Genome Biology and Evolution最新文献

筛选
英文 中文
Challenges in Assembling the Dated Tree of Life. 组装有日期的生命之树所面临的挑战。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae229
Carlos G Schrago, Beatriz Mello
{"title":"Challenges in Assembling the Dated Tree of Life.","authors":"Carlos G Schrago, Beatriz Mello","doi":"10.1093/gbe/evae229","DOIUrl":"10.1093/gbe/evae229","url":null,"abstract":"<p><p>The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545107","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}
引用次数: 0
Campylobacter fetus Plasmid Diversity: Comparative Analysis of Fully Sequenced Plasmids and Proposed Classification Scheme. 胎儿弯曲杆菌质粒多样性:完全测序质粒的比较分析和拟议的分类方案。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae203
Nerea Pena-Fernández, Linda van der Graaf-van Bloois, Birgitta Duim, Aldert Zomer, Jaap A Wagenaar, Medelin Ocejo, Jose Luís Lavín, Esther Collantes-Fernández, Ana Hurtado, Gorka Aduriz
{"title":"Campylobacter fetus Plasmid Diversity: Comparative Analysis of Fully Sequenced Plasmids and Proposed Classification Scheme.","authors":"Nerea Pena-Fernández, Linda van der Graaf-van Bloois, Birgitta Duim, Aldert Zomer, Jaap A Wagenaar, Medelin Ocejo, Jose Luís Lavín, Esther Collantes-Fernández, Ana Hurtado, Gorka Aduriz","doi":"10.1093/gbe/evae203","DOIUrl":"10.1093/gbe/evae203","url":null,"abstract":"<p><p>Campylobacter fetus is an animal pathogen that contains 2 mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv) including its biovar intermedius that exhibit different biochemical traits and differences in pathogenicity. Although plasmids are important in the horizontal transfer of antimicrobial resistance genes and virulence factors, C. fetus plasmids are understudied. Here, the closed sequences of 12 plasmids from Spanish C. fetus isolates were compared with the publicly available DNA sequences of C. fetus plasmids and other members of the Campylobacterales order. Sizes of C. fetus plasmids from Spanish isolates ranged between 4 and 50 kb and most of them (10/12) were potentially conjugative. Comparative analysis of the plasmids' gene content revealed a close genetic relationship between the plasmids of C. fetus isolated in Spain and those from other geographical regions, while being clearly distinct from plasmids of other Campylobacter species. Furthermore, C. fetus plasmids were grouped into two main clusters regardless of their geographic location or lineage. The distribution pattern of relaxase, replicase, and single-stranded DNA binding SSB protein encoding genes showed a clustering comparable to that resulting from plasmid whole gene content analysis, suggesting its potential use for the classification of C. fetus plasmids. Most of the larger plasmids harbored mobile genetic elements. These results can help to better understand the evolutionary dynamics and pathogenic implications of C. fetus plasmids.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11467750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400022","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}
引用次数: 0
Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies. ithomiine蝴蝶触角转录组中新的性别特异性基因和多样的种间表达。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae218
Francesco Cicconardi, Billy J Morris, Jacopo Martelossi, David A Ray, Stephen H Montgomery
{"title":"Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies.","authors":"Francesco Cicconardi, Billy J Morris, Jacopo Martelossi, David A Ray, Stephen H Montgomery","doi":"10.1093/gbe/evae218","DOIUrl":"10.1093/gbe/evae218","url":null,"abstract":"<p><p>The olfactory sense is crucial for organisms, facilitating environmental recognition and interindividual communication. Ithomiini butterflies exemplify this importance not only because they rely strongly on olfactory cues for both inter- and intra-sexual behaviors, but also because they show convergent evolution of specialized structures within the antennal lobe, called macroglomerular complexes (MGCs). These structures, widely absent in butterflies, are present in moths where they enable heightened sensitivity to, and integration of, information from various types of pheromones. In this study, we investigate chemosensory evolution across six Ithomiini species and