricola DSM 14571, confirming their classification as E. miricola. Comprehensive comparative genomic analyses were conducted across 28 strains, including human isolates and strains from invertebrates like frogs. The strains exhibited open pan-genome characteristics. Mich-1 shared 3,199 genes (83.2%) with human isolates but fewer genes with frog-derived isolates (ranging from 3,319 to 3,375). This phylogenetic analysis highlights regional variation and the global diversity of E. miricola isolates, revealing connections between clinical and environmental strains. Antibiotic susceptibility testing revealed that the three clinical strains were resistant to 13 out of 16 tested drugs, with susceptibility only to trimethoprim/sulfamethoxazole and ciprofloxacin. The strains carried five β-lactamase-encoding genes (BlaB-10, BlaB-39, CME-1, CME-2, and GOB-25), conferring resistance to penams, cephalosporins, and carbapenems. Several virulence-associated genes were conserved across clinical and frog isolates. These genes contribute to stress adaptation, adherence, and immune modulation.

DISCUSSION: This study underscores the evolutionary adaptability of E. miricola genomes, highlighting their capacity to acquire genetic traits that enable survival in diverse niches. This adaptability facilitates the emergence of more resistant and virulent strains, posing significant threats to both human and animal health.},
}

@article {pmid40702183,
year = {2025},
author = {Logsdon, GA and Ebert, P and Audano, PA and Loftus, M and Porubsky, D and Ebler, J and Yilmaz, F and Hallast, P and Prodanov, T and Yoo, D and Paisie, CA and Harvey, WT and Zhao, X and Martino, GV and Henglin, M and Munson, KM and Rabbani, K and Chin, CS and Gu, B and Ashraf, H and Scholz, S and Austine-Orimoloye, O and Balachandran, P and Bonder, MJ and Cheng, H and Chong, Z and Crabtree, J and Gerstein, M and Guethlein, LA and Hasenfeld, P and Hickey, G and Hoekzema, K and Hunt, SE and Jensen, M and Jiang, Y and Koren, S and Kwon, Y and Li, C and Li, H and Li, J and Norman, PJ and Oshima, KK and Paten, B and Phillippy, AM and Pollock, NR and Rausch, T and Rautiainen, M and Song, Y and Söylev, A and Sulovari, A and Surapaneni, L and Tsapalou, V and Zhou, W and Zhou, Y and Zhu, Q and Zody, MC and Mills, RE and Devine, SE and Shi, X and Talkowski, ME and Chaisson, MJP and Dilthey, AT and Konkel, MK and Korbel, JO and Lee, C and Beck, CR and Eichler, EE and Marschall, T},
title = {Complex genetic variation in nearly complete human genomes.},
journal = {Nature},
volume = {644},
number = {8076},
pages = {430-441},
pmid = {40702183},
issn = {1476-4687},
support = {R21 CA259309/CA/NCI NIH HHS/United States ; R35 GM138212/GM/NIGMS NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; R01 HG011649/HG/NHGRI NIH HHS/United States ; P30 CA034196/CA/NCI NIH HHS/United States ; R01 CA261934/CA/NCI NIH HHS/United States ; U01 HG013748/HG/NHGRI NIH HHS/United States ; K99 HG012798/HG/NHGRI NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; R00 GM147352/GM/NIGMS NIH HHS/United States ; U01 AI090905/AI/NIAID NIH HHS/United States ; },
abstract = {Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps[1,2] and reaching telomere-to-telomere status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8 and AMY1/AMY2, and fully resolve 1,852 complex structural variants. In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite higher-order repeat array length and characterize the pattern of mobile element insertions into α-satellite higher-order repeat arrays. Although most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference[1] significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference[3] to a median quality value of 45. Using this approach, 26,115 structural variants per individual are detected, substantially increasing the number of structural variants now amenable to downstream disease association studies.},
}

@article {pmid40697987,
year = {2025},
author = {Boondech, A and Ainmani, P and Khieokhajonkhet, A and Boonsrangsom, T and Pongcharoen, P and Rungrat, T and Sujipuli, K and Ratanasut, K and Aeksiri, N},
title = {Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697987},
issn = {2516-8290},
abstract = {Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.},
}

