Genome Biology and Evolution最新文献_第2页

ParallelEvolCCM: Quantifying co-evolutionary patterns among genomic features. ParallelEvolCCM：量化基因组特征之间的共同进化模式。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-17 DOI: 10.1093/gbe/evaf092

Robert G Beiko, Chaoyue Liu, João Vitor Cavalcante, Ryan C Fink

引用次数: 0

Exploring the relationship of transposable elements and ageing: causes and consequences. 探讨转座因子与衰老的关系：原因与后果。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-15 DOI: 10.1093/gbe/evaf088

Miriam Merenciano, Anaïs Larue, Chloé Garambois, William Vilas Boas Nunes, Cristina Vieira

引用次数: 0

The First De Novo HiFi Genome Assemblies for Three Clownfish-hosting Sea Anemone Species (Anthozoa: Actiniaria). 三种小丑鱼寄主海葵物种（珊瑚虫目：猕猴桃属）的第一个全新的HiFi基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf064

Aurélien De Jode, Benjamin M Titus

{"title":"The First De Novo HiFi Genome Assemblies for Three Clownfish-hosting Sea Anemone Species (Anthozoa: Actiniaria).","authors":"Aurélien De Jode, Benjamin M Titus","doi":"10.1093/gbe/evaf064","DOIUrl":"10.1093/gbe/evaf064","url":null,"abstract":"The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome-scale reference genomes are available for all clownfish species, yet only short reads-based reference genomes are available for five species of host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high-quality long-read assemblies for three species of clownfish-hosting sea anemones belonging to each of these clades: Entacmaea quadricolor, Stichodactyla haddoni, and Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads for E. quadricolor, S. haddoni, and R. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4 Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948, and 17,056 protein-coding genes in E. quadricolor, S. haddoni, and R. doreensis genome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811178","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

Robust Binding Capability and Occasional Gene Loss of Telomere-Binding Proteins Underlying Telomere Evolution in Nematoda. 线虫端粒进化中端粒结合蛋白的强大结合能力和偶尔的基因丢失。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf085

Hobum Song, Seonhong Kim, Daisy Sunghee Lim, Hee-Jung Choi, Junho Lee

{"title":"Robust Binding Capability and Occasional Gene Loss of Telomere-Binding Proteins Underlying Telomere Evolution in Nematoda.","authors":"Hobum Song, Seonhong Kim, Daisy Sunghee Lim, Hee-Jung Choi, Junho Lee","doi":"10.1093/gbe/evaf085","DOIUrl":"10.1093/gbe/evaf085","url":null,"abstract":"Telomeres, the nucleoprotein complexes that protect the ends of linear chromosomes, are essential for maintaining the stability of eukaryotic genomes. As telomeres generally consist of repetitive DNA associated with specifically bound proteins, telomeric repeat motifs are thought to be difficult to evolve. However, a recent study identified nematodes with telomeric repeats distinct from the canonical TTAGGC motif. Here, we investigated how telomere repeats could have evolved despite the challenge posed by the specificity of telomere-binding proteins (TBPs) to the telomeric DNA in Nematoda. We performed a phylogenetic analysis and electrophoresis mobility shift assays to assess the binding affinities of two TBPs, which displayed different conservation patterns. Our results revealed that the well-conserved protein CEH-37 exhibits limited specificity, unable to distinguish telomeric repeats found in nematodes except for the TTAGGG motif, while the less conserved POT proteins displayed rigid specificity. These findings suggest that the emergence of novel telomeric repeat motifs correlated with the characteristics and evolutionary outcomes of TBPs in Nematoda. Our study not only revealed the dynamics of telomere evolution but also enhanced the understanding of the evolutionary relationship between proteins and DNAs.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143963328","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 Analyses of Human Respiratory Syncytial Viruses Provide Insights into Evolutionary Dynamics. 人类呼吸道合胞病毒的全基因组分析提供了进化动力学的见解。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf093

Lu-Lu Chen, Chu-Ci Tong, Yu-Xian Zhao, Yan-Peng Zheng, Xiang-Lei Peng, Yuan-Hui Fu, Jin-Sheng He, Jie-Mei Yu