identify possible links between expression profiles and neuroanatomical. To enable this, we sequenced four new high-quality genome assemblies and six sex-specific antennal transcriptomes for three of these species with different MGC morphologies. With extensive genomic analyses, we found that the expression of antennal transcriptomes across species exhibit profound divergence, and identified highly expressed ORs, which we hypothesize may be associated to MGCs, as highly expressed ORs are absent in Methona, an Ithomiini lineage which also lacks MGCs. More broadly, we show how antennal sexual dimorphism is prevalent in both chemosensory genes and non-chemosensory genes, with possible relevance for behavior. As an example, we show how lipid-related genes exhibit consistent sexual dimorphism, potentially linked to lipid transport or host selection. In this study, we investigate the antennal chemosensory adaptations, suggesting a link between genetic diversity, ecological specialization, and sensory perception with the convergent evolution of MCGs. Insights into chemosensory gene evolution, expression patterns, and potential functional implications enhance our knowledge of sensory adaptations and sexual dimorphisms in butterflies, laying the foundation for future investigations into the genetic drivers of insect behavior, adaptation, and speciation.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380634","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}
引用次数: 0
Examining the Effects of Environment, Geography, and Elevation on Patterns of DNA Methylation Across Populations of Two Widespread Bumble Bee Species. 研究环境、地理和海拔对两种广泛分布的熊蜂种群 DNA 甲基化模式的影响。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae207
Sam D Heraghty, Sarthok Rasique Rahman, Kelton M Verble, Jeffrey D Lozier
{"title":"Examining the Effects of Environment, Geography, and Elevation on Patterns of DNA Methylation Across Populations of Two Widespread Bumble Bee Species.","authors":"Sam D Heraghty, Sarthok Rasique Rahman, Kelton M Verble, Jeffrey D Lozier","doi":"10.1093/gbe/evae207","DOIUrl":"10.1093/gbe/evae207","url":null,"abstract":"<p><p>Understanding the myriad avenues through which spatial and environmental factors shape evolution is a major focus in biological research. From a molecular perspective, much work has been focused on genomic sequence variation; however, recently there has been increased interest in how epigenetic variation may be shaped by different variables across the landscape. DNA methylation has been of particular interest given that it is dynamic and can alter gene expression, potentially offering a path for a rapid response to environmental change. We utilized whole genome enzymatic methyl sequencing to evaluate the distribution of CpG methylation across the genome and to analyze patterns of spatial and environmental association in the methylomes of two broadly distributed montane bumble bees (Bombus vancouverensis Cresson and Bombus vosnesenskii Radoszkowski) across elevational gradients in the western US. Methylation patterns in both species are similar at the genomic scale with ∼1% of CpGs being methylated and most methylation being found in exons. At the landscape scale, neither species exhibited strong spatial or population structuring in patterns of methylation, although some weak relationships between methylation and distance or environmental variables were detected. Differential methylation analysis suggests a stronger environment association in B. vancouverensis given the larger number of differentially methylated CpG's compared to B. vosnesenskii. We also observed only a handful of genes with both differentially methylated CpGs and previously detected environmentally associated outlier SNPs. Overall results reveal a weak but present pattern in variation in methylation over the landscape in both species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11474243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345130","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}
引用次数: 0
Unveiling the Genome-Wide Consequences of Range Expansion and Mating System Transitions in Primula vulgaris. 揭示报春花分布范围扩大和交配系统转变的全基因组后果。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae208