@article {pmid40697354,
year = {2025},
author = {Hölzer, M and Reuschel, C and Vorimore, F and Laroucau, K and Sachse, K},
title = {Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs.},
journal = {Access microbiology},
volume = {7},
number = {2},
pages = {},
pmid = {40697354},
issn = {2516-8290},
abstract = {Recently discovered obligate intracellular bacteria belonging to the genus Chlamydiifrater with the species of Chlamydiifrater phoenicopteri and Chlamydiifrater volucris were studied to explore the composition of their genomes and their relatedness to Chlamydia, the other genus of the family Chlamydiaceae. We investigated 4 isolates of Cf. volucris, 2 of them newly sequenced, and one of Cf. phoenicopteri alongside 12 representatives of the Chlamydia species. Our study uncovers previously unrecognized genomic structures within Chlamydiifrater using a hybrid sequencing approach and advanced annotation pipelines, providing insights into species-specific adaptations and evolutionary dynamics. The integration of long-read sequencing data, comprehensive re-annotation strategies and pan-genomics enabled the localization of the unique plasticity zone and the identification of novel gene clusters in Chlamydiifrater strains, which improves our understanding of chlamydial genome architecture and plasticity in the family Chlamydiaceae. Our analysis revealed that 761 CDS (~80%) are shared among members of both genera. We further identified 158 unique genes of Chlamydiifrater species, but their annotation remains challenging because of the absence of functionally annotated orthologs in public databases. A full-length ompA gene encoding the major outer membrane porin was seen in all Chlamydiifrater strains. We also describe the localization and structure of multiple truncated CDS of ompA family members, representing one of this study's most interesting findings. While genome analysis of Chlamydiifrater spp. confirmed numerous common features shared with representatives of the genus Chlamydia, many unique genomic elements were identified that underpin the distinct phenotype and separate genetic position of these new microorganisms.},
}

@article {pmid40696396,
year = {2025},
author = {Chen, Y and Bao, R and Li, N and Fang, T and Yin, X and Qin, L and Hu, B and Miao, Q},
title = {Whole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {44},
pmid = {40696396},
issn = {1476-0711},
support = {2024ZSFZ39//Zhongshan Hospital/ ; 2024J08352//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification ; Humans ; Anti-Bacterial Agents/pharmacology ; *Genome, Bacterial ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Phenotype ; *Recombination, Genetic ; Macrolides/pharmacology ; Genetic Variation ; Mycobacterium Infections, Nontuberculous/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.

METHODS: We performed whole-genome sequencing and phenotypic antimicrobial susceptibility testing on 109 Mab isolates collected at zhongshan hospital from 2018 to 2023.

RESULTS: The results indicate that recombination, especially distributed conjugation transfer, promotes the formation and sustained diversity of Mab subspecies. Through pangenome analysis, the synergistic gain/loss of accessory genes was found to contribute to different metabolic profiles and the ability to adapt to oxidative stress, facilitating strain adaptation to host environments. We conducted phenotypic antimicrobial susceptibility testing, revealing resistance to macrolide antibiotics differed among subspecies. We identified 24 genes whose gain or loss may increase the likelihood of macrolide resistance, including those involved in biofilm formation, the stress response, virulence, biotin synthesis, and fatty acid metabolism. Genomic variations within Mab species may have significant implications for disease epidemiology, infection pathogenesis, and host interactions.

CONCLUSIONS: Our findings provide a valuable genetic basis for the success of Mab as a highly adaptive and drug-resistant pathogen, informing current efforts to control and treat Mab infections, including strategies targeting specific sequence types or lineages.},
}

*Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification
Humans
Anti-Bacterial Agents/pharmacology
*Genome, Bacterial
Whole Genome Sequencing
Microbial Sensitivity Tests
Phenotype
*Recombination, Genetic
Macrolides/pharmacology
Genetic Variation
Mycobacterium Infections, Nontuberculous/microbiology
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid40695073,
year = {2025},
author = {Hinthong, W and Phelan, J and Hussain, A and Mazumder, R and Azra, and Haq, IU and Ullah, I and Roberts, T and Thawong, N and Billows, N and Campino, S and Khan, TA and Mondal, D and Clark, TG},
title = {Genomic insights into Klebsiella pneumoniae: Virulence, resistance, and transmission in South and Southeast Asia.},
journal = {International journal of medical microbiology : IJMM},
volume = {320},
number = {},
pages = {151666},
doi = {10.1016/j.ijmm.2025.151666},
pmid = {40695073},
issn = {1618-0607},
abstract = {BACKGROUND: Klebsiella pneumoniae has long posed a significant challenge in clinical settings worldwide, particularly due to its carbapenemase production and multidrug-resistant (MDR) characteristics. While extensive genomic studies of K. pneumoniae have been conducted globally, research in Asia, particularly South Asia, remains limited.

OBJECTIVES: This study aims to address and compare the genomic characteristics of K. pneumoniae isolates from South Asia and Southeast Asia, including virulence, antimicrobial resistance (AMR), plasmids, and mobile genetic elements (MGE) profiles, as well as potential transmission dynamics.

METHODS: A total of 463 K. pneumoniae genomes were included from collected samples and public databases. All genomes underwent comprehensive analysis, including pan-genome profiling, multi-locus sequence typing (MLST), annotation of virulence factors, AMR genes, plasmids, and MGEs, as well as SNP distance-based analysis to infer transmission dynamics, using established bioinformatic tools.