{"title":"Genome-Wide Analyses of Human Respiratory Syncytial Viruses Provide Insights into Evolutionary Dynamics.","authors":"Lu-Lu Chen, Chu-Ci Tong, Yu-Xian Zhao, Yan-Peng Zheng, Xiang-Lei Peng, Yuan-Hui Fu, Jin-Sheng He, Jie-Mei Yu","doi":"10.1093/gbe/evaf093","DOIUrl":"10.1093/gbe/evaf093","url":null,"abstract":"Human Respiratory syncytial virus (HRSV) is a leading cause of acute lower respiratory tract infections. It is essential to monitor its genomic characteristics. In this study, we analyzed the variation and evolutionary features of HRSV A and HRSV B using whole-genome data, with a focus on their evolutionary features post-COVID-19. Our findings revealed: (i) the mutation rates of HRSV A genes were generally higher than those of HRSV B genes, with the primary mutation directions for both subtypes being C to T, T to C, G to A, and A to G; (ii) multiple lineages of both subtypes that were prevalent during the pandemic are no longer circulating, likely related to the founder effect caused by non-pharmaceutical interventions; (iii) the lineage-defining amino acids on the neutralizing antigens F and G of the circulating lineages post SARS-CoV-2 pandemic exhibited significant temporal specificity; (iv) HRSV B predominated over A in 2023, and the lineage-defining amino acids of the HRSV B F protein located on or very close to major neutralizing antigenic sites, and several lineage-defining amino acids of the G protein were under strong positive selection. These observations suggested that the HRSV B showed stronger adaptive evolutionary features compared to HRSV A post-pandemic. Combining with the fact that several lineage-defining amino acids are located in the replication-related proteins, we hypothesized a potential model of synergistic evolution mediated by multi-protein mutations in the adaptive evolution of circulating strains. However, the impact of these amino acid changes on the viral properties requires further experimental validation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144150272","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 Demographic Analyses of Balaenid Whales Revealed Complex History of Gene Flow Associated with Past Climate Oscillation. balaenid鲸的全基因组人口统计分析揭示了与过去气候振荡相关的基因流动的复杂历史。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf081

Bai-Wei Lo, Francisca Martinez Real, Andreas Magg, John Pierce Wise, Stefan Mundlos, Paolo Franchini

{"title":"Genome-Wide Demographic Analyses of Balaenid Whales Revealed Complex History of Gene Flow Associated with Past Climate Oscillation.","authors":"Bai-Wei Lo, Francisca Martinez Real, Andreas Magg, John Pierce Wise, Stefan Mundlos, Paolo Franchini","doi":"10.1093/gbe/evaf081","DOIUrl":"10.1093/gbe/evaf081","url":null,"abstract":"The balaenid whale, comprising three species of right whales and the bowhead whale, represents an ancient and highly endangered lineage of marine mammals. To unravel the evolutionary history of balaenid whales with respect to gene flow, a comprehensive analysis based on whole-genome data was conducted for all species within this group. Employing population genomic methodologies, we revealed that extant right whales form an unresolved branching pattern, identified evidence of historical transequatorial migration, and provided estimates of the age of the group. Furthermore, we investigated the impact of glacial cycles on the connectivity of bowhead whale populations. By employing multiple complementary approaches to detect gene flow, we identified and characterized gene flow events from bowhead whales to North Atlantic right whales, offering detailed insights into the process. Lastly, we assessed the phenotypic consequences of interspecies gene flow. Our study sheds light on the intricate evolutionary history of modern balaenid whales, which have been profoundly shaped by ancient climate events.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985172","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

Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses. 四鞭毛虫衣藻叶绿体基因组的六个新测序：系统发育和比较基因组分析。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf074

Yangliang Chen, Qian Xiong, Qingyu Dai, Guoxiang Liu

{"title":"Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses.","authors":"Yangliang Chen, Qian Xiong, Qingyu Dai, Guoxiang Liu","doi":"10.1093/gbe/evaf074","DOIUrl":"https://doi.org/10.1093/gbe/evaf074","url":null,"abstract":"Several quadriflagellate genera were revealed as the members of deep branches in Chlamydomonadales. However, the phylogenetic relationships among these quadriflagellate genera remained unresolved, and little information is known about the chloroplast genome structure for the chlamydomonadalean early-diverging lineages due to the limited data. In this study, we conducted phylogenetic and comparative genomic analyses with 6 newly sequenced quadriflagellate chlamydomonadalean chloroplast genomes. Four phylogenetic inferences based on different datasets recovered the robust topology, with Staurocarteria-Hafniomonas as the earliest-diverging lineage, followed by Corbierea within Chlamydomonadales and Spermatozopsis included in Sphaeropleales. The amino acid dataset combined with the site-heterogeneous model received the highest support for key nodes and may better fit the inferences of the deep relationships in Chlamydomonadales. Moreover, Sp. similis chloroplast genome is also more structurally similar to its close relatives than to other quadriflagellate chlamydomonadaleans. Phylogeny and genome structure features both indicated the taxonomic position of Spermatozopsis should be reconsidered. The loss of large inverted repeats (IRs) was first reported in chlamydomonadaleans (Co. pseudopalmata), and may occur at least 4 times in Chlamydomonadales. Comparative genome analyses demonstrated the highly divergent large IRs and a high level of rearrangements across the entire genome. IR expansions/contractions and inversions contribute to changes in gene content and gene order in this region. This study provides a foundation for future research on the phylogenetic relationships as well as chloroplast genomic features and evolution of the entire Chlamydomonadales.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998893","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

