Genome Biology and Evolution最新文献

{"title":"A Chromosome-Level Genome Assembly of the Potato Leafhopper Empoasca fabae (Hemiptera: Cicadellidae).","authors":"Joshua Molligan, Florent Sylvestre, Edel Pérez-López","doi":"10.1093/gbe/evag207","DOIUrl":"10.1093/gbe/evag207","url":null,"abstract":"<p><p>The potato leafhopper, Empoasca fabae (Harris, 1841), is a highly polyphagous, migratory insect pest of eastern North America that feeds on more than 200 herbaceous and woody plant species, causing substantial losses to forage and field crops. Despite its agricultural and ecological importance, no genome has been available for this species. Here, we present the first chromosome-level genome assembly of E. fabae, generated from Oxford Nanopore long reads, Illumina short reads, and Omni-C proximity-ligation data. The final assembly spans 908 Mb across 132 scaffolds, with 99.8% of the assembly captured in ten chromosome-length scaffolds (nine autosomes and an X chromosome) with a scaffold N50 of 96.2 Mb. The assembly is highly complete, recovering 92.9% of conserved hemipteran single-copy orthologs from protein annotations, and is composed of 47.6% repetitive sequence, dominated by long terminal repeat retrotransposons and unclassified elements. Read-depth comparison between male and female individuals supports assignment of a single sex-linked chromosome, consistent with an XO sex determination system. BRAKER3 gene annotation predicted 31,406 protein-coding genes after retaining the longest isoform per locus. Comparative genome analysis of the two closest related Typhlocybinae species with genomes available, Matsumurasca onukii and Hebata decipiens, revealed extensive chromosome-scale collinearity while defining a shared core gene repertoire. This reference genome provides a foundation for comparative and population genomic studies and for investigating genetic traits in this economically important crop pest species.</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/PMC13537132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792305","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 Evidence for Natural Selection Underlying High-Altitude Adaptive Hemoglobin Levels Among Peruvian Andeans.","authors":"Kimberly Zhu, Kelsey C Jorgensen, Julien Weinstein, Melisa Kiyamu, Gianpietro Elías, Jenna L Isherwood, Abagail M Breidenstein, Obed A Garcia, Greta Gerdes, Laurel N Pearson, Frank S Lee, Maria Rivera-Ch, Fabiola Leon-Velarde, Tom D Brutsaert, Abigail W Bigham","doi":"10.1093/gbe/evag164","DOIUrl":"10.1093/gbe/evag164","url":null,"abstract":"<p><p>High-altitude hypoxia presents an extreme environmental pressure that challenges human survival, growth, and reproduction. Despite this challenge, humans have thrived on the Andean Altiplano for millennia, displaying several unique physiological responses to hypoxia such as elevated hemoglobin concentration ([Hb]). This trait closely resembles the acclimatization response observed among high-altitude sojourners but is distinct from the sea-level normative [Hb] that characterizes the Tibetan adaptive response. As recent candidate-gene efforts to understand the role of natural selection in shaping Andean [Hb] have produced conflicting results, it remains unclear what role natural selection may have played in shaping this unique hematopoietic response. Using genome-wide array data from Peruvian Andeans, we identified two genomic regions containing three genes, PDE1B, PPP1R1A, and RASGEF1B, that show evidence of recent positive selection and are associated with [Hb]. Importantly, Andean alleles within these regions are associated with lowered [Hb], suggesting that recent polygenic selection may be acting to reduce [Hb] within this population. We observe the greatest divergence of Andean allele frequencies from other global populations within the PDE1B/PPP1R1A region and use WGS data and publicly available expression and Hi-C data to more closely identify how natural selection may be acting within this region to impact [Hb]. We identify a selective sweep that favors 11 PDE1B expression-decreasing alleles and is located at the boundary of a topologically associating domain spanning several hemoglobin-linked genes. In sum, this study provides novel evidence that polygenic natural selection may be acting to lower Andean [Hb] in a manner phenotypically convergent with Tibetan populations.