Genome Biology and Evolution最新文献_第4页

Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae). 由 Euwallacea fornicatus (Eichhoff) 和 Euwallacea similis (Ferrari) 的基因组揭示的外来入侵单倍体伏甲的染色体结构重排（鞘翅目，瘤甲科，鞘翅目）。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae226

James R M Bickerstaff, Tom Walsh, Leon Court, Gunjan Pandey, Kylie Ireland, David Cousins, Valerie Caron, Thomas Wallenius, Adam Slipinski, Rahul Rane, Hermes E Escalona

{"title":"Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).","authors":"James R M Bickerstaff, Tom Walsh, Leon Court, Gunjan Pandey, Kylie Ireland, David Cousins, Valerie Caron, Thomas Wallenius, Adam Slipinski, Rahul Rane, Hermes E Escalona","doi":"10.1093/gbe/evae226","DOIUrl":"10.1093/gbe/evae226","url":null,"abstract":"Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny, and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed Euwallacea similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance, and management. Using a combination of long and short read sequencing platforms, we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome-level genomes for these species. Comparative macrosynteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542627/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463285","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

Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies. 同域和异域的森蝶物种 Z 染色体进化速度加快。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae227

Manuela López Villavicencio, Joséphine Ledamoisel, Riccardo Poloni, Céline Lopez-Roques, Vincent Debat, Violaine Llaurens

{"title":"Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies.","authors":"Manuela López Villavicencio, Joséphine Ledamoisel, Riccardo Poloni, Céline Lopez-Roques, Vincent Debat, Violaine Llaurens","doi":"10.1093/gbe/evae227","DOIUrl":"10.1093/gbe/evae227","url":null,"abstract":"Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome vs. autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in prezygotic and postzygotic isolation mechanisms.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11562113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463296","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

Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict. 真核生物基因组结构的多样性可能是对遗传冲突的回应。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae239

Elinor G Sterner, Auden Cote-L'Heureux, Xyrus X Maurer-Alcalá, Laura A Katz

引用次数: 0

AncestryPainter 2.0: Visualizing Ancestry Composition and Admixture History Graph. AncestryPainter 2.0：可视化祖先构成和混血历史图表。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae249

Shuanghui Chen, Chang Lei, Xiaohan Zhao, Yuwen Pan, Dongsheng Lu, Shuhua Xu

{"title":"AncestryPainter 2.0: Visualizing Ancestry Composition and Admixture History Graph.","authors":"Shuanghui Chen, Chang Lei, Xiaohan Zhao, Yuwen Pan, Dongsheng Lu, Shuhua Xu","doi":"10.1093/gbe/evae249","DOIUrl":"10.1093/gbe/evae249","url":null,"abstract":"The earlier version of AncestryPainter is a Perl program that displays the ancestry composition of numerous individuals using a rounded graph. Motivated by the requests of users in practical applications, we updated AncestryPainter to version 2.0 by coding in an R package and improving the layout, providing more options and compatible statistical functions for graphing. Apart from improving visualization functions per se in this update, we added an extra graphing module to visualize genetic distance through radial bars of varying lengths surrounding a core. Notably, AncestryPainter 2.0 allows for multiple pie charts at the center of the graph to display the ancestry composition of more than one target population and implements a method admixture history graph to infer the admixture sequence of multiple ancestry populations. We validated the six admixture history graph metrics using both simulated and real data and implemented a Pearson coefficient-based metric with the best performance in AncestryPainter 2.0. Furthermore, a statistical module was implemented to merge ancestry proportion matrices. AncestryPainter 2.0 is freely available at https://github.com/Shuhua-Group/AncestryPainterV2 and https://pog.fudan.edu.cn/#/Software.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638642","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

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 : 2024-11-01 DOI: 10.1093/gbe/evae233

Alexandre Gouy, Xuejing Wang, Adamandia 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, Adamandia Kapopoulou, Samuel Neuenschwander, Emanuel Schmid, Laurent Excoffier, Gerald Heckel","doi":"10.1093/gbe/evae233","DOIUrl":"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 odors 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":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579656/pdf/","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":"OA","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 : 2024-11-01 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":"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 mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial 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 mitochondrial 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 mitochondrial tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mitochondrial 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 loss of mitochondrial tRNAs as well as a resource for further improvements of annotation workflows for mitochondrial tRNA annotation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11571959/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation. 单细胞顺式调控元件的特征说明了细胞分化的意义。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae241

