Genome BiologyPub Date : 2026-03-30DOI: 10.1186/s13059-026-04056-4
Ayun Luo, Hang-Yu Tian, Song Li, Christian Roos, Sheng Wang, Dong-Dong Wu
{"title":"Predicting extinction risk of gibbons from genomes of extinct Yunnan lar gibbon.","authors":"Ayun Luo, Hang-Yu Tian, Song Li, Christian Roos, Sheng Wang, Dong-Dong Wu","doi":"10.1186/s13059-026-04056-4","DOIUrl":"https://doi.org/10.1186/s13059-026-04056-4","url":null,"abstract":"<p><strong>Background: </strong>All species of gibbons are endangered, with the Yunnan lar gibbons (Hylobates lar yunnanensis) officially declared extinct in the wild in 2022. While human activities are frequently cited as major factor, the population structure, evolutionary history, and patterns of genomic erosion of endangered or extinct species remain poorly understood.</p><p><strong>Results: </strong>We obtain genomic data from museum specimens of the extinct Yunnan lar gibbon, as well as from extant gibbon populations, and conduct a comprehensive assessment of population history and the genomic consequences of recent declines. Our findings indicate that Pleistocene climate change greatly impacted the available habitats of the lar gibbon. In addition to climatic factors, we observe a bimodal distribution of heterozygosity in the Yunnan lar gibbon, likely resulting from a severe recent inbreeding event following a population bottleneck, which pushed the population to the brink of collapse. By integrating genomic data from other gibbon species, we propose that the heterozygosity distribution serves as a better indicator for assessing the conservation status of gibbon species.</p><p><strong>Conclusions: </strong>The interaction between genomic features and external factors, such as environmental conditions, likely contributed to the extinction of the Yunnan lar gibbon. The insights and resources generated from this study will boost the research in gibbon conservation genomics and assist in determining conservation priorities, evaluating, and improving conservation measures.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147582881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"EMF2b-1 regulates endosperm cell cycling through PRC2 recruitment in maize.","authors":"Jiameng Xu, Ying Zhang, Ke Qing, Nianguo Xue, Jie Chen, Xu Zhang, Wenjing Zhao, Xing Tian, Hengyu Yan, Yubin Li, Jiaqiang Dong","doi":"10.1186/s13059-026-04049-3","DOIUrl":"https://doi.org/10.1186/s13059-026-04049-3","url":null,"abstract":"<p><strong>Background: </strong>Polycomb Repressive Complex 2 (PRC2) establishes H3K27me3 to regulate gene expression, yet how its genomic targeting is achieved in large crop genomes remains unclear. Cereal endosperm development relies on tightly coordinated transitions between mitosis and endoreduplication, which is essential for determining final kernel size. Here we identify the maize SUZ12 homolog EMF2b-1 as a key regulator of endosperm cell cycling and kernel growth.</p><p><strong>Results: </strong>Loss-of-function mutations in EMF2b-1 lead to reduced kernel size and enhanced endoreduplication. We also find emf2b-1 mutants exhibit decreased cell size and delayed cell differentiation, accompanied by a substantial decrease in H3K27me3 levels. Transcriptome and H3K27me3 ChIP-seq analysis identify 353 downstream target genes with reduced H3K27me3 and increased expression, among which 98 are direct target genes enriched for functions in cell cycling and endoreduplication. Notably, the seed size regulator ZmDA1, a homolog of DA1 that suppresses cell division while promoting endoreduplication, is directly targeted by the EMF2b 1-PRC2 complex and is upregulated in emf2b-1 mutants, consistent with its known role in restricting kernel size. Further motif enrichment and EMF2b-1 immunoprecipitation-mass spectrometry demonstrate that the endosperm specific transcription factor, BZR1-9, recruits EMF2b-1-PRC2 complex to the ZmDA1, thereby repressing its expression to regulate cell cycling and endoreduplication.</p><p><strong>Conclusions: </strong>These findings demonstrate that EMF2b-1 is essential for cell cycling during maize endosperm development, and uncover a transcription factor-guided mechanism of PRC2 recruitment in maize, an evolutionarily conserved strategy paralleling Polycomb targeting in Arabidopsis and Drosophila.