RESULTS: K. pneumoniae isolates exhibited diverse virulence determinants. Hypervirulent isolates were primarily associated with ST23 and ST86, and commonly harbour aerobactin, salmochelin, and rmpA. The majority of isolates were predicted to be MDR, with those from Southeast Asia showing a higher relative abundance of AMR genes associated with the antibiotic classes examined in this study. Among all isolates, the predominant carbapenemase-associated gene was blaNDM-1. Col440I_1 was the most prevalent plasmid replicon, although it did not co-occur with any AMR genes. Association between the IncFII_1_pKP9 plasmid replicon and resistance genes sul-5, blaCTX-M, and blaTEM was found. ISSen9 was the dominant MGE, frequently co-occurring with the plasmid replicons IncFIB(K)_1_Kpn3 and IncFII_1_pKP91. Transmission analysis indicated that the highest isolate similarity occurred within MLST and country. However, clustering based on plasmid replicon profiles revealed that some clusters comprised isolates from multiple countries.

CONCLUSION: This study provides a comprehensive analysis of the genomic characteristics and transmission patterns of K. pneumoniae in South and Southeast Asia, contributing to our understanding of its virulence and resistance mechanisms. These findings further suggest that plasmid replicons may play a critical role in shaping transmission dynamics and provide valuable insights to inform future AMR surveillance and control strategies.},
}

@article {pmid40694258,
year = {2025},
author = {Popov, IV and Chikindas, ML and Popov, IV},
title = {Genomic insights into Streptomyces albidoflavus SM254: tracing the putative signs of anti-Pseudogymnoascus destructans properties.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {3},
pages = {2121-2131},
pmid = {40694258},
issn = {1678-4405},
support = {25-24-00351//Russian Science Foundation/ ; },
abstract = {White-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, has devastated bat populations across North America. Streptomyces albidoflavus SM254 was previously reported to exhibit antifungal activity against this pathogen, but no comprehensive genomic characterization has been performed to date. Here, we analyzed 34 S. albidoflavus genomes, including the antifungal strain SM254 and 33 publicly available references, to investigate its metabolic potential and functional distinctiveness. Using pangenome reconstruction, phylogenomics, average nucleotide identity, and KEGG pathway profiling, we found that S. albidoflavus SM254 shares high nucleotide identity (> 99%) with five closely related strains but displays a unique combination of complete ethanol fermentation capacity and asparagine biosynthesis deficiency. These traits were exclusive to SM254 and may reflect adaptation to the oxygen-limited, nutrient-variable sediment environment. Functional annotation further revealed high completeness in central energy, redox, and stress-response pathways. Although direct antifungal mechanisms remain to be experimentally validated, S. albidoflavus SM254's unique metabolic profile and ecological specialization suggest potential relevance in biocontrol contexts.},
}

@article {pmid40693537,
year = {2025},
author = {Lovell, JT and Walstead, R and Lawrence, A and Stark-Dykema, E and Farnitano, MC and Harder, A and Brůna, T and Barry, K and Goodstein, D and Jenkins, J and Lipzen, A and Boston, L and Webber, J and Chovatia, M and Eichenberger, J and Talag, J and Grimwood, J and Schmutz, J and Kelly, JK and Sweigart, AL and Fishman, L and Willis, JH},
title = {Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70012},
doi = {10.1111/1755-0998.70012},
pmid = {40693537},
issn = {1755-0998},
support = {DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; DEB-1856180//Division of Environmental Biology/ ; },
abstract = {Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.},
}

@article {pmid40690081,
year = {2025},
author = {Li, Y and Yang, X and Su, J and Alwathnani, H and Ye, J and Rensing, C},
title = {Isolation and pan-genome analysis of Acinetobacter junii SC22, a heavy metal(loid)s resistant and plant growth promoting bacterium, from the Zijin Gold and Copper mine.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {40690081},
issn = {1572-8773},
support = {2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; RSP-2024/205//King Saud University/ ; },
abstract = {Excess heavy metals can be toxic to plants and microbes. The application of plant growth promoting bacteria (PGPB) in agriculture has gained global attention for promising sustainable development, including in heavy metals polluted soil. However, the metal resistance and plant growth promoting determinants of strains belonging to the genus Acinetobacter remain poorly understood. Here, we characterize strain SC22, and analyzed the complete genome of strain SC22. The influence of inoculating with this strain on soybean growth by pot experiment was also analyzed. Our results showed that strain SC22 displayed high As(III) and Cu(II) resistance and high IAA production. The presence of operons such as, merRACDT, zntA and 4 znuABC, czcABCD and arsRBCH, and trpRABCDFS encode functions enabling strain SC22 to survive under extremely highly heavy metal contaminated environments and also produce plant hormones. The inoculation of strain SC22 stimulated soybean growth. Strains belonging to the genus Acinetobacter have an open pan-genome, and ArsH encoded on the core genome displayed differences to ArsH encoded on the genome of other Acinetobacter that were isolated from different habitats. These findings suggest the potential use of strain Acinetobacter junii SC22 in bioremediation and subsequent plant growth promotion in heavy metal polluted environments.},
}

