Genomics最新文献

{"title":"Geogenomic mapping of drug-resistant Mycobacterium tuberculosis from Ireland and overseas.","authors":"Cian Ennis, Gaetan Thilliez, Ronan F O'Toole","doi":"10.1016/j.ygeno.2025.111132","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111132","url":null,"abstract":"<p><p>In this study, we performed an in-depth comparison of genome-sequenced Mycobacterium tuberculosis isolates from Ireland with isolates from other countries. The sequenced isolates from Ireland mostly belonged to Lineage 4 (64.15 %) with Lineages 2 (17.27 %), 1 (13.21 %), 3 (5.22 %), and 5 (0.15 %) also represented. Of these, Lineages 2 (47.57 %) and 4 (34.95 %) accounted for most of the isolates that were resistant to at least rifampicin. By performing hierarchical clustering of the genomes, we determined that many drug-resistant (DR) strains of Lineage 2 collected in Ireland belonged to larger international clusters of the bacterium that were dominant in countries that included Estonia, Georgia, Ukraine, and Moldova. Lineage 4 DR-TB strains isolated in Ireland were also commonly part of large international clusters but the major countries differed i.e. Eswatini, Germany, United Kingdom, and Mozambique. Based on single nucleotide polymorphism (SNP) analysis, there was no evidence found of widespread onward transmission of DR-TB isolates in Ireland. This indicates that a key source of DR-TB in Ireland is translocation of M. tuberculosis from countries where specific genetic clusters of drug-resistant strains are prevalent. This study has implications for interpreting future trends in TB drug resistance. As an open economy with extensive international travel connections, Ireland is sensitive to the emergence of resistant isolates of M. tuberculosis elsewhere. In addition to caution being applied with respect to TB presenting in individuals from high multi-drug resistant (MDR) TB burden countries, vigilance is also needed for TB in persons from countries where large clusters of DR-TB occur.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111132"},"PeriodicalIF":3.0,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strategic intercropping with mulberry (Morus alba L.) predictably modulates rhizosphere microbiome assembly and enriches pathways for secondary metabolite production.","authors":"Zhou Hu, Yuheng Lei, Tianrui Li, Tingfu Zhang, Qian Yang, Jun Yang, Gaiqun Huang, Delong Guan, Jian Zou","doi":"10.1016/j.ygeno.2025.111129","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111129","url":null,"abstract":"<p><p>Intercropping is a key strategy for sustainable agriculture, but its effects on the rhizosphere microbiome remain poorly understood. Here, we investigated how intercropping mulberry (Morus alba L.) with functionally distinct partners-a nitrogen-fixing legume (Pisum sativum), a saprotrophic fungus (Morchella esculenta), and a medicinal plant (Polygonatum sibiricum)-shapes its rhizosphere bacterial community. Compared to monoculture, all intercropping systems significantly increased bacterial diversity and established unique community structures and functional signatures. Legume intercropping specifically enriched nitrogen-cycling bacteria like Bradyrhizobium and enhanced nitrogen metabolism pathways, whereas fungal intercropping fostered anaerobic decomposers. Crucially, all systems enriched pathways for secondary metabolite biosynthesis, suggesting a potential to enhance mulberry's economic value. Our findings establish that strategic partner selection is a powerful microbiome design tool, enabling predictable modulation of rhizosphere function for sustainable mulberry cultivation.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111129"},"PeriodicalIF":3.0,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets.","authors":"Zhiling Guan, Patrick Lindsey, Rick Kamps, Hubert J M Smeets","doi":"10.1016/j.ygeno.2025.111122","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111122","url":null,"abstract":"<p><p>Mitochondrial DNA (mtDNA) single nucleotide variants (SNVs) are associated with various pathologies, predominantly in energy-demanding tissues like muscles and brain. Characterizing these SNVs at the single-cell level is crucial for understanding their mechanism and clinical manifestation. Publicly available single-cell RNA sequencing (scRNA-seq) data could be an invaluable resource, but existing pipelines fall short in reliable detection of mtDNA SNVs from scRNA-seq data. Therefore, we developed a novel bioinformatics pipeline, that includes quality control, alignment to the mitochondrial genome, SNV calling, and annotation, and that filters-out sequencing errors. Coverage-dependent thresholds are customizable for detecting heteroplasmic SNVs. Duplicate reads can be retained as the majority were valid biological duplicates. Strand bias errors, exceeding a 1:3 ratio, RNA modification-induced errors, identified by the presence of multiple alternative alleles at the same position, and overrepresented SNVs were removed. Our data demonstrated that this pipeline effectively detects homoplasmic and heteroplasmic mtDNA SNVs in scRNA-Seq data.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111122"},"PeriodicalIF":3.0,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the landscape of genome-wide chromatin interaction sites of the lncRNA TUG1 in bovine cell lines and liver tissue.","authors":"Rosemarie Weikard, Raghu Bhushan, Doreen Becker, Frieder Hadlich, Carole Charlier, Gabriel Costa Monteiro Moreira, Christa Kuehn","doi":"10.1016/j.ygeno.2025.111135","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111135","url":null,"abstract":"<p><p>Long-noncoding RNA (lncRNA) interact with DNA, RNA and proteins to regulate the epigenome and fundamental biological processes. In the bovine genome, the nature and mechanisms of lncRNA interactions with specific chromatin regions are unexplored yet. Here, we aimed to unravel the chromatin interaction sites of the evolutionary conserved lncRNA TUG1 in the bovine genome using ChIRP-seq (chromatin isolation by RNA precipitation) in two popular bovine cell lines (MDBK, MAC-T) and liver tissue. About half of the genome-wide TUG1 chromatin occupancy in the genome (3225, 3587 and 3977 interaction sites in MDBK, MAC-T and liver, respectively) was associated with protein-coding genes. Observation of numerous concordant TUG1 chromatin interaction sites between MDBK and MAC-T cells and liver tissue was consistent with the known ubiquitous expression of TUG1. Analysis of overlaps between ChIRP-seq peaks and ATAC-seq peaks in MDBK and MAC-T cells pinpointed TUG1 chromatin interaction sites relevant for modulating chromatin accessibility.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111135"},"PeriodicalIF":3.0,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome sequence of the lichen-forming fungus Cetrariella delisei reveals an expanded repertoire of biosynthetic gene clusters","authors":"Minjoo Cho ,&nbsp;Eunkyung Choi ,&nbsp;Seung Jae Lee ,&nbsp;Soyun Choi ,&nbsp;Inseo Kim ,&nbsp;Doyoon Shin ,&nbsp;Wonyong Kim ,&nbsp;Jae-Seoun Hur ,&nbsp;Jeong-Hoon Kim ,&nbsp;Jae-Sung Rhee ,&nbsp;Hyun Park","doi":"10.1016/j.ygeno.2025.111131","DOIUrl":"10.1016/j.ygeno.2025.111131","url":null,"abstract":"<div><div>Lichens represent a distinctive symbiotic relationship between fungi and photosynthetic algae, allowing them to persist in harsh and extreme habitats. While known for their adaptability, the genomic features of lichen-forming fungi remain relatively understudied. In this study, the genome of the lichen-forming fungus <em>Cetrariella delisei</em> was assembled into 40 contigs, spanning 45.8 Mbp, with a BUSCO completeness of 96.7 %. Repetitive sequences comprised 18.14 % of the genome. A total of 11,716 genes were annotated, including 401 putative carbohydrate-active enzymes (CAZymes), though polysaccharide lyases were absent. Comparative analysis with five additional Parmeliaceae species showed that <em>C. delisei</em> contains a markedly higher number of auxiliary activity genes. Notably, <em>C. delisei</em> harbors 79 biosynthetic gene clusters (BGCs), exceeding the 50 to 65 clusters typically observed in related species, reflecting an expanded biosynthetic repertoire potentially underlying enhanced natural product diversity. These results improve our understanding of lichen symbiosis and provide a valuable genomic resource for future research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111131"},"PeriodicalIF":3.0,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput characterization of 5886 HER2 variants identifies 112 new in cellulo gain-of-function