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.","authors":"Xiaokun Guo, Linyang Jiang, Jiajun Li, Mengdi Yuan, Dianke Li, Wenyu Shi, Ziding Zhang, Stefan Wuchty","doi":"10.1186/s13059-026-04057-3","DOIUrl":"10.1186/s13059-026-04057-3","url":null,"abstract":"<p><p>Isoforms from the same gene can significantly rewire protein interaction networks, but proteome-wide computational evaluation of these effects remains challenging. In this work, we present DeepISO, a deep learning framework for predicting isoform-specific interactions. DeepISO integrates two graph convolutional neural networks and a random forest model via a logistic regression model. To the best of our knowledge, this is the first approach to jointly leverage AlphaFold-predicted structures and ESM2 language model embeddings for this task. Compared with state-of-the-art PPI prediction tools, DeepISO demonstrates superior performance.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-27DOI: 10.1186/s13059-026-04046-6
Hu Li, Huiling Jin, Min Ning, Fenglin Deng, Wenyi Chen, Ou Yang, Jianhui Cheng, Xiaoping Lian, Lin Shao, Shilai Zhang, Naoki Yamaji, Fengyi Hu, Jian Feng Ma, Gui Jie Lei
{"title":"Functional characterization of transporter genes in rice node at single-cell resolution through multi-omics technologies.","authors":"Hu Li, Huiling Jin, Min Ning, Fenglin Deng, Wenyi Chen, Ou Yang, Jianhui Cheng, Xiaoping Lian, Lin Shao, Shilai Zhang, Naoki Yamaji, Fengyi Hu, Jian Feng Ma, Gui Jie Lei","doi":"10.1186/s13059-026-04046-6","DOIUrl":"10.1186/s13059-026-04046-6","url":null,"abstract":"<p><strong>Background: </strong>The rice node is a critical hub for the distribution of mineral nutrients, mediated by transporters. Manganese (Mn) is an essential micronutrient for plant growth. However, the precise cell types and the cell-type-enriched transporter genes in rice node, and the molecular mechanisms underlying the translocation and distribution of Mn in rice remain poorly understood.</p><p><strong>Results: </strong>We characterize 11 distinct cell types using multiple cluster-enriched genes in rice node I through single-nucleus RNA sequencing (snRNA-seq), systematically profile the expression patterns of putative 1,144 transporter genes within 11 cell types, and identify six candidate transporter genes linked to the tissue-specific deposition of six elements through combining spatial ionomics in node, respectively. Furthermore, we functionally characterize OsMTP7 that is highly expressed in phloem cells in node, as well as in root stele cells and anther. OsMTP7 is localized to plasma membrane in rice and shows efflux activity for Mn. OsMTP7 knockout inhibites Mn uptake and xylem-mediated Mn translocation in root and Mn distribution in node, leading to decreased Mn concentration in various organs and root xylem sap, resulting in reduced biomass and yield. We reveal that OsMTP7 knockout alters expression of genes for multiple biological processes in spikelets using bulk RNA-seq, resulting in increased oxidative stress in anther and low fertility.</p><p><strong>Conclusions: </strong>Our study reveals the precise cell types and the cell-type-enriched transporter genes in node, identifies candidate transporters for elements deposition in node, and demonstrates a novel and critical Mn efflux transporter mediating Mn uptake, translocation and distribution for improving growth and yield in rice.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-26DOI: 10.1186/s13059-026-04039-5
Limin Jiang, Ivy Hurwitz, Lukasz S Wylezinski, Michael K Racke, Fengyao Yan, Fei Ye, Quanhu Sheng, Shuguang Leng, Cecilia P Chung, C Michael Stein, Chung-I Li, Naresh Kumar, Michele Ceccarelli, Steven F Baker, Douglas J Perkins, Charles F Spurlock, Leng Han, Yan Guo
