Genome Biology and Evolution最新文献_第2页

Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography. 微生物组地理种群结构 (mGPS) 可检测微观地理。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae209

Yali Zhang, Leo McCarthy, Emil Ruff, Eran Elhaik

{"title":"Microbiome Geographic Population Structure (mGPS) Detects Fine-Scale Geography.","authors":"Yali Zhang, Leo McCarthy, Emil Ruff, Eran Elhaik","doi":"10.1093/gbe/evae209","DOIUrl":"10.1093/gbe/evae209","url":null,"abstract":"Over the past decade, sequencing data generated by large microbiome projects showed that taxa exhibit patchy geographical distribution, raising questions about the geospatial dynamics that shape natural microbiomes and the spread of antimicrobial resistance genes. Answering these questions requires distinguishing between local and nonlocal microorganisms and identifying the source sites for the latter. Predicting the source sites and migration routes of microbiota has been envisioned for decades but was hampered by the lack of data, tools, and understanding of the processes governing biodiversity. State-of-the-art biogeographical tools suffer from low resolution and cannot predict biogeographical patterns at a scale relevant to ecological, medical, or epidemiological applications. Analyzing urban, soil, and marine microorganisms, we found that some taxa exhibit regional-specific composition and abundance, suggesting they can be used as biogeographical biomarkers. We developed the microbiome geographic population structure, a machine learning-based tool that utilizes microbial relative sequence abundances to yield a fine-scale source site for microorganisms. Microbiome geographic population structure predicted the source city for 92% of the samples and the within-city source for 82% of the samples, though they were often only a few hundred meters apart. Microbiome geographic population structure also predicted soil and marine sampling sites for 86% and 74% of the samples, respectively. We demonstrated that microbiome geographic population structure differentiated local from nonlocal microorganisms and used it to trace the global spread of antimicrobial resistance genes. Microbiome geographic population structure's ability to localize samples to their water body, country, city, and transit stations opens new possibilities in tracing microbiomes and has applications in forensics, medicine, and epidemiology.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expansion of MHC-IIB Has Constrained the Evolution of MHC-IIA in Passerines. MHC-IIB 的扩展限制了鸟类中 MHC-IIA 的进化。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae236

Iris Liesbeth Ruesink-Bueno, Anna Drews, Emily Amelia O'Connor, Helena Westerdahl

{"title":"Expansion of MHC-IIB Has Constrained the Evolution of MHC-IIA in Passerines.","authors":"Iris Liesbeth Ruesink-Bueno, Anna Drews, Emily Amelia O'Connor, Helena Westerdahl","doi":"10.1093/gbe/evae236","DOIUrl":"10.1093/gbe/evae236","url":null,"abstract":"The major histocompatibility complex (MHC) is central in adaptive immunity, with the highly polymorphic MHC genes encoding antigen-presenting molecules. Two MHC class II (MHC-II) loci, DA1 and DA2, predate the radiation of extant birds and persist throughout much of the avian phylogeny. Within each locus, the MHC-II molecules are encoded by A-genes (DAA) and B-genes (DAB), which are arranged in A-B dyads. However, in passerines (order Passeriformes), the DA2 locus has been lost, and the ancestral A-B dyad at the DA1 locus has been replaced by a putatively single A-gene (DAA1) and an array of highly polymorphic B-genes (DAB1). In this study, we genotyped the DAA1 gene of 15 passerine species and confirmed that passerines possess just one copy of DAA1. We then compared selection patterns in DAA1 between passerines and nonpasserines and found that exon 2, which encodes the antigen-presenting domain, has been subject to weaker positive selection and stronger negative selection in passerines compared with nonpasserines. Additional comparisons showed that the patterns of selection in the passerine DAA1 gene are unlikely to be related to the loss of the DA2 locus. Instead, our findings suggest that the expansion of DAB1 (MHC-IIB) has imposed an evolutionary constraint on the passerine DAA1 (MHC-IIA) gene. We speculate that this constraint may be the result of each DAA1 chain forming heterodimers with many different DAB1 chains.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus. 曲霉次生代谢物基因簇的基因组定位偏差及其与组蛋白修饰的关联。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae228

