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 Q2 EVOLUTIONARY BIOLOGY

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

{"title":"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。","authors":"Jacob F Warner, Ryan R Range, Jennifer Fenner, Cheikouna Ka, Damien S Waits, Kristen Boddy, Kyle T David, Andrew R Mahon, Kenneth Halanych","doi":"10.1093/gbe/evae237","DOIUrl":null,"url":null,"abstract":"The Antarctic sea urchin Sterechinus neumayeri (Echinoida;Echinidae) is routinely used as a model organism for Antarctic biology. Here, we present a high-quality genome of S. neumayeri. This chromosomal-level assembly was generated using PacBio long-read sequencing and HiC chromatin conformation capture sequencing. This 885.3 Mb assembly exhibits high contiguity with a scaffold length N50 of 36.7Mb assembled into 20 chromosomal length scaffolds. These putative chromosomes exhibit a high degree of synteny compared to other sea urchin models. We used transcript evidence gene modeling combined with sequence homology to identify 21,638 gene models that capture 97.4% of BUSCO orthologs. Among these, we were able to identify and annotate conserved developmental gene regulatory network orthologs, positioning S. neumayeri as a tractable model for comparative studies on evolution and development.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2000,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Chromosomal-level genome assembly of the Antarctic sea urchin Sterechinus neumayeri, a model for Antarctic invertebrate biology.\",\"authors\":\"Jacob F Warner, Ryan R Range, Jennifer Fenner, Cheikouna Ka, Damien S Waits, Kristen Boddy, Kyle T David, Andrew R Mahon, Kenneth Halanych\",\"doi\":\"10.1093/gbe/evae237\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The Antarctic sea urchin Sterechinus neumayeri (Echinoida;Echinidae) is routinely used as a model organism for Antarctic biology. Here, we present a high-quality genome of S. neumayeri. This chromosomal-level assembly was generated using PacBio long-read sequencing and HiC chromatin conformation capture sequencing. This 885.3 Mb assembly exhibits high contiguity with a scaffold length N50 of 36.7Mb assembled into 20 chromosomal length scaffolds. These putative chromosomes exhibit a high degree of synteny compared to other sea urchin models. We used transcript evidence gene modeling combined with sequence homology to identify 21,638 gene models that capture 97.4% of BUSCO orthologs. Among these, we were able to identify and annotate conserved developmental gene regulatory network orthologs, positioning S. neumayeri as a tractable model for comparative studies on evolution and development.\",\"PeriodicalId\":12779,\"journal\":{\"name\":\"Genome Biology and Evolution\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.2000,\"publicationDate\":\"2024-10-30\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gbe/evae237\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gbe/evae237","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

南极海胆 Sterechinus neumayeri（棘皮动物门；棘皮动物科）通常被用作南极生物学的模式生物。在这里，我们展示了 S. neumayeri 的高质量基因组。这个染色体级的基因组是通过 PacBio 长线程测序和 HiC 染色质构象捕获测序生成的。这个 885.3 Mb 的基因组具有很高的连续性，其支架长度 N50 为 36.7 Mb，组装成 20 个染色体长度的支架。与其他海胆模型相比，这些假定染色体表现出高度的同源性。我们利用转录本证据基因建模与序列同源性相结合的方法，确定了 21,638 个基因模型，这些模型捕获了 97.4% 的 BUSCO 同源物。其中，我们能够识别并注释出保守的发育基因调控网络直向同源物，从而将 S. neumayeri 定位为进化和发育比较研究的可操作模型。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

Chromosomal-level genome assembly of the Antarctic sea urchin Sterechinus neumayeri, a model for Antarctic invertebrate biology.

The Antarctic sea urchin Sterechinus neumayeri (Echinoida;Echinidae) is routinely used as a model organism for Antarctic biology. Here, we present a high-quality genome of S. neumayeri. This chromosomal-level assembly was generated using PacBio long-read sequencing and HiC chromatin conformation capture sequencing. This 885.3 Mb assembly exhibits high contiguity with a scaffold length N50 of 36.7Mb assembled into 20 chromosomal length scaffolds. These putative chromosomes exhibit a high degree of synteny compared to other sea urchin models. We used transcript evidence gene modeling combined with sequence homology to identify 21,638 gene models that capture 97.4% of BUSCO orthologs. Among these, we were able to identify and annotate conserved developmental gene regulatory network orthologs, positioning S. neumayeri as a tractable model for comparative studies on evolution and development.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY

CiteScore

5.80

自引率

6.10%

发文量

169

审稿时长

1 months

期刊介绍： About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.