Genome Biology and Evolution最新文献_第10页

Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes. 真核生物DNA损伤反应蛋白长度变异的进化见解。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf089

Dominic Wiredu-Boakye, Laurence Higgins, Ondřej Gahura, Anzhelika Butenko, Guy Leonard, Mark A Freeman, Árni Kristmundsson, Karen Moore, Jamie W Harrison, Shani Mac Donald, Vyacheslav Yurchenko, Bryony A P Williams, Richard Chahwan

{"title":"Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes.","authors":"Dominic Wiredu-Boakye, Laurence Higgins, Ondřej Gahura, Anzhelika Butenko, Guy Leonard, Mark A Freeman, Árni Kristmundsson, Karen Moore, Jamie W Harrison, Shani Mac Donald, Vyacheslav Yurchenko, Bryony A P Williams, Richard Chahwan","doi":"10.1093/gbe/evaf089","DOIUrl":"10.1093/gbe/evaf089","url":null,"abstract":"Across the tree of life, DNA damage response (DDR) proteins play a pivotal, yet dichotomous role in organismal development and evolution. Here, we present a comprehensive analysis of 432 DDR proteins encoded by 68 genomes, including that of Nucleospora cyclopteri, an intranuclear microsporidia sequenced in this study. We compared the DDR proteins encoded by these genomes to those of humans to uncover the DNA repair-ome across phylogenetically distant eukaryotes. We also performed further analyses to understand if organismal complexity and lifestyle play a role in the evolution of DDR protein length and conserved domain architecture. We observed that the genomes of extreme parasites such as Paramicrocytos, Giardia, Spironucleus, and certain microsporidian lineages encode the smallest eukaryotic repertoire of DDR proteins and that pathways involved in modulation of nucleotide pools and nucleotide excision repair are the most preserved DDR pathways in the eukaryotic genomes analysed here. We found that DDR and DNA repair proteins are consistently longer than housekeeping and metabolic proteins. This is likely due to the higher number of physical protein-protein interactions which DDR proteins are involved. We find that although DNA repair proteins are generally longer than housekeeping proteins, their functional domains occupy a relatively smaller footprint. Notably, this pattern holds true across diverse organisms and shows no dependence on either lifestyle or mitochondrial status. Finally, we observed that unicellular organisms harbour proteins that are tenfold longer than their human homologues, with the extra amino acids forming interdomain regions with a clearly novel albeit undetermined function.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101722","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

Temporal Dynamics of Gene Expression During Metamorphosis in Two Distant Drosophila Species. 两个远缘果蝇物种变态过程中基因表达的时间动态。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf100

Aleksandra M Ozerova, Dina A Kulikova, Mikhail B Evgen'ev, Mikhail S Gelfand

引用次数: 0

Discovering Intron Gain Events in Humans Through Large-Scale Evolutionary Comparisons. 通过大规模进化比较发现人类内含子获得事件。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf091

Celine Hoh, Steven L Salzberg

引用次数: 0

Genomic Organization of Trypanosoma cruzi tRNA Genes. 克氏锥虫tRNA基因的基因组组织。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf108

Florencia Díaz-Viraqué, Ricardo Ehrlich, Carlos Robello

{"title":"Genomic Organization of Trypanosoma cruzi tRNA Genes.","authors":"Florencia Díaz-Viraqué, Ricardo Ehrlich, Carlos Robello","doi":"10.1093/gbe/evaf108","DOIUrl":"10.1093/gbe/evaf108","url":null,"abstract":"A frequently overlooked category of genes in large-scale genome analyses is the nonprotein-coding genes. Specifically, the genomic organization of tRNA genes in Trypanosoma cruzi-a unicellular eukaryotic pathogen responsible for causing the debilitating human disease Chagas disease-has largely remained uncharted due to the previous incompleteness of the genome assembly. By utilizing advanced genomic techniques and improved assembly methods, the quality of genome assemblies has significantly improved, making these studies feasible. Here, we analyzed the genic content and distribution of tRNA genes in the nuclear genome of various strains compared with the genome organization of other related trypanosomatids. We found synteny in most of the tDNAs clusters between T. cruzi and Trypanosoma brucei, highlighting the significance of the genomic location of these Pol III-transcribed genes. A vast majority of the isoacceptor species are encoded by two genes, except for tDNASeC, which comprises a tandem of 11 copies in the core compartment associated with well-positioned nucleosomes. Finally, we describe a group of tRNA genes located at chromatin folding domain boundaries, potentially acting as chromatin insulators in T. cruzi.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12204681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144368787","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