{"title":"ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.","authors":"Limin Jiang, Ivy Hurwitz, Lukasz S Wylezinski, Michael K Racke, Fengyao Yan, Fei Ye, Quanhu Sheng, Shuguang Leng, Cecilia P Chung, C Michael Stein, Chung-I Li, Naresh Kumar, Michele Ceccarelli, Steven F Baker, Douglas J Perkins, Charles F Spurlock, Leng Han, Yan Guo","doi":"10.1186/s13059-026-04039-5","DOIUrl":"10.1186/s13059-026-04039-5","url":null,"abstract":"<p><p>HLA typing from sequencing data is crucial for studying immune gene families, but high allele similarity challenges existing tools. We present ImmuSeeker, comprehensive software for extracting HLA genotypes, expression, and diversity at gene, one-field, and two-field allele levels, with improved Bayesian zygosity inference and graphical phylogenetic visualization. ImmuSeeker was benchmarked against nine established tools using gold-standard HLA datasets, repeated RNA sequencing (RNA-seq) and Isoform Sequencing (Iso-Seq) data, and a longitudinal patient cohort, demonstrating superior accuracy, consistency, and analytical utility. ImmuSeeker provides a scalable, robust framework for comprehensive HLA typing and immune system analyses.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13154904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147522480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-18DOI: 10.1186/s13059-026-04033-x
Liang Dong, Yonghao Sun, Lu Kang, Zichao Li, Yameng Liang, Huangjun Sheng, Feng Tian, David Jackson, Fang Yang
{"title":"Dynamic and cell-type specific transcriptional reprogramming underlies the floral transition in the maize shoot apical meristem.","authors":"Liang Dong, Yonghao Sun, Lu Kang, Zichao Li, Yameng Liang, Huangjun Sheng, Feng Tian, David Jackson, Fang Yang","doi":"10.1186/s13059-026-04033-x","DOIUrl":"10.1186/s13059-026-04033-x","url":null,"abstract":"<p><strong>Background: </strong>The floral transition in maize represents a pivotal developmental switch that determines flowering time, environmental adaptation, and yield-related traits. However, the molecular mechanisms governing shoot apical meristem reprogramming and cell identity changes during this process remain poorly understood.</p><p><strong>Results: </strong>By integrating time-course bulk RNA-seq, single-cell transcriptomics, chromatin accessibility, and transcription factor binding profiles, we construct a spatiotemporal molecular framework of the maize shoot apical meristem floral transition. Our analyses reveal global transcriptional reprogramming accompanied by pronounced cell type-specific regulation dynamics. At a global level, our transcriptional-level inference suggests that pathways associated with chromatin remodeling, environmental response, and reproductive development are sequentially activated. We further identify a ZmMADS69-ZmRap2.7-ZMM4 regulatory module that fine-tunes the floral transition within the shoot apical meristem. At single-cell resolution, we find that the floral transition is not driven by a uniform transcriptional switch, but instead emerges from the coordinated action of spatially distinct shoot apical meristem domains. Through differential expression, trajectory, and co-expression module analyses, we further identify previously unrecognized roles for the inflorescence regulators UNBRANCHED2 and UNBRANCHED3 in promoting the floral transition, suggesting that they coordinate floral induction with subsequent inflorescence development.</p><p><strong>Conclusions: </strong>Our study establishes a comprehensive spatiotemporal regulatory framework for the maize floral transition, providing mechanistic insights into shoot apical meristem reprogramming and offering a foundation for identifying new regulators to improve maize adaptation and yield.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13112620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147482102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-18DOI: 10.1186/s13059-026-04023-z
Wenjia Wang, Jia-Jun Liu, Yuzhen Li, Sungjin Ko, Ning Feng, Manling Zhang, Qingqi Lin, Mengying Xia, Yan P Yu, Jian-Hua Luo, Pedro L Baldoni, George C Tseng, Silvia Liu