Genomic Exploration of Climate-driven Evolution and Evolutionary Convergence in Forest Pathogens. 森林病原体气候驱动进化和进化趋同的基因组探索。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf069

Pauline Hessenauer, Nicolas Feau, Renate Heinzelmann, Richard C Hamelin

引用次数: 0

The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation. 种群分支统计在识别局部适应基因组特征中的准确性和效力。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf080

Max Shpak, Kadee N Lawrence, John E Pool

{"title":"The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation.","authors":"Max Shpak, Kadee N Lawrence, John E Pool","doi":"10.1093/gbe/evaf080","DOIUrl":"10.1093/gbe/evaf080","url":null,"abstract":"Population branch statistics, which estimate the degree of genetic differentiation along a focal population's lineage, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. Beyond the population branch statistic (PBS), the normalized PBSn1 adjusts focal branch length with respect to outgroup branch lengths at the same locus, whereas population branch excess (PBE) incorporates median branch lengths at other loci. PBSn1 and PBE were proposed to be more specific to local selective sweeps as opposed to geographically ubiquitous selection. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or (approximated) background selection, with local selective sweeps or geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. Particularly when parallel sweeps are introduced, PBSn1 and PBE correctly identify local sweeps among their top outliers more frequently than PBS. Additionally, we evaluate versions of these statistics based on maximal site differentiation within a window, finding that site-based PBE and PBSn1 are particularly effective at identifying local soft sweeps. These results validate the greater specificity of the rescaled branch statistics PBE and PBSn1 to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997677","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

Evolution of Pineal Nonvisual Opsins in Lizards and the Tuatara and Identification of Lepidopsin: A New Opsin Gene. 蜥蜴和蜥蜴松果体非视蛋白的进化和鳞翅目蛋白的鉴定：一个新的视蛋白基因。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-04-30 DOI: 10.1093/gbe/evaf058

Ricardo D Romero, Flávio S J de Souza

{"title":"Evolution of Pineal Nonvisual Opsins in Lizards and the Tuatara and Identification of Lepidopsin: A New Opsin Gene.","authors":"Ricardo D Romero, Flávio S J de Souza","doi":"10.1093/gbe/evaf058","DOIUrl":"https://doi.org/10.1093/gbe/evaf058","url":null,"abstract":"Many lizards (Squamata), as well as the tuatara (Rhynchocephalia), are distinguished among vertebrate groups for the presence of the parietal eye, or \"third eye\", a structure derived from the pineal complex containing a simplified retina with photoreceptor cells. The parietal eye expresses nonvisual opsins that differ from the visual opsin repertoire of the lateral eyes. These are pinopsin (OPNP), parapinopsin (OPNPP), and parietopsin (OPNPT), all being evolutionary close to visual opsins. Here, we searched over 60 lepidosaurian genomes for pineal nonvisual opsins to check for the evolutionary trajectory of these genes in reptiles. Unexpectedly, we identified a novel opsin gene, which we termed \"lepidopsin\" (OPNLEP), that is present solely in the genomes of the tuatara and most lizard groups but absent from other vertebrates. Remnants of the gene are found in the coelacanth and some ray-finned fishes, implying that OPNLEP is an ancient opsin that has been repeatedly lost during vertebrate evolution. We found that the tuatara and most lizards of the Iguania, Anguimorpha, Scincoidea, and Lacertidae clades, which possess a parietal eye, harbor all pineal opsin genes. Lizards missing the parietal eye, like geckos, teiids, and a fossorial amphisbaenian, lack most or all pineal nonvisual opsins. In summary, our survey of pineal nonvisual opsins reveals (i) the persistence of a previously unknown ancient opsin gene-OPNLEP-in lepidosaurians; (ii) losses of nonvisual opsins in specific lizard clades; and (iii) a correlation between the presence of a parietal eye and the genomic repertoire of pineal nonvisual opsins.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 5","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998036","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