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13428292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148390727","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":"Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness.","authors":"Madison Chapel, Carl G de Boer","doi":"10.1093/gbe/evag196","DOIUrl":"10.1093/gbe/evag196","url":null,"abstract":"<p><p>The gene regulatory networks of eukaryotes are dramatically more complex than the gene regulatory networks of prokaryotes, but we lack a complete picture of the selective pressures that have shaped this difference. Here, we use a biochemically informed model of gene regulation to simulate gene regulatory network evolution and explore the role that reproductive strategy plays in shaping regulatory complexity. We find that recombining and nonrecombining populations converge to the same level of complexity, even in the absence of selection. However, recombination modifies the rate at which complexity emerges, accelerating convergence to the complexity plateau in changing environments while slowing the process in static environments. Our results suggest that, rather than being under direct selection, regulatory complexity may emerge as a byproduct of other evolutionary processes. These results highlight how reproductive strategy and environmental change interact to influence evolutionary trajectories.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678262","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":"New Country for Old Mice: The Recent Colonization History of Mus musculus domesticus in the Americas.","authors":"Kennedy D Agwamba, Sofia I Gabriel, Jeremy B Searle, Jeff Wall, Michael W Nachman","doi":"10.1093/gbe/evag187","DOIUrl":"10.1093/gbe/evag187","url":null,"abstract":"<p><p>Humans have profoundly influenced the distribution of organisms globally, particularly those that live in close association with human societies. The western house mouse, Mus musculus domesticus, expanded from the Fertile Crescent into Europe several thousand years ago alongside early agricultural societies and was subsequently introduced worldwide through European maritime expansion. Given their close ecological association, human commensals, such as the house mouse, are expected to reflect historic patterns of human movement. Using a dataset of 276 exome sequences of mice sampled from Western Europe, North America, and South America, we reconstruct the demographic history of house mice in the Americas and draw genetic connections to contemporary European population from which they were historically sourced. Admixture graphs reveal that house mice from the Atlantic coast of the Iberian Peninsula are the sister group to all American populations, and a secondary contribution from southern UK populations is evident in North America. Analyses of population structure further support shared ancestry between the Atlantic coast of the Iberian Peninsula and both American continents, between the United Kingdom and North America, between Portugal and Brazil, and between Spain and Argentina. Demographic modeling reveals that American mouse populations diverged roughly within the last 500 years, consistent with the post-15th century arrival of Western European people to the Americas. Together, these results identify Western European mouse populations that share close ancestry with American mouse populations and illustrate how the demographic history of a widespread human commensal species can mirror fine-scale patterns of human migration.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13469698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591245","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":"Inferring the Relative Contributions of Evolutionary Processes Shaping X Chromosome Dynamics in the Common Marmoset (Callithrix jacchus) in the Presence of Twinning and Hematopoietic Chimerism.","authors":"Vivak Soni, Cyril J Versoza, Devangana Shah, Susanne P Pfeifer, Jeffrey D Jensen","doi":"10.1093/gbe/evag200","DOIUrl":"10.1093/gbe/evag200","url":null,"abstract":"<p><p>The common marmoset (Callithrix jacchus) is a biomedically important species that is characterized by two unusual biological traits-a high frequency of twin births and hematopoietic chimerism-that preclude the application of many commonly used population genomic approaches for quantifying evolutionary processes. In this study, we directly account for both factors in order to estimate fine-scale mutation and recombination rate maps, as well as to infer the demographic and selective processes shaping variation, on the common marmoset X chromosome. Comparing our findings to estimates recently inferred on the autosomes of this species, we find reduced rates of mutation and recombination on the X, as expected. Furthermore, population sex ratios are inferred to be nearly equal, and the appropriately rescaled autosomal population history fits the X chromosome well. Finally, we report evidence of recent selective sweeps targeting a number of X-linked genes, including several of significant biomedical relevance. Overall, these analyses provide novel insights into the evolutionary processes shaping X chromosome evolution in this biomedically relevant primate model.