Ying-Ying Ren, Zhen Liu

{"title":"Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation.","authors":"Ying-Ying Ren, Zhen Liu","doi":"10.1093/gbe/evae241","DOIUrl":"10.1093/gbe/evae241","url":null,"abstract":"Cis-regulatory elements govern the specific patterns and dynamics of gene expression in cells during development, which are the fundamental mechanisms behind cell differentiation. However, the genomic characteristics of single-cell cis-regulatory elements closely linked to cell differentiation during development remain unclear. To explore this, we systematically analyzed ∼250,000 putative single-cell cis-regulatory elements obtained from snATAC-seq analysis of the developing mouse cerebellum. We found that over 80% of these single-cell cis-regulatory elements show pleiotropic effects, being active in 2 or more cell types. The pleiotropic degrees of proximal and distal single-cell cis-regulatory elements are positively correlated with the density and diversity of transcription factor binding motifs and GC content. There is a negative correlation between the pleiotropic degrees of single-cell cis-regulatory elements and their distances to the nearest transcription start sites, and proximal single-cell cis-regulatory elements display higher relevance strengths than distal ones. Furthermore, both proximal and distal single-cell cis-regulatory elements related to cell differentiation exhibit enhanced sequence-level evolutionary conservation, increased density and diversity of transcription factor binding motifs, elevated GC content, and greater distances from their nearest genes. Together, our findings reveal the general genomic characteristics of putative single-cell cis-regulatory elements and provide insights into the genomic and evolutionary mechanisms by which single-cell cis-regulatory elements regulate cell differentiation during development.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11580522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142590223","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 Highly Repetitive Genome of Myxobolus rasmusseni, an Emerging Myxozoan Parasite of Fathead Minnows. 一种新出现的黑头鲦寄生虫--Myxobolus rasmusseni 的高度重复基因组。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae220

Viraj R Muthye, Aralia Leon Coria, Hongrui Liu, Cameron P Goater, Constance A M Finney, James D Wasmuth

{"title":"The Highly Repetitive Genome of Myxobolus rasmusseni, an Emerging Myxozoan Parasite of Fathead Minnows.","authors":"Viraj R Muthye, Aralia Leon Coria, Hongrui Liu, Cameron P Goater, Constance A M Finney, James D Wasmuth","doi":"10.1093/gbe/evae220","DOIUrl":"10.1093/gbe/evae220","url":null,"abstract":"Myxozoans are a monophyletic taxon of approximately 2,400 described species of parasites from the phylum Cnidaria. The recent focus on their negative impacts on fisheries, on their evolution from free-living ancestors, and on their emergence into new fish host populations has stressed the critical need for genomic resources for this parasitic group. Here, we describe the genome assembly and annotation of Myxobolus rasmusseni, an emerging parasite of fathead minnows in Alberta, Canada. The assembly is 174.6 Mb in size, 68% of which is made up of repetitive elements, making it one of the most repetitive animal genomes sequenced to date. Through comparisons to other myxozoans, we show that widespread gene loss, a known phenomenon of this group of parasites, is consistent with closely related species. Additionally, we assembled the M. rasmusseni mitochondrial genome, which is nearly twice the size of the typical animal mitochondrial genome yet contains only five of the canonical mitochondrial protein-coding genes and open reading frames not found in other myxozoans. These results add to our understanding of the gene- and genome-level diversity observed in myxozoans.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11557904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463300","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

Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei. 牙买加咖啡浆果螟（Hypothenemus hampei）种群的遗传变异。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae217

Mohammed Errbii, Ameka Myrie, Dwight Robinson, Eva Schultner, Lukas Schrader, Jan Oettler

引用次数: 0

Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community. 从复杂的微生物群落中组装出线虫 Rhabditoides Inermis 的基因组。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae230

Christian Rödelsperger, Waltraud Röseler, Marina Athanasouli, Sara Wighard, Matthias Herrmann, Ralf J Sommer

{"title":"Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.","authors":"Christian Rödelsperger, Waltraud Röseler, Marina Athanasouli, Sara Wighard, Matthias Herrmann, Ralf J Sommer","doi":"10.1093/gbe/evae230","DOIUrl":"10.1093/gbe/evae230","url":null,"abstract":"Free-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of specific traits or genes, a robust phylogenomic framework is indispensable. In the context of the nematode family Diplogastridae to which P. pacificus belongs, the identity of a sister group has long been debated. In this work, we generated a pseudochromosome level genome assembly of the nematode Rhabditoides inermis, which has previously been proposed as the sister taxon. The genome was assembled from a complex microbial community that is stably associated with R. inermis isolates and that consists of multiple bacteria and a fungus, which we identified as a strain of Vanrija albida. The R. inermis genome spans 173.5Mb that are largely assembled into five pseudochromosomes. This chromosomal configuration likely arose from two recent fusions of different Nigon elements. Phylogenomic analysis did not support a sister group relationship between R. inermis and diplogastrids, but rather supports a sister group relationship between the monophyletic Diplogastridae and a group of genera of Rhabditidae including C. elegans and R. inermis. Thus, our work addresses for the first time the long lasting question about the sister group to diplogastrids at the phylogenomic level and provides with the genomes of R. inermis and the associated fungus V. albida valuable resources for future genomic comparisons.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 11","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11542624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604408","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