@article {pmid40681976,
year = {2025},
author = {Hu, H and Chang, A and Cao, L and Wei, Y and Yu, F},
title = {Identification of Rcr12, a single dominant clubroot resistance gene near Rcr6 on chromosome B3 of Brassica nigra.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {925},
pmid = {40681976},
issn = {1471-2229},
mesh = {*Disease Resistance/genetics ; *Plant Diseases/genetics/parasitology/immunology ; *Mustard Plant/genetics/parasitology ; *Plasmodiophorida/physiology ; *Chromosomes, Plant/genetics ; *Genes, Plant ; *Plant Proteins/genetics ; Chromosome Mapping ; },
abstract = {BACKGROUND: Clubroot disease, caused by the soil-borne protist Plasmodiophora brassicae, is a major threat to Brassica crops worldwide, leading to significant yield losses. Genetic resistance is the most effective and sustainable management strategy; however, the identification and characterization of clubroot resistance (CR) genes remain a challenge, particularly in Brassica nigra. Despite its abundant CR resources, only one CR gene, Rcr6, has been identified in the B genome of B. nigra, leaving much of its genetic potential unexplored. Understanding the genomic distribution and diversity of CR genes in B. nigra is crucial for expanding resistance breeding options, especially for canola (B. napus).

RESULTS: This study identified Rcr12, a single dominant CR gene on chromosome B3 of the highly resistant B. nigra line BRA19278. Using bulked segregant RNA sequencing (BSR-seq) and fine mapping in segregating populations derived from a cross between CR2748 (a susceptible B. nigra line) and BRA19278, together with single-root protoplast-derived isolates (SPIs) of P. brassicae and comparative analysis across multiple reference genomes, we established that Rcr12 is distinct from Rcr6 despite their close physical proximity. Evidence supporting its distinctiveness includes differential resistance patterns against various SPIs, unique SNP marker associations, and pangenomic analyses. Fine mapping refined the Rcr12 locus to a 0.33 Mb region on chromosome B3, containing multiple resistance gene candidates, in contrast to the single candidate identified for Rcr6. This study is the first to report an nucleotide-binding leucine-rich repeat (NLR) cluster-type CR locus near an NLR singleton in Brassica crops, underscoring the evolutionary and functional significance of this gene arrangement.

CONCLUSION: The discovery of Rcr12 expands our understanding of NLR gene organization and its role in host resistance evolution. Beyond advancing clubroot resistance breeding, this discovery lays the groundwork for studying functional interactions between NLR singletons and clusters in plant immunity. Additionally, the use of purified SPIs as a pathogen differentiation tool offers a novel approach to resolving ambiguities in clubroot research, addressing the complexity of host-pathogen interactions and facilitating future investigations, especially with the anticipated release of a new pathogen classification system.},
}

*Disease Resistance/genetics
*Plant Diseases/genetics/parasitology/immunology
*Mustard Plant/genetics/parasitology
*Plasmodiophorida/physiology
*Chromosomes, Plant/genetics
*Genes, Plant
*Plant Proteins/genetics
Chromosome Mapping

@article {pmid40672531,
year = {2025},
author = {Wang, Z and Hou, X and Guo, Z and Lei, X and Peng, M},
title = {Biodegradation of sodium selenite by a highly tolerant strain Rhodococcus qingshengii PM1: Biochemical characterization and comparative genome analysis.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100426},
pmid = {40672531},
issn = {2666-5174},
abstract = {BACKGROUND: Rhodococcus is an important genus of soil bacteria known for its metabolic diversity and environmental adaptability under harsh and contaminated conditions. However, few studies have reported on the selenium metabolism of Rhodococcus species.

RESULTS: Here, we isolated a highly selenite-resistance strain PM1 (up to 100 mM) from a selenium-rich mine in Enshi City. This strain reduced 50 mM sodium selenite by 99 % within 72 h. SEM and XPS revealed that PM1 reduced selenite to selenium nanorods (SeNRs). Phylogenetic analysis identified PM1 as R. qingshengii. The whole genome of strain PM1 was sequenced, and a comparative genome analysis of strain PM1with 64 other genomes of Rhodococcus was performed. Whole genome sequencing identified a total of 97 heavy metal resistance genes in strain PM1. Comparative genomics revealed that Rhodococcus species possess an open pan-genome, indicating adaptability to diverse environments. Genomic analysis revealed a total of 96 putative selenite-reducing proteins in strain PM1. Four gene clusters, involved in the pentose phosphate pathway, iron-sulfur cluster assembly, sulfate reductase cluster, and sulfate transport complex, showed high conservation of sequence identity within these species.