Xin Zhang, Iseult Leahy, Jérȏme Collemare, Michael F Seidl

{"title":"Genomic Localization Bias of Secondary Metabolite Gene Clusters and Association with Histone Modifications in Aspergillus.","authors":"Xin Zhang, Iseult Leahy, Jérȏme Collemare, Michael F Seidl","doi":"10.1093/gbe/evae228","DOIUrl":"10.1093/gbe/evae228","url":null,"abstract":"Fungi are well-known producers of bioactive secondary metabolites (SMs), which have been exploited for decades by humankind for various medical applications like therapeutics and antibiotics. SMs are synthesized by biosynthetic gene clusters (BGCs)-physically co-localized and co-regulated genes. Because BGCs are often regulated by histone post-translational modifications (PTMs), it was suggested that their chromosomal location is important for their expression. Studies in a few fungal species indicated an enrichment of BGCs in sub-telomeric regions; however, there is no evidence that BGCs with distinct genomic localization are regulated by different histone PTMs. Here, we used 174 Aspergillus species covering 22 sections to determine the correlation between BGC genomic localization, gene expression, and histone PTMs. We found a high abundance and diversity of SM backbone genes across the Aspergillus genus, with notable unique genes within sections. Being unique or conserved in many species, BGCs showed a strong bias for being localized in low-synteny regions, regardless of their position in chromosomes. Using chromosome-level assemblies, we also confirmed a significantly biased localization in sub-telomeric regions. Notably, SM backbone genes in sub-telomeric regions and about half of those in low-synteny regions exhibit higher gene expression variability, likely due to the similar higher variability in H3K4me3 and H3K36me3 histone PTMs; while variations in histone H3 acetylation and H3K9me3 are not correlated to genomic localization and expression variation, as analyzed in two Aspergillus species. Expression variability across four Aspergillus species further supports that BGCs tend to be located in low-synteny regions and that regulation of expression in those regions likely involves different histone PTMs than the most commonly studied modifications.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499148","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 Evolution of Gene Expression Plasticity During Adaptation to Salt in Chlamydomonas reinhardtii. 莱茵衣藻在适应盐分过程中基因表达可塑性的演变。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae214

Yeshoda Y Harry-Paul, Josianne Lachapelle, Rob W Ness

{"title":"The Evolution of Gene Expression Plasticity During Adaptation to Salt in Chlamydomonas reinhardtii.","authors":"Yeshoda Y Harry-Paul, Josianne Lachapelle, Rob W Ness","doi":"10.1093/gbe/evae214","DOIUrl":"10.1093/gbe/evae214","url":null,"abstract":"When environmental change is rapid or unpredictable, phenotypic plasticity can facilitate adaptation to new or stressful environments to promote population persistence long enough for adaptive evolution to occur. However, the underlying genetic mechanisms that contribute to plasticity and its role in adaptive evolution are generally unknown. Two main opposing hypotheses dominate-genetic compensation and genetic assimilation. Here, we predominantly find evidence for genetic compensation over assimilation in adapting the freshwater algae Chlamydomonas reinhardtii to 36 g/L salt environments over 500 generations. More canalized genes in the high-salt (HS) lines displayed a pattern of genetic compensation (63%) fixing near or at the ancestral native expression level, rather than genetic assimilation of the salt-induced level, suggesting that compensation was more common during adaptation to salt. Network analysis revealed an enrichment of genes involved in energy production and salt-resistance processes in HS lines, while an increase in DNA repair mechanisms was seen in ancestral strains. In addition, whole-transcriptome similarity among ancestral and HS lines displayed the evolution of a similar plastic response to salt conditions in independently reared HS lines. We also found more cis-acting regions in the HS lines; however, the expression patterns of most genes did not mimic that of their inherited sequence. Thus, the expression changes induced via plasticity offer temporary relief, but downstream changes are required for a sustainable solution during the evolutionary process.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389919","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

LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins. LukProt：真核生物预测蛋白质数据库，用于研究动物起源。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae231

Łukasz F Sobala

{"title":"LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.","authors":"Łukasz F Sobala","doi":"10.1093/gbe/evae231","DOIUrl":"10.1093/gbe/evae231","url":null,"abstract":"The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463297","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

Chromosomal-level genome assembly of the Antarctic sea urchin Sterechinus neumayeri, a model for Antarctic invertebrate biology. 南极无脊椎动物生物学模型--南极海胆 Sterechinus neumayeri 的染色体级基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-30 DOI: 10.1093/gbe/evae237

Jacob F Warner, Ryan R Range, Jennifer Fenner, Cheikouna Ka, Damien S Waits, Kristen Boddy, Kyle T David, Andrew R Mahon, Kenneth Halanych

引用次数: 0

Genomes of Microtus rodents highlight the importance of olfactory and immune systems in their fast radiation. 微型啮齿动物的基因组突显了嗅觉和免疫系统在其快速辐射中的重要性。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-24 DOI: 10.1093/gbe/evae233

Alexandre Gouy, Xuejing Wang, Adamantia Kapopoulou, Samuel Neuenschwander, Emanuel Schmid, Laurent Excoffier, Gerald Heckel