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148706304","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":"Massive Genetic Diversity Loss Within Asian Elephant Subspecies: New Insights for Determining Conservation Priorities.","authors":"Jeroen Kappelhof, Julia Höglund, Emma Diepeveen, Reeta Sharma, Rebekah L Rogers, Michael G Campana, Natalia A Prado, Jesús E Maldonado, Janine L Brown, Patrick Arnold, Benoit Goossens, Symphorosa Sipangkui, Martijn F L Derks, Jack J Windig, Martien A M Groenen, Mirte Bosse","doi":"10.1093/gbe/evag183","DOIUrl":"10.1093/gbe/evag183","url":null,"abstract":"<p><p>In this study, we provide a comprehensive genomic analysis of population structure, genetic diversity, and load across the four Asian elephant (Elephas maximus) subspecies using whole-genome sequencing data of 81 wild-born individuals, with most of them currently living under human care. Our results reveal striking contrast in inbreeding: the Bornean subspecies (E.m. borneensis) exhibits the highest level of inbreeding, with ∼65% of its genome in runs of homozygosity (ROH), and the lowest genome-wide heterozygosity (∼46 heterozygous sites per 100 kb). The Sumatran subspecies (E.m. sumatranus) shows intermediate levels of inbreeding (35% ROH) and heterozygosity (∼101 sites per 100 kb), while the mainland and Sri Lankan subspecies (E.m indicus and E.m. maximus) display similarly low inbreeding (∼10% to 11% ROH) and high heterozygosity (∼130 to 134 sites per 100 kb). Notably, when correcting for ROH coverage, heterozygosity levels are comparable across all four subspecies (∼136 to 155 sites per 100 kb), indicating that differences in genetic diversity are primarily driven by loss of heterozygosity within ROHs due to inbreeding. Genetic load remains relatively low in all subspecies, especially in highly conserved genomic regions. The high genetic diversity observed in the island-dwelling E.m. maximus subspecies likely reflects historical gene flow linked to intensive human-mediated elephant trade, raising questions about its taxonomic status. Given its high inbreeding, E.m. borneensis represents the highest conservation priority, with genetic rescue as a potential management strategy. This study highlights the urgent need for focused conservation efforts and further genomic research to safeguard the unique genetic diversity and long-term viability of Asian elephants.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148520148","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 to: Lineage-Specific Gene Family Innovations Underpin the Pathogenicity of Woody-Plant Pathogens in Botryosphaeriaceae.","authors":"","doi":"10.1093/gbe/evag205","DOIUrl":"https://doi.org/10.1093/gbe/evag205","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 8","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13480124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792260","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":"Evolutionary Rate Covariation Across Malaria Parasite Species Enables Inference of Protein Interactions.","authors":"Helena D Hopson, Radoslaw Igor Omelianczyk, Anayansi Ramirez, Jordan H Little, Nathan Clark, Paul A Sigala, Ellen M Leffler","doi":"10.1093/gbe/evag203","DOIUrl":"10.1093/gbe/evag203","url":null,"abstract":"<p><p>Despite publication of the Plasmodium falciparum reference genome over 20 years ago, one-third of its genes remain functionally unannotated, and information is limited for many others. Proteins that act in the same pathway or complex tend to experience similar shifts in evolutionary pressure, such that correlated constraints across species can indicate co-functional proteins. To investigate this connection, we calculated relative evolutionary rates across the genome on a phylogeny of 22 Plasmodium species and assigned each protein-protein pair a score representing the strength of evolutionary rate covariation (ERC). We show that known pathways and interacting proteins across lifecycle stages in Plasmodium have strong ERC signals. By scanning genome-wide for additional proteins showing high ERC with established interacting proteins, we find enrichment of stage expression and physically interacting protein pairs supporting new candidate functions for proteins. More generally, we demonstrate the utility of ERC to prioritize proteins for hypothesis-driven functional follow-up by showing that a protein with little functional characterization (PF3D7_0811600) shows high ERC and co-localizes with high molecular weight rhoptry proteins 2 and 3 (RhopH2 and RhopH3), which form an ion channel that enhances parasite permeability of infected red blood cells. The ERC matrix can be queried to extract Plasmodium proteins showing high ERC with any protein of interest to prioritize candidate genes and accelerate discovery of novel functional connections.