Genome Biology and Evolution最新文献_第10页

Correction to: The Enigmatic Non-Transposon PIWI-interacting RNAs. Correction to：谜一般的非转座子 PIWI-interacting RNAs。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae202

引用次数: 0

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Oikopleura dioica 线粒体基因组的进化启示：测序挑战、RNA 编辑、基因转移到细胞核以及 tRNA 丢失。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae181

Yael Klirs, Maria Novosolov, Carmela Gissi, Rade Garić, Tal Pupko, Thomas Stach, Dorothée Huchon

{"title":"Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.","authors":"Yael Klirs, Maria Novosolov, Carmela Gissi, Rade Garić, Tal Pupko, Thomas Stach, Dorothée Huchon","doi":"10.1093/gbe/evae181","DOIUrl":"10.1093/gbe/evae181","url":null,"abstract":"Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004081","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

Assessing Mechanisms of Potential Local Adaptation Through a Seascape Genomic Approach in a Marine Gastropod, Littoraria flava. 通过海景基因组学方法评估海洋腹足类动物 Littoraria flava 的潜在本地适应机制。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae194

Thainá Cortez, Gabriel G Sonoda, Camilla A Santos, Sónia Cristina da Silva Andrade

{"title":"Assessing Mechanisms of Potential Local Adaptation Through a Seascape Genomic Approach in a Marine Gastropod, Littoraria flava.","authors":"Thainá Cortez, Gabriel G Sonoda, Camilla A Santos, Sónia Cristina da Silva Andrade","doi":"10.1093/gbe/evae194","DOIUrl":"10.1093/gbe/evae194","url":null,"abstract":"Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava, a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11413584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132539","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

Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila. 嗜仙人掌果蝇染色体长基因组揭示结构进化的基本模式

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae191

Kyle M Benowitz, Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin

{"title":"Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila.","authors":"Kyle M Benowitz, Carson W Allan, Coline C Jaworski, Michael J Sanderson, Fernando Diaz, Xingsen Chen, Luciano M Matzkin","doi":"10.1093/gbe/evae191","DOIUrl":"10.1093/gbe/evae191","url":null,"abstract":"A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11411373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125502","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 Diversity Illuminates the Environmental Adaptation of Drosophila suzukii. 基因组多样性揭示苏氏果蝇的环境适应性

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae195

Siyuan Feng, Samuel P DeGrey, Christelle Guédot, Sean D Schoville, John E Pool

{"title":"Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii.","authors":"Siyuan Feng, Samuel P DeGrey, Christelle Guédot, Sean D Schoville, John E Pool","doi":"10.1093/gbe/evae195","DOIUrl":"10.1093/gbe/evae195","url":null,"abstract":"Biological invasions carry substantial practical and scientific importance and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype-environment association pipeline for our dataset. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as the prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132540","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

Tracing Homopolymers in Oikopleura dioica's Mitogenome. 追踪 Oikopleura dioica 有丝分裂基因组中的同源多聚物。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae182

Nicolas Dierckxsens, Kosei Watanabe, Yongkai Tan, Aki Masunaga, Michael J Mansfield, Jiashun Miao, Nicholas M Luscombe, Charles Plessy

引用次数: 0

Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes. 关键氧感应基因的进化与鱼类耐缺氧能力有关。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae183

Courtney H Babin, Félix P Leiva, Wilco C E P Verberk, Bernard B Rees

{"title":"Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes.","authors":"Courtney H Babin, Félix P Leiva, Wilco C E P Verberk, Bernard B Rees","doi":"10.1093/gbe/evae183","DOIUrl":"10.1093/gbe/evae183","url":null,"abstract":"Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)-HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (Pcrit) of the corresponding species. Our results demonstrate that Pcrit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A, two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in Pcrit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008674","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

Correction to: Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. 更正：遗传和功能多样性有助于解释黄单胞菌属的致病性、弱致病性和共生生活方式。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-09-03 DOI: 10.1093/gbe/evae178

引用次数: 0

Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus. 胎生鳗鱼 Zoarces viviparus 染色体级基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-08-05 DOI: 10.1093/gbe/evae155

Nico Fuhrmann, Marie V Brasseur, Christina E Bakowski, Lars Podsiadlowski, Stefan Prost, Henrik Krehenwinkel, Christoph Mayer

{"title":"Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus.","authors":"Nico Fuhrmann, Marie V Brasseur, Christina E Bakowski, Lars Podsiadlowski, Stefan Prost, Henrik Krehenwinkel, Christoph Mayer","doi":"10.1093/gbe/evae155","DOIUrl":"10.1093/gbe/evae155","url":null,"abstract":"The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141626573","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

Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes. 海蛇光谱上不同的短波长光视蛋白基因的动态扩展和视网膜表达。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-08-05 DOI: 10.1093/gbe/evae150

Isaac H Rossetto, Alastair J Ludington, Bruno F Simões, Nguyen Van Cao, Kate L Sanders

{"title":"Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes.","authors":"Isaac H Rossetto, Alastair J Ludington, Bruno F Simões, Nguyen Van Cao, Kate L Sanders","doi":"10.1093/gbe/evae150","DOIUrl":"10.1093/gbe/evae150","url":null,"abstract":"The photopigment-encoding visual opsin genes that mediate color perception show great variation in copy number and adaptive function across vertebrates. An open question is how this variation has been shaped by the interaction of lineage-specific structural genomic architecture and ecological selection pressures. We contribute to this issue by investigating the expansion dynamics and expression of the duplicated Short-Wavelength-Sensitive-1 opsin (SWS1) in sea snakes (Elapidae). We generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, and 81 SWS1 exon sequences for sea snakes, and analyzed these alongside 16 existing genomes for sea snakes and their terrestrial relatives. Our analyses revealed multiple independent transitions in SWS1 copy number in the marine Hydrophis clade, with at least three lineages having multiple intact SWS1 genes: the previously studied Hydrophis cyanocinctus and at least two close relatives of this species; Hydrophis atriceps and Hydrophis fasciatus; and an individual Hydrophis curtus. In each lineage, gene copy divergence at a key spectral tuning site resulted in distinct UV and Violet/Blue-sensitive SWS1 subtypes. Both spectral variants were simultaneously expressed in the retinae of H. cyanocinctus and H. atriceps, providing the first evidence that these SWS1 expansions confer novel phenotypes. Finally, chromosome annotation for nine species revealed shared structural features in proximity to SWS1 regardless of copy number. If these features are associated with SWS1 duplication, expanded opsin complements could be more common in snakes than is currently recognized. Alternatively, selection pressures specific to aquatic environments could favor improved chromatic distinction in just some lineages.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579513","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