{"title":"IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.","authors":"Wenjia Wang, Jia-Jun Liu, Yuzhen Li, Sungjin Ko, Ning Feng, Manling Zhang, Qingqi Lin, Mengying Xia, Yan P Yu, Jian-Hua Luo, Pedro L Baldoni, George C Tseng, Silvia Liu","doi":"10.1186/s13059-026-04023-z","DOIUrl":"10.1186/s13059-026-04023-z","url":null,"abstract":"<p><p>Long-read transcriptome sequencing (long-RNA-seq) revolutionizes transcriptome research by enabling full-length transcript analysis for comprehensive exploration of isoform diversity. We developed IFDlong, a probabilistic framework and software suite for detecting isoform and fusion transcripts from bulk or single-cell long-RNA-seq data. IFDlong annotates each long read, identifies novel isoforms, quantifies expression via an expectation-maximization algorithm, and profiles fusion transcripts. In large-scale simulation and real data analyses, IFDlong outperforms existing tools and demonstrated high accuracy and robustness across multiple in-house and public datasets, including healthy tissues, cell lines, and different diseases.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13113378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147482097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-13DOI: 10.1186/s13059-026-04002-4
Mario Acera-Mateos, Xian Adiconis, Jessica-Kanglin Li, Domenica Marchese, Ginevra Caratù, Chung-Chau Hon, Prabha Tiwari, Miki Kojima, Beate Vieth, Michael A Murphy, Sean K Simmons, Thomas Lefevre, Irene Claes, Christopher L O'Connor, Rajasree Menon, Edgar A Otto, Yoshinari Ando, Katy Vandereyken, Matthias Kretzler, Markus Bitzer, Ernest Fraenkel, Thierry Voet, Wolfgang Enard, Piero Carninci, Holger Heyn, Joshua Z Levin, Elisabetta Mereu
{"title":"Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.","authors":"Mario Acera-Mateos, Xian Adiconis, Jessica-Kanglin Li, Domenica Marchese, Ginevra Caratù, Chung-Chau Hon, Prabha Tiwari, Miki Kojima, Beate Vieth, Michael A Murphy, Sean K Simmons, Thomas Lefevre, Irene Claes, Christopher L O'Connor, Rajasree Menon, Edgar A Otto, Yoshinari Ando, Katy Vandereyken, Matthias Kretzler, Markus Bitzer, Ernest Fraenkel, Thierry Voet, Wolfgang Enard, Piero Carninci, Holger Heyn, Joshua Z Levin, Elisabetta Mereu","doi":"10.1186/s13059-026-04002-4","DOIUrl":"10.1186/s13059-026-04002-4","url":null,"abstract":"<p><strong>Background: </strong>The integration of multimodal single-cell data enables comprehensive organ reference atlases, yet its impact remains largely unexplored, particularly in complex tissues. Using the kidney as an emblematic example of a complex organ, we perform a systematic evaluation of multimodal single-cell integration strategies, with heart tissue used for additional methodological validation.</p><p><strong>Results: </strong>We generate a benchmarking dataset for the renal cortex by integrating 3' and 5' scRNA-seq with joint snRNA-seq and snATAC-seq, profiling 119,744 high-quality nuclei/cells from 19 donors. To align cell identities and enable consistent comparisons, we develop the interpretable machine learning tool scOMM (single-cell Omics Multimodal Mapping) and systematically assess integration strategies. \"Horizontal\" integration of scRNA and snRNA-seq improves cell-type identification, while \"vertical\" integration of snRNA-seq and snATAC-seq has an additive effect, enhancing resolution in homogeneous populations and difficult-to-identify states. Global integration is especially effective in identifying adaptive states and rare cell types, including WFDC2-expressing Thick Ascending Limb and Norn cells, previously undetected in kidney atlases.</p><p><strong>Conclusions: </strong>Our work establishes a robust framework for multimodal reference atlas generation, advancing single-cell analysis and extending its applicability to diverse tissues.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"27 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12983708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147444747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-12DOI: 10.1186/s13059-026-04026-w
Yuàn Wang, Zhi-Qing Xue, Ren-Gang Zhang, Zhi-Ying Zhu, Elvira Hörandl, Xiao-Ru Wang, Yan-Fei Mao, Deborah Charlesworth, Li He
