Chromosome-level assembly for the complex genome of land hermit crab Coenobita brevimanus.

IF 5.8 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Scientific Data Pub Date : 2024-11-02 DOI:10.1038/s41597-024-04031-3

Zhongkai Wang, Gang Wang, Haorong Li, Hui Jiang, Yishan Sun, Ge Han, Jinrui Ma, Qiuning Liu, Chen Zhang, Daizhen Zhang, Huabin Zhang, Yongxin Li, Boping Tang, Wen Wang

{"title":"Chromosome-level assembly for the complex genome of land hermit crab Coenobita brevimanus.","authors":"Zhongkai Wang, Gang Wang, Haorong Li, Hui Jiang, Yishan Sun, Ge Han, Jinrui Ma, Qiuning Liu, Chen Zhang, Daizhen Zhang, Huabin Zhang, Yongxin Li, Boping Tang, Wen Wang","doi":"10.1038/s41597-024-04031-3","DOIUrl":null,"url":null,"abstract":"<p><p>Land hermit crabs are a group of shell-carrying crabs that have evolved remarkable terrestrial adaptations in behavior, morphology, physiology, and biochemistry. However, the genetic mechanisms underlying these adaptations remain unclear. In addition, usually it is very difficult to get good genome assemblies for crustaceans. In this study, we managed to assemble the first chromosome-level genome for a land hermit crab (Coenobita brevimanus) with careful manual curation. The final assembly spans 4.74 Gb, with the contig N50 of 1.75 Mb and scaffold N50 of 42.95 Mb, encompassing 117 chromosomes that account for 96.54% of the genome. The evaluations including genome BUSCO (95.26%), Merqury qv (35.88) and the mapping ratio of pair-end short reads (99.48%) showed the high-continuity of C. brevimanus genome assembly, making it the genome with the highest quality in crustaceans with genome size bigger than 3 Gb. The availability of this chromosome-scale genome of crustaceans represents a valuable resource for the land hermit crab, which represents an independent water-to-land transition evolutionary event in the animal kingdom.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"11 1","pages":"1190"},"PeriodicalIF":5.8000,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11531507/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientific Data","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41597-024-04031-3","RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}

引用次数: 0

Abstract

Land hermit crabs are a group of shell-carrying crabs that have evolved remarkable terrestrial adaptations in behavior, morphology, physiology, and biochemistry. However, the genetic mechanisms underlying these adaptations remain unclear. In addition, usually it is very difficult to get good genome assemblies for crustaceans. In this study, we managed to assemble the first chromosome-level genome for a land hermit crab (Coenobita brevimanus) with careful manual curation. The final assembly spans 4.74 Gb, with the contig N50 of 1.75 Mb and scaffold N50 of 42.95 Mb, encompassing 117 chromosomes that account for 96.54% of the genome. The evaluations including genome BUSCO (95.26%), Merqury qv (35.88) and the mapping ratio of pair-end short reads (99.48%) showed the high-continuity of C. brevimanus genome assembly, making it the genome with the highest quality in crustaceans with genome size bigger than 3 Gb. The availability of this chromosome-scale genome of crustaceans represents a valuable resource for the land hermit crab, which represents an independent water-to-land transition evolutionary event in the animal kingdom.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

陆地寄居蟹Coenobita brevimanus复杂基因组的染色体组组装。

陆生寄居蟹是一类携带贝壳的蟹类，在行为、形态、生理和生化方面已经进化出显著的陆生适应性。然而，这些适应性背后的遗传机制仍不清楚。此外，甲壳类动物通常很难获得良好的基因组组装。在这项研究中，我们通过仔细的手工整理，成功地为陆地寄居蟹（Coenobita brevimanus）组装了第一个染色体组水平的基因组。最终组装的基因组跨度为 4.74 Gb，等位基因 N50 为 1.75 Mb，支架 N50 为 42.95 Mb，包含 117 条染色体，占基因组的 96.54%。包括基因组BUSCO（95.26%）、Merqury qv（35.88）和对端短读数的映射比（99.48%）在内的评估结果表明，C. brevimanus基因组组装具有很高的连续性，使其成为基因组大小大于3 Gb的甲壳类动物中质量最高的基因组。该染色体级甲壳类基因组的获得为陆地寄居蟹提供了宝贵的资源，代表了动物界一次独立的水陆过渡进化事件。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Scientific Data Social Sciences-Education

CiteScore

11.20

自引率

4.10%

发文量

689

审稿时长

16 weeks

期刊介绍： Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data. The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.