Emiliano Mora-Carrera, Rebecca L Stubbs, Giacomo Potente, Narjes Yousefi, Simon Aeschbacher, Barbara Keller, Rimjhim Roy Choudhury, Ferhat Celep, Judita Kochjarová, Jurriaan M de Vos, Peter Szövényi, Elena Conti
{"title":"Unveiling the Genome-Wide Consequences of Range Expansion and Mating System Transitions in Primula vulgaris.","authors":"Emiliano Mora-Carrera, Rebecca L Stubbs, Giacomo Potente, Narjes Yousefi, Simon Aeschbacher, Barbara Keller, Rimjhim Roy Choudhury, Ferhat Celep, Judita Kochjarová, Jurriaan M de Vos, Peter Szövényi, Elena Conti","doi":"10.1093/gbe/evae208","DOIUrl":"10.1093/gbe/evae208","url":null,"abstract":"<p><p>Genetic diversity is heterogeneously distributed among populations of the same species, due to the joint effects of multiple demographic processes, including range contractions and expansions, and mating systems shifts. Here, we ask how both processes shape genomic diversity in space and time in the classical Primula vulgaris model. This perennial herb originated in the Caucasus region and was hypothesized to have expanded westward following glacial retreat in the Quaternary. Moreover, this species is a long-standing model for mating system transitions, exemplified by shifts from heterostyly to homostyly. Leveraging a high-quality reference genome of the closely related Primula veris and whole-genome resequencing data from both heterostylous and homostylous individuals from populations encompassing a wide distribution of P. vulgaris, we reconstructed the demographic history of P. vulgaris. Results are compatible with the previously proposed hypothesis of range expansion from the Caucasus region approximately 79,000 years ago and suggest later shifts to homostyly following rather than preceding postglacial colonization of England. Furthermore, in accordance with population genetic theoretical predictions, both processes are associated with reduced genetic diversity, increased linkage disequilibrium, and reduced efficacy of purifying selection. A novel result concerns the contrasting effects of range expansion versus shift to homostyly on transposable elements, for the former, process is associated with changes in transposable element genomic content, while the latter is not. Jointly, our results elucidate how the interactions among range expansion, transitions to selfing, and Quaternary climatic oscillations shape plant evolution.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11469071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345131","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}
引用次数: 0
Enigmatic Pachytene PIWI-Interacting RNAs. 神秘的非转座子 PIWI-interacting RNAs。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae162
Ming-Min Xu, Xin Zhiguo Li
{"title":"Enigmatic Pachytene PIWI-Interacting RNAs.","authors":"Ming-Min Xu, Xin Zhiguo Li","doi":"10.1093/gbe/evae162","DOIUrl":"10.1093/gbe/evae162","url":null,"abstract":"<p><p>PIWI-interacting RNAs (piRNAs), a class of small RNAs, are renowned for their roles in sequencing-dependent targeting and suppressing transposable elements (TEs). Nevertheless, a majority of mammalian piRNAs, expressing at pachytene stage of meiosis, known as pachytene piRNAs, are devoid of discernible targets, casting a veil of enigma over their functional significance. Overturning the notion that this unusual class of piRNAs functions beyond TE silencing, we recently demonstrated that pachytene piRNAs play an essential and conserved role in silencing young and actively transposing TEs across amniotes. However, only 1% of pachytene piRNAs target active TEs. The biological significance of the abundant non-TE piRNAs, coproduced from the same precursors as TE piRNAs, remains unclear. Here, we provide a comprehensive summary of the potential roles of non-TE piRNAs, and thus propose that these non-TE piRNAs either bolster the action of TE piRNAs or provide the host genome a preexisting mechanism to suppress the potential invasion of novel TEs in the future.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11464241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758264","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}
引用次数: 0