CONCLUSIONS: To our knowledge, this research enhances our understanding of high selenite reduction in strain PM1 at genomic level and elucidates the biotechnological applications of selenite-reducing bacteria in environmental remediation.},
}

@article {pmid40671251,
year = {2025},
author = {Okumura, K and Ogura, K and Hashimoto, W},
title = {Distribution of Iron Importers and Ecological Traits in Pseudomonas Species Highlights the Potential Role of Efe System in Plant-Related Environments.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70128},
doi = {10.1111/1462-2920.70128},
pmid = {40671251},
issn = {1462-2920},
support = {23K18062//the Japan Society for the Promotion of Science/ ; JPMJSP2110//Japan Science and Technology Agency/ ; },
mesh = {*Iron/metabolism ; *Pseudomonas/genetics/metabolism/classification ; Phylogeny ; *Bacterial Proteins/genetics/metabolism ; Siderophores/genetics/metabolism ; Plant Roots/microbiology ; Genome, Bacterial ; *Plants/microbiology ; Multigene Family ; },
abstract = {Iron is essential for bacterial survival; however, the relationship of Pseudomonas species between iron import systems and environmental adaptation remains poorly understood. Multi-locus sequence and pan-genome analyses using 320 Pseudomonas genomes classified the species into four groups: P. aeruginosa, P. putida, P. syringae, and P. fluorescens, each exhibiting distinct patterns of iron importer and siderophore synthetic gene cluster. The P. aeruginosa group contained fewer iron importers, whereas the P. putida group exhibited a higher prevalence of xenosiderophore importers. The Fe[2+]-importing Efe system was predominantly detected in the P. syringae and P. fluorescens groups, both of which include plant pathogens and plant growth-promoting rhizobacteria. Reanalysis of publicly available transcriptome data revealed efeU, foxA, and fpvA were significantly upregulated in plant roots but not in insect hosts, and these genes were specifically suppressed during plant immune responses. Growth test and in planta competitive assay using P. fluorescens wild-type and Efe system-deficient mutant suggested that the Efe system gives an advantage under plant-related environments. Phylogenetic analysis indicated the Pseudomonas Efe system was inherited through vertical gene transfer from a common ancestor. Our comprehensive analysis revealed the distribution of iron importers across Pseudomonas groups, highlighting the importance of these systems in environmental adaptation.},
}

*Iron/metabolism
*Pseudomonas/genetics/metabolism/classification
Phylogeny
*Bacterial Proteins/genetics/metabolism
Siderophores/genetics/metabolism
Plant Roots/microbiology
Genome, Bacterial
*Plants/microbiology
Multigene Family

@article {pmid40667268,
year = {2025},
author = {Brose, J and Martin, D and Wang, YW and Wood, JC and Vaillancourt, B and Hamilton, JP and Buell, CR},
title = {An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40667268},
issn = {2692-8205},
support = {T32 GM142623/GM/NIGMS NIH HHS/United States ; },
abstract = {Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.},
}

@article {pmid40667000,
year = {2025},
author = {Hsieh, P and Soisangwan, N and Gordon, DS and Javidh, A and Harvey, WT and Porubsky, D and Hoekzema, K and Baker, C and Munson, KM and Kinipi, C and Leavesley, M and Brucato, N and Cox, MP and Ricaut, FX and Romero, IG and Eichler, EE},
title = {A global map for introgressed structural variation and selection in humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40667000},
issn = {2692-8205},
support = {K99 HG011041/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; },
abstract = {Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs ≥50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.},
}

@article {pmid40662827,
year = {2025},
author = {Rizzo, N and Cáceres, M and Mäkinen, V},
title = {Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i265-i274},
pmid = {40662827},
issn = {1367-4811},
support = {//European Union's Horizon 2020 research and innovation/ ; 956229//Marie Skłodowska-Curie/ ; 101060011//Marie Skłodowska-Curie/ ; //Helsinki Institute for Information Technology/ ; },
mesh = {*Software ; Humans ; *Sequence Alignment/methods ; Algorithms ; *Genomics/methods ; Telomere/genetics ; },
abstract = {SUMMARY: Sequence-to-graph alignment is a central challenge of computational pangenomics. To overcome the theoretical hardness of the problem, state-of-the-art tools use seed-and-extend or seed-chain-extend heuristics to alignment. We implement a complete seed-chain-extend alignment workflow based on indexable elastic founder graphs (iEFGs) that support linear-time exact searches unlike general graphs. We show how to construct iEFGs, find high-quality seeds, chain, and extend them at the scale of a telomere-to-telomere assembled human chromosome.