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 8","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13524075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850470","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":"Insights into the Phylogeny and Enigmatic Mitochondrial Biology of Eustigmatophyte Algae From Over 50 Newly Sequenced Organellar Genomes.","authors":"Michal Richtář, Eliška Klapuchová, Tatiana Yurchenko, Karen P Fawley, Marvin W Fawley, Dovilė Barcytė, Karin Jaške, Benjamin M Wolf, Fay-Wei Li, Tereza Ševčíková, Marek Eliáš","doi":"10.1093/gbe/evag169","DOIUrl":"10.1093/gbe/evag169","url":null,"abstract":"<p><p>Organellar genomes are both a resource for reconstructing organismal phylogenies and interesting subjects for evolutionary studies. Herein, we focused on the organellar genomes of eustigmatophytes (eustigs), a class of the algal phylum Ochrophyta with a growing biotechnological potential, and massively expanded the existing limited sample by 51 new organellar genomes. Analyses of this large dataset provided a robustly resolved eustig phylogeny and important insights into the evolution of unique features of eustig organellar genomes. Eustig plastomes are rather stable in terms of the gene content, with only minor differences stemming from differential gene loss and rare lineage-specific gains. In contrast, eustig mitogenomes contain a very stable core of conserved genes accompanied by a broadly varying shell comprising \"accessory\" genes. Notably, the new data illuminated the origin of two mitochondrial genes previously deemed eustig-specific, namely orfX and orfY that were found to have evolved, respectively, by rps4 duplication and extreme divergence of an rps1 ortholog. Most interestingly, we identified five previously unrecognized orthogroups of mysterious mitochondrial orfs that are patchily distributed across eustigs yet likely evolved in the ancestor of this class. These orfs have no discernible homologs outside eustigmatophytes but are predicted to encode multipass membrane proteins with a soluble C-terminal domain. Our results also revise some of the previous conclusions regarding the mitochondrial translation in eustigs and suggest the recruitment of a group of unusual tRNAs for a translation-independent function in the genus Vischeria. Our study thus provides a glimpse into a \"dark matter\" of mitochondrial biology in eustigmatophytes.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404536","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":"Interhaplotype Inversions and Repeat Expansion in the Sexually Deceptive Orchid Chiloglottis trapeziformis.","authors":"Zirui Zhang, Ashley Jones, Benjamin Schwessinger, Rod Peakall, Darren Wong","doi":"10.1093/gbe/evag190","DOIUrl":"10.1093/gbe/evag190","url":null,"abstract":"<p><p>High-quality nuclear genome resources remain scarce for most orchids, particularly Australia's diverse terrestrial lineages. Chiloglottis trapeziformis is a well-studied sexually deceptive orchid that provides a valuable system for investigating orchid genome evolution, structural variation, and the molecular basis of specialized pollination. Here, we integrated PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C chromatin-contact data to generate the first chromosome-scale, haplotype-resolved nuclear genome assembly for any Australian terrestrial orchid. Hi-C guided scaffolding resolved two haplotypes into 20 chromosomes each, consistent with the reported karyotype and genome size (2n = 40, haplotype sizes of 1.58 and 1.91 Gb). Genome completeness was high for both haplotypes, recovering 94.67% and 94.82% single-copy BUSCO genes for Haplotype 1 and Haplotype 2, respectively. De novo repeat annotation revealed a repeat-rich genome (85.79% to 88.25% repetitive sequence), dominated by LTR retrotransposons. Evidence-guided annotation identified 16,287 and 16,548 protein-coding genes in Haplotype 1 and Haplotype 2, respectively. Phylogenetically informed comparisons placed C. trapeziformis as sister to Anoectochilus roxburghii among sampled Orchidoideae and showed broad gene-order conservation. Comparing the two haplotypes for structural variation, we identified large interhaplotype inversions containing functionally annotated genes with detectable RNA expression, with focal examples further supported by local Hi-C contact patterns and breakpoint-level inspection. Inversion-overlapping genes did not show elevated dS relative to collinear background. This assembly and annotation resource provides a foundation for population and conservation genomics, structural and comparative analyses, and genome-enabled hypothesis testing of molecular traits underlying sexual deception in orchids.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591323","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}