{"title":"Recurrent sex chromosome turnover mediated by distinct ARR17 and PISTILLATA duplications in willows.","authors":"Yuàn Wang, Zhi-Qing Xue, Ren-Gang Zhang, Zhi-Ying Zhu, Elvira Hörandl, Xiao-Ru Wang, Yan-Fei Mao, Deborah Charlesworth, Li He","doi":"10.1186/s13059-026-04026-w","DOIUrl":"10.1186/s13059-026-04026-w","url":null,"abstract":"<p><strong>Background: </strong>Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species' SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.</p><p><strong>Results: </strong>Here we describe phased chromosomal assemblies of three Salix species with a ZW system derived from an XY system, including four lineages of the Salix polyclona complex (six assemblies in total). Their SLRs are within the same repeat-rich pericentromeric region of chromosome 15 as in the willows with XY system. Although these Z- and W- SLRs carry intact and/or partial ARR17 duplicates, few RNA products are detectable in our sampled tissues. However, the W-SLRs include partial duplicates of PISTILLATA (PI), a stamen development gene. These are arranged in inverted repeats and express small interfering RNAs targeting the autosomal intact Salix PI gene, suggesting that they reduce its expression, and therefore act as maleness-suppressing factors.</p><p><strong>Conclusions: </strong>The turnover events involving intact ARR17 and partial PI duplications in the 15ZW clade I species involve pericentromeric regions that recombine rarely, making changes possible in these Salix species that would be unlikely in other genome regions.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147445669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2026-03-12DOI: 10.1186/s13059-026-04018-w
Vincent F D F Thygesen, Motahare Feizabadi Farahani, Sofie Holtsmark Nielsen, Florentin Constancias, Michael Givskov, Jacqueline Abranches, Gabriele Scorrano, Marie Louise S Jørkov, Ghader Ebrahimi, Julio C Bendezu-Sarmiento, Fabrice Demeter, Kristian Kristiansen, Daniel Belstrøm, Martin Sikora
{"title":"The genomic history of Streptococcus mutans from the Mesolithic until modern times.","authors":"Vincent F D F Thygesen, Motahare Feizabadi Farahani, Sofie Holtsmark Nielsen, Florentin Constancias, Michael Givskov, Jacqueline Abranches, Gabriele Scorrano, Marie Louise S Jørkov, Ghader Ebrahimi, Julio C Bendezu-Sarmiento, Fabrice Demeter, Kristian Kristiansen, Daniel Belstrøm, Martin Sikora","doi":"10.1186/s13059-026-04018-w","DOIUrl":"10.1186/s13059-026-04018-w","url":null,"abstract":"<p><strong>Background: </strong>Streptococcus mutans is a member of the human oral microbiota and is considered one of the most important cariogenic organisms. Previous studies have suggested an expansion of S. mutans populations about 10,000 years ago with the onset of agriculture, yet direct molecular evidence of its presence from ancient DNA remains sparse.</p><p><strong>Results: </strong>Here, we present population genomic analyses of 25 ancient S. mutans genomes (average read depth 0.1X - 387X) recovered from archaeological remains across Eurasia spanning ~ 8,000 years of human evolution. Recombination-corrected phylogenomic analyses using Gubbins show a star-like phylogeny indicative of an early radiation, with the ancient genomes falling within the genomic diversity of modern isolates but restricted to one of the major clades of the phylogeny (D). Analyses of genes encoding present day virulence factors reveals that the presence of the mutanobactin operon involved in oxygen tolerance is restricted to specific subclades (A & B) and absent among the ancient samples. Using the MEGAHIT assembler followed by binning of contigs with CONCOCT, we recover metagenome-assembled genomes (MAG) of 7 high-coverage ancient S. mutans strains, including a 7,500-year-old sample from an early European Neolithic farmer. Pangenome analysis with modern isolates using the anvi'o's suite revealed the presence of specific functional genes in the ancient isolates, which were lost through time.</p><p><strong>Conclusions: </strong>Our study demonstrates that Streptococcus mutans DNA is well preserved in tooth samples from archaeological remains and show that it formed part of the human oral microbiota already before the onset of agriculture, consistent with a radiation and population expansion well before 8,000 years ago.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147444188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}