Our sequence-to-graph alignment tool and the scripts to replicate our experiments are available in https://github.com/algbio/SRFAligner.},
}

*Software
Humans
*Sequence Alignment/methods
Algorithms
*Genomics/methods
Telomere/genetics

@article {pmid40661756,
year = {2025},
author = {Xu, R and Wang, Z and Chen, Z and Wang, Z and Meng, Q and Li, N and Qin, Y},
title = {The Evolution and expression analysis of USP gene family in Solanum.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1546640},
pmid = {40661756},
issn = {1664-462X},
abstract = {As natural environments degrade and extreme weather events become more frequent, humanity increasingly faces the challenge of producing crops under various complex and adverse conditions. Improving crop adaptability has become crucial. Universal stress proteins (USPs) are a class of small molecular proteins widely found in plants, capable of withstanding various biotic and abiotic environmental stresses, including temperature stress, drought, nutrient deficiency, oxidative imbalance, salt and heavy ion toxicity, and pathogenic infections. Enhancing our understanding of USPs holds significant potential for improving plant stress resilience. This study focuses on 13 species of Solanum, including cultivated and wild tomatoes, and systematically identified 438 members of the USP gene family through bioinformatics approaches. Phylogenetic analysis reveals that major USP members are conserved within Solanum, with interspecies differences in USP numbers primarily attributed to copy number variation (CNV). Through synteny and homology analyses, we found that USP27 and USP28 are unique to tomatoes, while the homologous gene of USP19 is absent in cultivated tomatoes. Notably, five unique USP genes are present in S. pennellii, which is characterized by its early differentiation and resistance advantages. Ka/Ks analysis indicates that only the USP10/21 homologous gene pair has undergone positive selection in wild tomatoes, while all other genes are subject to strong negative selection. The USPs in Solanum exhibit high consistency in domain characteristics, sequence conservation, and types of promoter regulatory elements, although there are substantial differences in the number of these elements. Utilizing publicly available data, we identified eight USPs that have undergone domestication or improvement selection, particularly noting the tissue-specific expression patterns of domesticated SolycUSP3/28/30. Through graph pangenome analysis, we screened 12 USPs covered by high-confidence structural variants, which primarily disrupt the intron regions of USPs, leading to significant differences in their expression responses to salt stress. We anticipate that these findings will provide a theoretical foundation and prior knowledge for further understanding and application of USP in plants.},
}

@article {pmid40661132,
year = {2025},
author = {Liu, L and Shu, Y and Wang, Y and Liu, M and Xu, S and Lu, X and Zhang, Y and Yu, L and Tao, Z and Wang, J and Ge, B and Cui, P and Wu, C and Huang, J and Yan, K and Zheng, C and Yang, G and Tian, X and Zhang, S},
title = {The pan genome analysis of WOX gene family in apple and the two sides of MdWUS-1 in promoting leaf-borne shoot.},
journal = {Horticulture research},
volume = {12},
number = {8},
pages = {uhaf117},
pmid = {40661132},
issn = {2662-6810},
abstract = {Unlike animals, plants are sessile organisms that cannot move freely in response to fluctuating and complex environments. As a result, plant development follows post-embryonic processes, enabling flexible developmental strategies to adapt to changing environment. The WUSCHEL-related homeobox (WOX) gene family plays a crucial role in regulating these post-embryonic processes in plants. In this study, we performed an evolutionary analysis of the WOX gene family across 29 plant species, isolating a total of 330 WOX family genes. Our study identified a fern protein with similar length and conserved motifs to WUS gene of spermatophyte, suggesting that the modern clade of the WOX family may have already diverged in ferns. Furthermore, we conducted a pan-genome analysis of the WOX family in Malus, examining the number and gene characteristics of WOX family members across eight varieties. The promoter elements of WUS-1, WUS-2, WOX5-1, and WOX5-2 in different Malus varieties were analyzed further. Additionally, we examined the expression patterns of modern clade WOX family members in developing tissues and during leaf-borne shoot regeneration of Malus. We developed the transgenic lines with inducible overexpression of MdWUS-1 or MdWOX5-1, which revealed that mild upregulation of MdWUS-1 significantly promoted leaf-borne shoot formation, while strong upregulation of MdWUS-1 led to browning and death of explants, likely due to oxidative stress. These findings provide new insights into the evolution of the WOX gene family from ferns into seed plants and lay the foundation for further studies on the spatiotemporal regulation of gene expression during shoot regeneration.},
}

