Genome Biology and Evolution最新文献

{"title":"Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (Phrynosoma modestum).","authors":"Julia Amoroso, Keaka Farleigh, Erika Crispo, Christopher Blair","doi":"10.1093/gbe/evag217","DOIUrl":"10.1093/gbe/evag217","url":null,"abstract":"<p><p>Population divergence is promoted by divergent selection and inhibited by gene flow, but the mechanisms of and relationship between these two processes remain poorly understood. Developing a well-informed hypothesis of the selective pressures underlying divergence in a natural population requires a thorough understanding of both species structure and demographic history. In this study, we assess whole-genome sequences of round-tailed horned lizards (Phrynosoma modestum) from throughout the species range and combine phylogenetic analyses with genomic landscape scans to understand how current genetic diversity has been influenced by demographic histories and evolutionary pressures. Maximum likelihood (ML) phylogenetic analysis supports two lineages within the species, corresponding to a North/South population divide that developed around 7 million years ago (Ma) and displays little migration. However, intermediate genealogical divergence index values between the two lineages ultimately leave us unable to recommend a full taxonomic distinction. Genome-wide scans of population genetic statistics identified islands of divergence exhibiting differentiation patterns linked to models of reproductive isolation and within-population selection. Significantly negative values of Tajima's D and positive selection statistics in these islands offer support for selection acting on P. modestum, but patterns may also stem from recent population expansions. We posit that selection within populations has played a large role in shaping genomic divergence across the species' range. Taken together, our results provide perspective into how variable selective pressures shape the genomics of two divergent populations currently maintaining species integrity, despite significant signatures of geographic structure and divergence.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13554808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molting in Pancrustacea Is Characterized by Both Deeply Conserved and Recently Evolved Gene Modules.","authors":"Kenneth Kim, Giulia Campli, Sagane Joye, Ariel D Chipman, Robert M Waterhouse, Marc Robinson-Rechavi","doi":"10.1093/gbe/evag212","DOIUrl":"10.1093/gbe/evag212","url":null,"abstract":"<p><p>Arthropods such as insects and crustaceans, which together form the monophyletic group Pancrustacea, possess a rigid chitinous exoskeleton that must be periodically shed through molting to allow growth and morphological change. Although molting is a deeply conserved developmental process across Arthropoda, our understanding of its molecular mechanisms is still largely derived from insect model species. Lineage-specific innovations and losses of molting-related genes raise fundamental questions about the extent of its conservation outside noninsect arthropods. Here, we investigate the evolutionary conservation of molting gene expression across five representative pancrustacean species using publicly available transcriptomic datasets. Changes in gene expression during molting are characterized by both deeply conserved and lineage-specific gene modules. Temporal gene expression analyses reveal that these lineage-specific signatures are not uniformly distributed across the molting process: the middle transitional phase is more lineage-specific, thereby exhibiting an inverse hourglass pattern. This is likely due to life-history-specific processes, development of the cuticle, and specialized structures of the exoskeleton. Overall, this study provides evidence for both the evolutionary conservation and divergence of this key postembryonic developmental process and highlights the modular architecture of the molting program.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coli.","authors":"Otto Lindahl, Talía Berruga-Fernández, Jivanti Soekhoe, Douglas L Huseby, Diarmaid Hughes","doi":"10.1093/gbe/evag209","DOIUrl":"10.1093/gbe/evag209","url":null,"abstract":"<p><p>Escherichia coli is a prototroph and can synthesize all twenty proteinogenic amino acids when required to grow in minimal medium. There are approximately sixty protein-coding genes individually essential for amino acid synthesis. This is a large mutational target for the accumulation of detrimental mutations. E. coli can rewire biosynthetic pathways in response to mutational damage, but the limits of this capacity are poorly understood. Here, to address evolutionary robustness, we asked whether and how the phenotypes of irreversible mutations causing auxotrophy could be suppressed or bypassed in the absence of horizontal gene transfer (HGT). Spontaneous suppressors could be selected for only ten of fifty-nine mutants tested (detection limit ∼7 × 10-11). Mechanisms of suppression included regional amplifications, mutations increasing gene or operon expression, mutations relaxing enzyme specificity, and mutations causing biochemical pathway diversions. Overall, the data show that spontaneous suppression of auxotrophy caused by an irreversible mutation is an evolutionary survival mechanism relevant only to a minority of the genes essential for amino acid synthesis. As a consequence, the essential genetic foundations for amino acid prototrophy are expected to be degraded over time by mutations (Muller's ratchet) and metabolic rewiring alone will be insufficient to counteract this effect. This implies that maintaining phenotypes, including prototrophy in E. coli, and potentially other bacterial species, is likely to be reliant on HGT of housekeeping genes to counteract the effects of inevitable mutational inactivation. Accordingly, chromosomal HGT in bacteria may be critical for survival across diverse environmental niches.