New Genome Assemblies for Poeciliidae: A Foundation for Adaptation Studies. 新的水蛭科基因组组合：适应研究的基础。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf111

Kara Ryan, Rishi De-Kayne, Jeremy Davis, Lenin Arias-Rodriguez, Michael Tobler, Joanna L Kelley

引用次数: 0

The Role of Alternative Splicing in Marine-Freshwater Divergence in Threespine Stickleback. 选择性剪接在三刺棘鱼海洋-淡水分化中的作用。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf105

Carlos E Rodríguez-Ramírez, Catherine L Peichel

{"title":"The Role of Alternative Splicing in Marine-Freshwater Divergence in Threespine Stickleback.","authors":"Carlos E Rodríguez-Ramírez, Catherine L Peichel","doi":"10.1093/gbe/evaf105","DOIUrl":"10.1093/gbe/evaf105","url":null,"abstract":"Alternative splicing regulates which parts of a gene are kept in the messenger RNA and has long been appreciated as a mechanism to increase the diversity of the proteome within eukaryotic species. There is a growing body of evidence that alternative splicing might also play an important role in adaptive evolution. However, the relative contribution of differential alternative splicing (DS) to phenotypic evolution and adaptation is still unknown. In this study, we asked whether DS played a role in adaptation to divergent marine and freshwater habitats in threespine stickleback (Gasterosteus aculeatus). Using two published gill RNA-seq datasets, we identified differentially expressed and differentially spliced genes (DEGs and DSGs) between population pairs of marine-freshwater stickleback in the Northeast Pacific and tested whether they are preferentially found in regions of the genome involved in marine-freshwater divergence. We found over 100 DSGs, which were found more often than expected in peaks of genetic divergence and quantitative trait loci that underlie phenotypic divergence between ecotypes. DSGs and DEGs are similarly enriched in these regions. Among the different types of DS, mutually exclusive exon splicing is most strongly correlated with genetic divergence between ecotypes. Taken together, our results add support to the growing evidence that natural selection might have acted on DS and might have specifically played a role in the adaptive divergence of marine and freshwater sticklebacks. Our results also suggest that some types of DS events might contribute more than others to adaptation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157958","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

Exploiting Viral DNA Genomes to Explore the Dispersal History of African Swine Fever Genotype II Lineages in Europe. 利用病毒DNA基因组探索非洲猪瘟基因型ⅱ谱系在欧洲的传播历史。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2025-05-30 DOI: 10.1093/gbe/evaf102

Fabiana Gámbaro, Lynnette C Goatley, Thomas J Foster, Chandana Tennakoon, Graham L Freimanis, Steven Van Borm, Marius Masiulis, Paulius Bušauskas, Christopher L Netherton, Simon Dellicour

{"title":"Exploiting Viral DNA Genomes to Explore the Dispersal History of African Swine Fever Genotype II Lineages in Europe.","authors":"Fabiana Gámbaro, Lynnette C Goatley, Thomas J Foster, Chandana Tennakoon, Graham L Freimanis, Steven Van Borm, Marius Masiulis, Paulius Bušauskas, Christopher L Netherton, Simon Dellicour","doi":"10.1093/gbe/evaf102","DOIUrl":"10.1093/gbe/evaf102","url":null,"abstract":"African swine fever virus (ASFV) is a highly virulent DNA virus that causes African swine fever, a severe hemorrhagic disease affecting domestic and wild pigs, leading to significant animal health burdens and economic losses. Initially limited to the sub-Saharan African region, ASFV genotype II has spread globally and is now a major concern in Africa, Europe, Asia, the Pacific and, more recently, the Caribbean. In this study, we performed phylogenetic and phylogeographic analyses using newly sequenced ASFV genomes from Lithuania, combined with previously available complete genomes, to investigate the spatiotemporal dispersal dynamics of ASFV genotype II in Europe. Our analysis suggests that ASFV genotype II has not been recently imported to Europe from other regions; instead, the spread is largely driven by long-distance dispersal, followed by regional (within-country) circulation. The estimated dispersal metrics suggest that ASFV has a slower dispersion capacity compared to other pig-transmitted viruses and is associated with a notable degree of spatial structure. Despite these findings, significant uncertainty remains regarding certain ancestral locations, highlighting challenges related to applying phylodynamic methods to DNA viruses with low genetic variability. Nevertheless, in our study, we managed to implement a phylogeographic framework to investigate major patterns of ASFV dispersion in Europe and the contribution of international importations in the establishment of regional transmission chains. This framework could be further expanded as more genomes become available. Our study emphasizes the need for increased genomic surveillance to enlarge the ASFV genome database to support outbreak control.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 6","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247556","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

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