@article {pmid40659765,
year = {2025},
author = {Mondol, SM and Islam, MR and Mia, ME and Hassan, MH and Farhad, F and Akter, K and Shakil, SK and Islam, I and Rakhi, NN and Mustary, JF and Amiruzzaman, and Rahaman, MM},
title = {Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25445},
pmid = {40659765},
issn = {2045-2322},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification/pathogenicity ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Bangladesh/epidemiology ; *Burns/microbiology/complications ; *Pseudomonas Infections/microbiology/epidemiology/drug therapy ; *Wound Infection/microbiology/epidemiology ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Genomics ; Genome, Bacterial ; Male ; Female ; },
abstract = {The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa represents a significant challenge in managing nosocomial infections, particularly in vulnerable populations such as burn patients. This study provides genomic and molecular characterization of MDR and XDR P. aeruginosa strains isolated from burn patients at Sheikh Hasina National Institute of Burn and Plastic Surgery (SHNIBPS) in Dhaka, Bangladesh. Over an 8-month period, 110 wound swabs were collected, with 91 isolates identified as P. aeruginosa. Antimicrobial susceptibility testing demonstrated a multidrug-resistant pattern in 30 isolates and an extensive drug-resistant pattern in the remaining 61 isolates analyzed in this study. PCR assays detected beta-lactamase genes from all four Ambler classes, revealing a notable prevalence of blaNDM-1 (16.48%) and blaVIM-2 (31.87%), with both genes co-occurring in 3.30% of the isolates. Additionally, blaPER-1 (15.38%), blaCTX-M (4.40%), blaOXA-1 (84.62%), and blaOXA-48 (51.65%) genes were detected. Class I integrons were detected in 84 isolates. A total of 21% of the isolates exhibited strong biofilm-forming capabilities. Key biofilm-associated genes (pelB, pilT, rhlB) were detected in most of the isolates. Whole genome sequence analysis of two selected XDR isolates identified different beta-lactamase genes such as blaPDC-98, blaPDC-374, blaOXA-50, blaOXA-677 and blaOXA-847. Virulence factor genes, metal resistance genes, and prophage sequences were also identified in the analysis. The genomic epidemiology analysis of 9,055 P. aeruginosa strains, based on MLST data, revealed the dominance of ST235. The blaPDC and blaOXA genes were found to be notably prominent worldwide. The comparative genomic analysis of P. aeruginosa strains from Bangladesh demonstrated an expanding pangenome as well as high degree of genetic variability. The study emphasized the dynamic nature of the P. aeruginosa pangenome and underscored the necessity for stringent infection control measures in burn units to manage and mitigate the spread of these highly resistant strains.},
}

*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification/pathogenicity
Humans
*Drug Resistance, Multiple, Bacterial/genetics
Bangladesh/epidemiology
*Burns/microbiology/complications
*Pseudomonas Infections/microbiology/epidemiology/drug therapy
*Wound Infection/microbiology/epidemiology
beta-Lactamases/genetics
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
Genomics
Genome, Bacterial
Male
Female

@article {pmid40657825,
year = {2025},
author = {Bai, Y and Luo, X and Qian, W and Geng, X and Bi, X and Zhang, Y},
title = {Identification and Analysis of the AP2/ERF Gene Family in Barley Based on Pan-Genome and Pan-Transcriptome.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {29},
pages = {18448-18455},
doi = {10.1021/acs.jafc.5c05138},
pmid = {40657825},
issn = {1520-5118},
mesh = {*Hordeum/genetics/classification/metabolism ; *Plant Proteins/genetics/metabolism ; Multigene Family ; Genome, Plant ; Phylogeny ; Gene Expression Regulation, Plant ; *Transcription Factors/genetics/metabolism ; Transcriptome ; },
abstract = {AP2/ERF gene family is an important family of plant transcription factors, widely involved in various life activities. This study systematically identified the AP2/ERF gene family in 76 barley genomes based on the barley pan-genome, revealing a total of 22,681 family members. Through orthologous gene group analysis, these genes were categorized into 383 orthologous gene groups (OGGs), with core and noncore genes identified. The results indicate that the AP2/ERF gene family in barley cultivars and landraces exhibits greater genetic diversity compared to wild barley, while wild barley is enriched in noncore genes and subjected to stronger selective pressures. Furthermore, two significant AP2/ERF genes, HvTEM1 and HvCRF4, were uncovered through selective pressure analysis, with pan-genome analysis suggesting their important roles in barley reproduction. This is the first pan-genomic analysis of the AP2/ERF gene family in barley, which reveals the evolutionary patterns and functional characteristics of the family in different barley categories. The findings provide new theoretical insights for the genetic improvement and precision breeding of barley.},
}