Parallel Spectral Tuning of a Cone Visual Pigment Provides Evidence for Ancient Deep-Sea Adaptations in Cetaceans. 一种锥体视觉色素的平行光谱调谐为鲸目动物古老的深海适应性提供了证据。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae223
Hai Chi, Linxia Sun, Na Li, Yue Zhan, Jinqu Guo, Lei Lei, David M Irwin, Guang Yang, Shixia Xu, Yang Liu
{"title":"Parallel Spectral Tuning of a Cone Visual Pigment Provides Evidence for Ancient Deep-Sea Adaptations in Cetaceans.","authors":"Hai Chi, Linxia Sun, Na Li, Yue Zhan, Jinqu Guo, Lei Lei, David M Irwin, Guang Yang, Shixia Xu, Yang Liu","doi":"10.1093/gbe/evae223","DOIUrl":"10.1093/gbe/evae223","url":null,"abstract":"<p><p>Dichromatic color vision is mediated by two cone visual pigments in many eutherian mammals. After reentry into the sea, early cetaceans lost their violet-sensitive visual pigment (short wavelength-sensitive 1) independently in the baleen and toothed whale ancestors and thus obtained only monochromatic cone vision. Subsequently, losses of the middle/long wavelength-sensitive (M/LWS) pigment have also been reported in multiple whale lineages, leading to rhodopsin (RH1)-mediated rod monochromatic vision. To further elucidate the phenotypic evolution of whale visual pigments, we assessed the spectral tuning of both M/LWS and RH1 from representative cetacean taxa. Interestingly, although the coding sequences for M/LWS are intact in both the pygmy right whale and the Baird's beaked whale, no spectral sensitivity was detected in vitro. Pseudogenization of other cone vision-related genes is observed in the pygmy right whale, suggesting a loss of cone-mediated vision. After ancestral sequence reconstructions, ancient M/LWS pigments from cetacean ancestors were resurrected and functionally measured. Spectral tuning of M/LWS from the baleen whale ancestor shows that it is green sensitive, with a 40-nm shift in sensitivity to a shorter wavelength. For the ancestor of sperm whales, although no spectral sensitivity could be recorded for its M/LWS pigment, a substantial sensitivity shift (20 to 30 nm) to a shorter wavelength may have also occurred before its functional inactivation. The parallel phenotypic evolution of M/LWS to shorter wavelength sensitivity might be visual adaptations in whales allowing more frequent deep-sea activities, although additional ecological differentiations may have led to their subsequent losses.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463298","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}
引用次数: 0
Evolutionary Modes of wtf Meiotic Driver Genes in Schizosaccharomyces pombe. 奇异酵母菌减数分裂驱动基因的进化模式
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae221
Yan-Hui Xu, Fang Suo, Xiao-Ran Zhang, Tong-Yang Du, Yu Hua, Guo-Song Jia, Jin-Xin Zheng, Li-Lin Du
{"title":"Evolutionary Modes of wtf Meiotic Driver Genes in Schizosaccharomyces pombe.","authors":"Yan-Hui Xu, Fang Suo, Xiao-Ran Zhang, Tong-Yang Du, Yu Hua, Guo-Song Jia, Jin-Xin Zheng, Li-Lin Du","doi":"10.1093/gbe/evae221","DOIUrl":"10.1093/gbe/evae221","url":null,"abstract":"<p><p>Killer meiotic drivers are a class of selfish genetic elements that bias inheritance in their favor by destroying meiotic progeny that do not carry them. How killer meiotic drivers evolve is not well understood. In the fission yeast, Schizosaccharomyces pombe, the largest gene family, known as the wtf genes, is a killer meiotic driver family that causes intraspecific hybrid sterility. Here, we investigate how wtf genes evolve using long-read-based genome assemblies of 31 distinct S. pombe natural isolates, which encompass the known genetic diversity of S. pombe. Our analysis, involving nearly 1,000 wtf genes in these isolates, yields a comprehensive portrayal of the intraspecific diversity of wtf genes. Leveraging single-nucleotide polymorphisms in adjacent unique sequences, we pinpoint wtf gene-containing loci that have recently undergone gene conversion events and infer their ancestral state. These events include the revival of wtf pseudogenes, lending support to the notion that gene conversion plays a role in preserving this gene family from extinction. Moreover, our investigation reveals that solo long terminal repeats of retrotransposons, frequently found near wtf genes, can act as recombination arms, influencing the upstream regulatory sequences of wtf genes. Additionally, our exploration of the outer boundaries of wtf genes uncovers a previously unrecognized type of directly oriented repeats flanking wtf genes. These repeats may have facilitated the early expansion of the wtf gene family in S. pombe. Our findings enhance the understanding of the mechanisms influencing the evolution of this killer meiotic driver gene family.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400020","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}
