Genome Biology and Evolution最新文献

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 : 2024-11-07 DOI: 10.1093/gbe/evae239

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

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 : 2024-11-07 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 (CREs) 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 CREs (scCREs) closely linked to cell differentiation during development remain unclear. To explore this, we systematically analyzed ∼250,000 putative scCREs obtained from snATAC-seq analysis of the developing mouse cerebellum. We found that over 80% of these scCREs show pleiotropic effects, being active in two or more cell types. The pleiotropic degrees of proximal and distal scCREs are positively correlated with the density and diversity of transcription factor (TF) binding motifs and GC content. There is a negative correlation between the pleiotropic degrees of scCREs and their distances to the nearest TSSs, and proximal scCREs display higher relevance strengths than distal ones. Furthermore, both proximal and distal scCREs related to cell differentiation exhibit enhanced sequence-level evolutionary conservation, increased density and diversity of TF binding motifs, elevated GC content, and greater distances from their nearest genes. Together, our findings reveal the general genomic characteristics of putative scCREs and provide insights into the genomic and evolutionary mechanisms by which scCREs regulate cell differentiation during development.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comprehensive Review on Plant Cytochrome P450 Evolution: Copy Number, Diversity, and Motif Analysis from Chlorophyta to Dicotyledoneae. 植物细胞色素 P450 进化综述：从叶绿体到双子叶植物的拷贝数、多样性和动因分析。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-07 DOI: 10.1093/gbe/evae240

Yuanpeng Fang, Zheng Tai, Keyi Hu, Lingfeng Luo, Sanwei Yang, Mengmeng Liu, Xin Xie

{"title":"Comprehensive Review on Plant Cytochrome P450 Evolution: Copy Number, Diversity, and Motif Analysis from Chlorophyta to Dicotyledoneae.","authors":"Yuanpeng Fang, Zheng Tai, Keyi Hu, Lingfeng Luo, Sanwei Yang, Mengmeng Liu, Xin Xie","doi":"10.1093/gbe/evae240","DOIUrl":"10.1093/gbe/evae240","url":null,"abstract":"Cytochrome P450 enzymes (CYPs) are widely distributed among various plant groups and constitute approximately 1% of the total number of protein-coding genes. Extensive studies suggest that CYPs are involved in nearly all molecular processes that occur in plants. Over the past two decades, the identification of CYP genes has expanded rapidly, with more than 40,000 CYP genes and 819 CYP families being discovered. Copy number variation is a significant evolutionary characteristic of gene families, yet a systematic characterization of the copy evolution patterns in plant CYP gene families has been lacking, resulting in confusion and challenges in understanding CYP functions. To address these concerns, this review provides comprehensive statistics and analyses of the copy number and diversity of almost all plant CYP gene families, focusing on CYP evolution from Chlorophyta to Dicotyledoneae. Additionally, we examined the subfamily characteristics of certain CYP families with restricted copy changes and identify several CYP subfamilies that play pivotal roles in this event. Furthermore, we analyzed the structural conservation of CYPs across different taxa and compiled a comprehensive database to support plant CYP studies. Our analysis revealed differences in the six core conserved motifs of plant CYP proteins among various clans and plant taxa, while demonstrating similar conservation patterns for the ERR (Glutamic Acid-Arginine-Arginine) triad motifs. These findings will significantly facilitate the understanding of plant CYP gene evolution and metabolic diversity and serve as a valuable reference for researchers studying CYP enzymes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142590133","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

Chromosome-level genome assembly of the Australian rainforest tree Rhodamnia argentea (malletwood). 澳大利亚热带雨林树种红木（Rhodamnia argentea）的染色体级基因组组装。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-02 DOI: 10.1093/gbe/evae238

Stephanie H Chen, Ashley Jones, Patricia Lu-Irving, Jia-Yee S Yap, Marlien van der Merwe, Jason G Bragg, Richard J Edwards

{"title":"Chromosome-level genome assembly of the Australian rainforest tree Rhodamnia argentea (malletwood).","authors":"Stephanie H Chen, Ashley Jones, Patricia Lu-Irving, Jia-Yee S Yap, Marlien van der Merwe, Jason G Bragg, Richard J Edwards","doi":"10.1093/gbe/evae238","DOIUrl":"https://doi.org/10.1093/gbe/evae238","url":null,"abstract":"Myrtaceae are a large family of woody plants, including hundreds that are currently under threat from the global spread of a fungal pathogen, Austropuccinia psidii (G.Winter) Beenken, which causes myrtle rust. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp assembly anchored to 11 chromosomes (2n = 22). The R. argentea genome will inform conservation efforts for Myrtaceae species threatened by myrtle rust, against which it shows variable resistance. We observed contamination in the sequencing data and further investigation revealed an arthropod source. This study emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of a tree that faces conservation challenges, contributing to broader biodiversity initiatives.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142564292","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

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":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/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":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":"142463296","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

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":"https://doi.org/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":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":"142604408","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

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":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":"142463300","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

Comparative Genomics of the World's Smallest Mammals Reveals Links to Echolocation, Metabolism, and Body Size Plasticity. 世界上最小哺乳动物的比较基因组学揭示了回声定位、新陈代谢和体型可塑性之间的联系。

IF 3.2 2区生物学

Genome Biology and Evolution Pub Date : 2024-11-01 DOI: 10.1093/gbe/evae225

Marie-Laurence Cossette, Donald T Stewart, Aaron B A Shafer

{"title":"Comparative Genomics of the World's Smallest Mammals Reveals Links to Echolocation, Metabolism, and Body Size Plasticity.","authors":"Marie-Laurence Cossette, Donald T Stewart, Aaron B A Shafer","doi":"10.1093/gbe/evae225","DOIUrl":"10.1093/gbe/evae225","url":null,"abstract":"Originating 30 million years ago, shrews (Soricidae) have diversified into around 400 species worldwide. Shrews display a wide array of adaptations, with some species having developed distinctive traits such as echolocation, underwater diving, and venomous saliva. Accordingly, these tiny insectivores are ideal to study the genomic mechanisms of evolution and adaptation. We conducted a comparative genomic analysis of four shrew species and 16 other mammals to identify genomic variations unique to shrews. Using two existing shrew genomes and two de novo assemblies for the maritime (Sorex maritimensis) and smoky (Sorex fumeus) shrews, we identified mutations in conserved regions of the genomes, also known as accelerated regions, gene families that underwent significant expansion, and positively selected genes. Our analyses unveiled shrew-specific genomic variants in genes associated with the nervous, metabolic, and auditory systems, which can be linked to unique traits in shrews. Notably, genes suggested to be under convergent evolution in echolocating mammals exhibited accelerated regions in shrews, and pathways linked to putative body size plasticity were detected. These findings provide insight into the evolutionary mechanisms shaping shrew species, shedding light on their adaptation and divergence over time.","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/PMC11544316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463295","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