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De Novo Assembly of the Trypanosoma congolense Genome Reveals an Organization Influenced by Antigenic Variation but Distinct from Trypanosoma brucei.","authors":"Marija Krasiļņikova, Jane C Munday, Dario Beraldi, Stephen D Larcombe, Guy R Oldrieve, Craig Lapsley, Liam J Morrison, Keith R Matthews, Richard McCulloch","doi":"10.1093/gbe/evag213","DOIUrl":"10.1093/gbe/evag213","url":null,"abstract":"<p><p>Antigenic variation allows pathogens to evade mammalian adaptive immunity through the continuous change in exposed antigens. In African trypanosomes, antigenic variation involves changes in expressed Variant Surface Glycoproteins (VSGs). Understanding of VSG expression control and change amongst African trypanosomes is most advanced in Trypanosoma brucei. In the important animal trypanosome, Trypanosoma congolense, incomplete genome assembly has held back understanding of the mechanics of antigenic variation. Here, we have used long-read DNA sequencing and Hi-C DNA interaction analysis to provide a telomere-to-telomere assembly of the T. congolense genome. This assembly reveals a genome comprising 12 diploid chromosomes, one tetraploid chromosome, and more than 100 small chromosomes. With this assembly we reveal several features of VSG organization and expression that differ from T. brucei. The majority of the T. congolense VSG archive, estimated at ∼1,500 genes, localizes to subtelomeres in 12 of the 13 large chromosomes, but these loci are notably smaller than are found in T. brucei. Furthermore, transcriptome analysis suggests expression of VSGs across the T. congolense subtelomeres, which are not separated within the nucleus from non-VSG chromosome regions, suggesting that there is no dedicated VSG expression site. Strikingly, one chromosome contains approximately 40% of the VSG archive and is largely transcriptionally silent, potentially acting as the major reservoir of new VSG variants. Finally, we show that VSG expression can be detected from multiple small chromosomes. In summary, the new genome assembly provides a platform for understanding a potentially unusual operation of VSG expression and switching in T. congolense.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13547854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148812440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.","authors":"Alexander Kwakye, Natalie Dzikowski, Matthew A Wund, Krishna R Veeramah","doi":"10.1093/gbe/evag222","DOIUrl":"10.1093/gbe/evag222","url":null,"abstract":"<p><p>Whole genome scans have identified numerous adaptive alleles in many species; however, linking these alleles to specific phenotypes remains a major challenge. A promising alternative to direct genotype-phenotype mapping, particularly given the complexities introduced by epistasis, pleiotropy, and environmental variability, is to assess whether differentially expressed genes (DEGs) are enriched in regions of genetic divergence between populations adapted to contrasting environments. Here, we study gene expression patterns in threespine stickleback populations adapting to contrasting environments (marine vs. freshwater) and investigate signatures of selection associated with gene expression evolution during adaptation. We performed transcriptomic experiments of the brain and gill tissues of wild-caught sticklebacks sampled from one marine and two freshwater environments using TagSeq. We found that DEGs in the freshwater environments harbor single nucleotide polymorphisms (SNPs) previously identified to be involved in rapid adaptation and FST outliers. A majority of these SNPs were located in cis-regulatory regions of the genes with predicted low to moderate effects on protein function and structure, although we found a high-impact SNP in the gene col8a1b. Genes such as pvalb4 and acsl4a, involved in calcium regulation in the gill and fatty acid metabolism in the brain, respectively, were enriched with SNPs showing signatures of selection. By linking signatures of selection to tissue-specific gene expression patterns, our study bridges the gap between genomic divergence and the molecular mechanisms underlying physiological adaptation to new environments and identifies specific pathways that can be targeted for future functional studies.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13583502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148857322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Evolution of Francisella: Metabolic Innovation, Endosymbiotic Transitions to Ticks, and Biogeographic History.","authors":"Juan S Echeverry-Pérez, Michele Castelli, Sebastián Muñoz-Leal, Santiago Nava, Davide Sassera, Alberto Sánchez-Vialas, A Sonia Olmeda, Félix Valcárcel, Juan E Uribe","doi":"10.1093/gbe/evag135","DOIUrl":"10.1093/gbe/evag135","url":null,"abstract":"<p><p>Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provide essential B vitamins lacking in their blood-based diet. The most extensively studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. The genus Francisella encompasses endosymbionts (FE), pathogens (FP), opportunistic pathogens (FO) and free-living environmental strains (FL), making it a powerful system for evolutionary and comparative genomic analyses. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to generate new FE genomes. Seven deeply sequenced public metagenomes were also assembled, yielding 69 Francisella, and as outgroup, three Allofrancisella, a Parafrancisella, and a Pseudofrancisella strains. This dataset supported phylogenomic reconstruction and comparison of genomic features, including vitamin biosynthesis and virulence pathways, with a focus on transitions to tick endosymbiosis. A densely sampled multi-locus sequence typing phylogeny was constructed to explore biogeographic patterns. Our results show that, except for FE, no ecological trait is monophyletic, supporting an origin of Francisella diversity from free-living ancestors. Biogeography suggests Palearctic and Afrotropical FE strains are derived and may involve horizontal transfers. Francisella comparative genomics reveals two contrasting profiles: environmental generalists and host-restricted specialists. These findings reinforce the role of tick FEs as nutritional mutualists, retaining key pathways such as riboflavin, shikimate, and biotin biosynthesis. In contrast, virulence is not ancestrally conserved but an innovation in pathogenic lineages, largely degraded in tick FEs. These results advance understanding of endosymbiont evolution and provide genomic insights with potential for disease control.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De Novo Genome Sequence Assembly of the Algal Endosymbiont Micractinium conductrix Derived From Its Host Paramecium bursaria 186b.","authors":"Guy Leonard, Irma Vitonytė, Fiona R Savory, Erika M Hansson, Duncan D Cameron, Michael A Brockhurst, Thomas A Richards","doi":"10.1093/gbe/evag194","DOIUrl":"10.1093/gbe/evag194","url":null,"abstract":"<p><p>Endosymbiosis is a major driver of evolutionary innovation and underpins the function of diverse ecosystems. The origins and evolution of endosymbiosis are challenging to study experimentally due to the short-lived culturability of many microbial strains derived from endosymbiotic interactions. The facultative endosymbiosis between the ciliate, Paramecium bursaria, and the green alga, Micractinium conductrix (Chlorellaceae, Trebouxiophyceae), is ecologically widespread and has emerged as a powerful lab-tractable model system. This endosymbiosis is founded upon a reciprocal nutrient exchange, but each of the species can be cultured independently enabling quantification of symbiotic fitness effects, new partnerships to be generated in the lab, and co-associations to be subject to experimental evolution. To date, evolve-and-resequence approaches have been limited due to a lack of high-quality genome assemblies enabling gene variants to be identified. Here, we report a near telomere-to-telomere genome assembly for M. conductrix 186b, using a range of sequencing technologies. Comparative analysis shows that this is one of the most complete Chlorellaceae algal genome assemblies available to date. To aid accurate gene calling and annotation, we conducted both RNAseq and Iso-Seq transcriptome sequencing experiments. Collectively, these 'omics datasets will facilitate: (i) comparative genomics studies of endosymbiont evolution, (ii) evolve-and-resequence experiments, (iii) genome-scale metabolic modeling studies, and (iv) identification of targets for genetic modification experiments and biotechnological applications.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148619748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: A Chromosome-Level Genome Assembly and Resequencing Data Reveal Low DNA Methylation and Reduced Diversity in the Solitary Bee Pollinator Osmia cornuta.","authors":"","doi":"10.1093/gbe/evag210","DOIUrl":"10.1093/gbe/evag210","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 9","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13537320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early Origin of the Human Seminal Plasma Proteome During Vertebrate Evolution.","authors":"Jose M Ranz, Alberto Civetta","doi":"10.1093/gbe/evag236","DOIUrl":"10.1093/gbe/evag236","url":null,"abstract":"<p><p>Seminal fluid proteins (SFPs)-encoding genes are rapidly evolving at the sequence level and often considered prone to frequent phylogenetic turnover. One mechanism underlying such rapid turnover is the lineage-restricted origin of new SFP genes, which results in a complement of phylogenetically young genes. Recent advances in genome resources and comparative genomics now enable more comprehensive cross-taxa analyses, providing improved estimates of the timing of gene origin during evolution. Using these resources alongside proteomic data from human seminal plasma, we traced the evolutionary origins of 646 putative human SFP genes. We find that most SFPs trace back to the bony vertebrate (Euteleostomi) radiation. These ancient SFP genes are more pleiotropic than younger ones, which are enriched in immunity-related functions and regulate proteolytic activity, particularly peptidase inhibitors. Together, these results underscore that the human proteome components of the seminal plasma originated early during vertebrate evolution, providing insights into the history of reproductive biology in deuterostomes.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148989809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissecting Fluctuating Selection: A Unified Population and Quantitative Genetics Framework.","authors":"Esdras Tuyishimire, Molly K Burke, Elizabeth G King","doi":"10.1093/gbe/evag225","DOIUrl":"10.1093/gbe/evag225","url":null,"abstract":"<p><p>One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (eg heritability, number of causative loci) and ecological factors (eg season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148891632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}