{"title":"Genomes of Microtus rodents highlight the importance of olfactory and immune systems in their fast radiation.","authors":"Alexandre Gouy, Xuejing Wang, Adamantia Kapopoulou, Samuel Neuenschwander, Emanuel Schmid, Laurent Excoffier, Gerald Heckel","doi":"10.1093/gbe/evae233","DOIUrl":"https://doi.org/10.1093/gbe/evae233","url":null,"abstract":"The characterization of genes and biological functions underlying functional diversification and the formation of species is a major goal of evolutionary biology. In this study, we investigated the fast radiation of Microtus voles, one of the most speciose group of mammals, which shows strong genetic divergence despite few readily observable morphological differences. We produced an annotated reference genome for the common vole, Microtus arvalis, and resequenced the genomes of 10 different species and evolutionary lineages spanning the Microtus speciation continuum. Our full genome sequences illustrate the recent and fast diversification of this group, and we identified genes in highly divergent genomic windows that have likely particular roles in their radiation. We found three biological functions enriched for highly divergent genes in most Microtus species and lineages: olfaction, immunity and metabolism. In particular, olfaction-related genes (mostly olfactory receptors and vomeronasal receptors) are fast evolving in all Microtus species indicating the exceptional importance of the olfactory system in the evolution of these rodents. Of note is e.g. the shared signature among vole species on Olfr1019 which has been associated with fear responses against predator odours in rodents. Our analyses provide a genome-wide basis for the further characterization of the ecological factors and processes of natural and sexual selection that have contributed to the fast radiation of Microtus voles.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution. 线粒体 tRNA 基因畸变在动物进化中频繁出现

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-22 DOI: 10.1093/gbe/evae232

Iuliia Ozerova, Jörg Fallmann, Mario Mörl, Matthias Bernt, Sonja J Prohaska, Peter F Stadler

{"title":"Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.","authors":"Iuliia Ozerova, Jörg Fallmann, Mario Mörl, Matthias Bernt, Sonja J Prohaska, Peter F Stadler","doi":"10.1093/gbe/evae232","DOIUrl":"https://doi.org/10.1093/gbe/evae232","url":null,"abstract":"Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mt-tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mt-tRNAs with a uniform workflow. Here, we report our results on the complete reannotation of all mitogenomes available in the RefSeq database by September 2022 using mitos2. Based on the individual cases of mt-tRNA variants reported throughout the literature, our data pinpoint the respective hotspots of change, i.e. Acanthocephala (Lophotrochozoa), Nematoda, Acariformes and Araneae (Arthropoda). Less dramatic deviations of mt-tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mt-tRNA clearly is a phenomenon that occurred independently many times, not limited to a small number of specific clades. The summary data here provide a starting point for systematic investigations into the detailed evolutionary processes of structural reduction and and loss of mt-tRNAs as well as a resource for further improvements of annotation workflows for mt-tRNA annotation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142499145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Chromosome-Scale and Annotated Reference Genome Assembly of Plecia longiforceps Duda, 1934 (Diptera: Bibionidae). Plecia longiforceps Duda, 1934 (Diptera: Bibionidae) 的染色体尺度和注释参考基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae205

Jonghwan Choi, Taemin Kang, Sun-Jae Park, Seunggwan Shin

{"title":"A Chromosome-Scale and Annotated Reference Genome Assembly of Plecia longiforceps Duda, 1934 (Diptera: Bibionidae).","authors":"Jonghwan Choi, Taemin Kang, Sun-Jae Park, Seunggwan Shin","doi":"10.1093/gbe/evae205","DOIUrl":"10.1093/gbe/evae205","url":null,"abstract":"Urbanization is a leading factor effecting global biodiversity, driving rapid evolutionary processes in the local biota. Species that adapt and proliferate in city environments can become pests, with human activities facilitating their dispersal and excessive outbreaks. Here we present the first genome data of Plecia longiforceps, a lovebug pest in Eastern Asia with intensive aggregations recently occurring in the Seoul Metropolitan Area of Korea. PacBio HiFi and ONT Pore-C sequencing data were used to construct a highly continuous assembly with a total size of 707 Mb and 8 major pseudochromosomes, its integrity supported by the N50 length of 98.1 Mb and 96.8% BUSCO completeness. Structural and functional annotation using transcriptome data and ab initio predictions revealed a high proportion (69.3%) of repeat sequences, and synteny analysis with Bibio marci showed high levels of genomic collinearity. The genome will serve as an essential resource for both population genomics and molecular research on lovebug dispersal and outbreaks, and also implement studies on the eco-evolutionary processes of insects in urbanizing habitats.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11474240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345128","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 Effect of the Presence and Absence of DNA Repair Genes on the Rate and Pattern of Mutation in Bacteria. DNA 修复基因的存在与否对细菌突变率和突变模式的影响。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-10-09 DOI: 10.1093/gbe/evae216

Georgios Kalogiannis, Adam Eyre-Walker

引用次数: 0