引用次数: 0
Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter. 揭开野生鸟类病毒组的神秘面纱:探索 CRESS-DNA 病毒暗物质。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae206
Ziyuan Dai, Haoning Wang, Juan Xu, Xiang Lu, Ping Ni, Shixing Yang, Quan Shen, Xiaochun Wang, Wang Li, Xiaolong Wang, Chenglin Zhou, Wen Zhang, Tongling Shan
{"title":"Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.","authors":"Ziyuan Dai, Haoning Wang, Juan Xu, Xiang Lu, Ping Ni, Shixing Yang, Quan Shen, Xiaochun Wang, Wang Li, Xiaolong Wang, Chenglin Zhou, Wen Zhang, Tongling Shan","doi":"10.1093/gbe/evae206","DOIUrl":"10.1093/gbe/evae206","url":null,"abstract":"<p><p>Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of \"viral dark matter,\" the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11463337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345132","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}
引用次数: 0
Genome-Wide Comparisons Reveal Extensive Divergence Within the Lichen Photobiont Genus, Trebouxia. 全基因组比较揭示地衣光生菌属 Trebouxia 的广泛分化
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae219
Rosa Celia Poquita-Du, Jürgen Otte, Anjuli Calchera, Imke Schmitt
{"title":"Genome-Wide Comparisons Reveal Extensive Divergence Within the Lichen Photobiont Genus, Trebouxia.","authors":"Rosa Celia Poquita-Du, Jürgen Otte, Anjuli Calchera, Imke Schmitt","doi":"10.1093/gbe/evae219","DOIUrl":"10.1093/gbe/evae219","url":null,"abstract":"<p><p>The green algal genus Trebouxia is the most frequently encountered photobiont of the lichen symbiosis. The single-celled symbionts have a worldwide distribution, including all continents and climate zones. The vast, largely undescribed, diversity of Trebouxia lineages is currently grouped into four phylogenetic clades (A, C, I, and S), based on a multilocus phylogeny. Genomes are still scarce, however, and it is unclear how the phylogenetic diversity, the broad ecological tolerances, and the ability to form symbioses with many different fungal host species are reflected in genome-wide differences. Here, we generated PacBio-based de novo genomes of six Trebouxia lineages belonging to the Clades A and S, isolated from lichen individuals of the genus Umbilicaria. Sequences belonging to Clade S have been reported in a previous study, but were reassembled and reanalyzed here. Genome sizes ranged between 63.08 and 73.88 Mb. Repeat content accounted for 9% to 16% of the genome sequences. Based on RNA evidence, we predicted 14,109 to 16,701 gene models per genome, of which 5,203 belonged to a core set of gene families shared by all 6 lineages. Between 121 and 454, gene families are specific to each lineage. About 53% of the genes could be functionally annotated. The presence of biosynthetic gene clusters (6 to 17 per genome) suggests that Trebouxia algae are able to synthesize alkaloids, saccharides, terpenes, NRPSs, and T3PKSs. Phylogenomic comparisons of the six strains indicate prevalent gene gain during Trebouxia evolution. Some of the gene families that exhibited significant evolutionary changes (i.e. gene expansion and contraction) are associated with metabolic processes linked to protein phosphorylation, which is known to have a role in photosynthesis regulation, particularly under changing light conditions. Overall, there is substantial genomic divergence within the algal genus Trebouxia, which may contribute to the genus' large ecological amplitude concerning fungal host diversity and climatic niches.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11523091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545108","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}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信