mutations","authors":"Christopher J. Giacoletto ,&nbsp;Liz J. Valente ,&nbsp;Lancer Brown ,&nbsp;Sara Patterson ,&nbsp;Rewatee Gokhale ,&nbsp;Susan M. Mockus ,&nbsp;Wayne W. Grody ,&nbsp;Hong-Wen Deng ,&nbsp;Jerome I. Rotter ,&nbsp;Martin R. Schiller","doi":"10.1016/j.ygeno.2025.111118","DOIUrl":"10.1016/j.ygeno.2025.111118","url":null,"abstract":"<div><div><em>ERBB2</em> (HER2) is a well-studied oncogene with several driver mutations apart from the well-known amplification defect in some breast cancers. We used the GigaAssay to test the functional effect of HER2 missense mutations on its receptor tyrosine kinase function. The GigaAssay is a modular high-throughput one-pot assay system for simultaneously measuring molecular function of thousands of genetic variants at very high accuracy. The activities of 5886 mutations were classified, significantly more mutants than previously reported. These variants include 112 new <em>in cellulo</em>, as well as 10 known and 9 new <em>in vivo</em> gain-of-function (GOF) mutations. Many of the GOFs spatially cluster in sequence and structure, supporting the activation mechanisms of heterodimerization with EGFR and release of kinase inhibition by the juxtamembrane domain. Retrospective analysis of patient outcomes from the Genomic Data Commons predicts survival with the newly identified HER2 GOF variants is better than with previously-identified GOFs, which likely represented the most severe variants.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111118"},"PeriodicalIF":3.0,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145228354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential m6A methylation landscapes in breast and leg muscles of Zhijin white geese: Epigenetic insights into muscle development","authors":"Zhonglong Zhao ,&nbsp;Hong Yang ,&nbsp;Yong Zhang ,&nbsp;Shijun Li ,&nbsp;Zhaobi Ai ,&nbsp;Runqian Yang ,&nbsp;Yixing Ou ,&nbsp;Tian Wang ,&nbsp;Li Ye ,&nbsp;Chang Shu","doi":"10.1016/j.ygeno.2025.111130","DOIUrl":"10.1016/j.ygeno.2025.111130","url":null,"abstract":"<div><div>Muscle growth is a crucial economic trait in poultry, influenced by a combination of environmental, nutritional, and genetic factors. N⁶-methyladenosine (m6A) modification, the most abundant form of RNA modification, has been identified in various poultry tissues. However, the m6A modification profiles during goose muscle development remain poorly understood. In this study, we characterized m6A modification profiles in breast (<em>n</em> = 5) and leg (n = 5) muscles of Zhijin white geese using MeRIP-seq and RNA-seq. Samples were collected from healthy 6-month-old male geese of similar body weight after euthanasia. Compared to breast muscles, leg muscles exhibited significant differences in muscle fiber morphology (cross-sectional area, diameter, and density), intramuscular fat content, and overall m6A levels (<em>P</em> &lt; 0.001). Leg muscles exhibited upregulation of m6A regulators (including <em>ALKBH5</em>, <em>METTL14</em>, <em>METTL16</em>, and <em>ZC3H13</em>) (<em>P</em> &lt; 0.05) and showed predominant m6A peaks in coding sequences (CDS) and 3′UTRs, with conserved RRACH motifs. Compared with breast muscles, 78 differentially methylated genes (DMGs) were identified by MeRIP-seq, including 43 hyper-methylated and 35 hypo-methylated genes in leg muscles. Integrated analysis with RNA-seq revealed 11 overlapping DMGs, comprising 7 hypo-methylated and 4 hyper-methylated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DMGs were significantly enriched in neuroactive ligand–receptor interaction, glycosaminoglycan biosynthesis, and regulation of actin cytoskeleton. Furthermore, we identified <em>LGI1</em>, <em>CDK18</em>, and <em>LPAR2</em> from the significantly enriched pathways as potential candidate genes influencing muscle development. This study provides a theoretical foundation for further investigation into the regulatory role of m6A modification in goose muscle development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111130"},"PeriodicalIF":3.0,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal shifts and cross-site relationships of oral, gut, and vaginal microbiota during the third trimester of pregnancy","authors":"Lulu Meng ,&nbsp;Haishan Xie ,&nbsp;Xia Duan ,&nbsp;Xinyuan Liang ,&nbsp;Xiaomei Tang ,&nbsp;Huijuan Luo ,&nbsp;Xiaomin Xiao ,&nbsp;Zhe Li","doi":"10.1016/j.ygeno.2025.111123","DOIUrl":"10.1016/j.ygeno.2025.111123","url":null,"abstract":"<div><h3>Background</h3><div>The maternal microbiome during pregnancy influences maternal and neonatal health, yet its dynamics and cross-site relationships in the third trimester remain unclear.