*Hordeum/genetics/classification/metabolism
*Plant Proteins/genetics/metabolism
Multigene Family
Genome, Plant
Phylogeny
Gene Expression Regulation, Plant
*Transcription Factors/genetics/metabolism
Transcriptome

@article {pmid40655353,
year = {2025},
author = {Manoharan, RS and Raghavan, K and Jayalakshmi, M},
title = {Genomic Diversity and Antimicrobial Resistance of Acinetobacter sp.-A Pan Genome Analysis.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1028-1036},
pmid = {40655353},
issn = {0046-8991},
abstract = {UNLABELLED: Acinetobacter baumannii has been associated with severe clinically acquired infections. The prevalence of non-A. baumannii-linked diseases is now equivalent to that of A. baumannii-associated illnesses. Hence, this study intends to explore the genomic linkage of virulence and antibiotic resistance amongst the five Acinetobacter spp. (A. baumannii, A. haemolyticus, A. johnsonni, and A. nosocomialis) using pan genome analysis. The results revealed open pan genome in Acinetobacter sp. with increase in number of additional genes in pan genome. The resistance gene identifier revealed that A. baumannii was resistant to macrolides, fluoroquinolone, lincosamide, carbapenem, cephalosporin, tetracycline, rifamycin, diaminopyrimidine, phenicol antibiotics, and penem. Non-A. baumannii sp. A. haemolyticus had the Oxa beta lactamase gene (Oxa) with resistance to carbapenem, cephalosporin, penem. A. johnsonii had no perfect hits for resistance but showed weak similarity to Oxa. A. nosocomialis had resistance genes to fluoroquinoids. The prevalence of Acinetobacter baumannii AbaQ gene was found with A. calcoaceticus and A. nosocomialis sequences used in this study supporting the transformation of resistance genes between Acinetobacter sp. This comparative research underlines the need of differentiating between distinct Acinetobacter sp. infections with their genetic profile for accurate diagnosis and management based on their anti microbial resistance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01411-6.},
}

@article {pmid40655291,
year = {2025},
author = {Song, Y and Jo, E and Kim, M and Lee, H and Cha, J},
title = {Harnessing genomic insights to identify antimicrobial traits in Bacillus velezensis MJ06 from Korean soybean-fermented Meju.},
journal = {Food science and biotechnology},
volume = {34},
number = {12},
pages = {2855-2865},
pmid = {40655291},
issn = {2092-6456},
abstract = {UNLABELLED: Bacillus velezensis, a key microorganism in traditional Korean soybean-fermented foods such as Meju, contributes to flavor and food safety. In this study, B. velezensis strains were isolated from Meju, and their morphological characteristics and biosynthetic gene clusters were analyzed using whole-genome sequencing. Pangenome analysis identified core and accessory genes, with MJ06 showing the highest number of genes associated with secondary metabolite biosynthesis, transport, and catabolism. Antimicrobial assays against six foodborne pathogenic bacteria and six fungi revealed MJ06 had the strongest antimicrobial activity, correlating with its enriched secondary metabolite biosynthetic gene clusters. Active antimicrobial compounds were extracted using C18 cartridges and anion exchange chromatography, and liquid chromatography-mass spectrometry analysis identified surfactin and bacillomycin D as major bioactive metabolites. This study highlights the power of comparative genomics in linking genetic potential to functional antimicrobial traits, facilitating the targeted selection of industrially valuable strains for food safety applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-025-01901-3.},
}

@article {pmid40654946,
year = {2025},
author = {Canalda-Baltrons, A and Silcocks, M and Hall, MB and Theys, D and Chang, X and Viberg, LT and Sherry, NL and Coin, L and Dunstan, SJ},
title = {Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40654946},
issn = {2692-8205},
support = {U19 AI162583/AI/NIAID NIH HHS/United States ; },
abstract = {Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (Mtb), remains a major global health concern. In this study, we harness long-read sequencing technologies and genome graph tools to construct a Mtb pangenome reference graph (PRG) from 859 high-quality, diverse, long-read assemblies. To enable accurate genotyping of SVs leveraging the PRG, we developed miniwalk, a tool that outperforms a traditional linear genome-based approach in precision for SV detection. We characterize patterns of structural variation genome-wide, revealing a virulence-associated ESX-5 deletion to be recurrent across the phylogeny, and fixed in a sub-lineage of L4. Systematic screens for additional genes that are recurrently affected by SVs implicated those related to metal homeostasis, including a copper exporter fixed in the widely distributed L1.2.1 sub-lineage. Lastly, we genotyped 41,134 isolates and found SVs putatively associated with resistance to various first and second-line drugs. These findings underscore the broader role of SVs in shaping Mtb diversity, highlighting their importance in both understanding evolution and designing strategies to combat drug-resistant TB.},
}

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}