</div></div><div><h3>Methods</h3><div>Oral, fecal, and vaginal samples were collected from 22 healthy pregnant women and analyzed using 16S rRNA gene sequencing.</div></div><div><h3>Results</h3><div>As pregnancy progressed, gut microbial richness significantly increased, while vaginal richness significantly declined. Source tracking showed that the majority of microbes originated from their respective niches, although low-level cross-site contributions were also observed. Correlation-based network analysis revealed complex associations among microbial communities across sites. The oral microbiome exhibited distinct relative contributions and network relationships to the gut and vaginal microbiomes. Moreover, some low-abundance genera (relative abundance &lt;1 %) played a critical role in maintaining ecological balance compared to high-abundance genera.</div></div><div><h3>Conclusions</h3><div>This study demonstrates dynamic, site-specific microbial changes and highlights potential microbial connections across body sites during late pregnancy, offering new ecological insights relevant to maternal–fetal health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111123"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease","authors":"Hongwei Jin ,&nbsp;Bin Feng ,&nbsp;Wenxiao Gong,&nbsp;Xiaoliang Chen,&nbsp;Dongli Wang,&nbsp;Yan Li,&nbsp;Weijun Huang,&nbsp;Wenting Peng","doi":"10.1016/j.ygeno.2025.111126","DOIUrl":"10.1016/j.ygeno.2025.111126","url":null,"abstract":"<div><div><ul><li><span>•</span><span><div>With the proposal of the concept of “metagenomics” and the development of sequencing technology, 16S rRNA gene profiling has been widely applied in the survey of microbial diversity. This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). This study investigated the gut microbiota of 24 children with asymptomatic and symptomatic hand, foot, and mouth disease (HFMD) and 19 healthy controls using 16S rRNA sequencing. The gut microbiota, both in asymptomatic and symptomatic HFMD patients, was distinct from the controls, with the composition of gut microbiota in the HFMD cases represented a significant difference. The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.</div></span></li></ul></div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111126"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ScASplicer: An interactive shiny/R application for alternative splicing analysis of single-cell sequencing.","authors":"Pengwei Hu, Jixiang Xing, Wuritu Yang, Hongxia Chi, Yongqiang Xing, Yongchun Zuo","doi":"10.1016/j.ygeno.2025.111116","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111116","url":null,"abstract":"<p><p>Alternative splicing (AS) in single cell is crucial for cell heterogeneity, gene expression and transcriptome diversity. However, given the complexity of AS analysis in single-cell RNA sequencing (scRNA-seq), employing a continuous and iterative process to refine data and uncover relevant latent information is crucial. While several tools have been developed to address various aspects of scRNA-seq AS analysis, a versatile and user-friendly web application that can perform all essential steps of AS analysis on scRNA-seq data is still lacking. Here, we made significant advancements in improving the usability and functionality of MARVEL. Firstly, we developed a Python package that can easily and efficiently generate input files, reducing the technical barrier. Secondly, we developed a Shiny-based R package that extends MARVEL's analysis capabilities to multiple cell populations, enabling interactive, code-free ex-ploration of AS and gene expression dynamics at single-cell level.The package, named ScASplicer (Single-Cell Alternative Splicing Shiny Explorer), provides a user-friendly platform for more efficient and comprehensive single-cell AS analysis.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111116"},"PeriodicalIF":3.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}