追踪 Oikopleura dioica 有丝分裂基因组中的同源多聚物。

IF 3.2 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Genome Biology and Evolution Pub Date : 2024-09-03 DOI:10.1093/gbe/evae182

Nicolas Dierckxsens, Kosei Watanabe, Yongkai Tan, Aki Masunaga, Michael J Mansfield, Jiashun Miao, Nicholas M Luscombe, Charles Plessy

{"title":"追踪 Oikopleura dioica 有丝分裂基因组中的同源多聚物。","authors":"Nicolas Dierckxsens, Kosei Watanabe, Yongkai Tan, Aki Masunaga, Michael J Mansfield, Jiashun Miao, Nicholas M Luscombe, Charles Plessy","doi":"10.1093/gbe/evae182","DOIUrl":null,"url":null,"abstract":"Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2000,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384890/pdf/","citationCount":"0","resultStr":"{\"title\":\"Tracing Homopolymers in Oikopleura dioica's Mitogenome.\",\"authors\":\"Nicolas Dierckxsens, Kosei Watanabe, Yongkai Tan, Aki Masunaga, Michael J Mansfield, Jiashun Miao, Nicholas M Luscombe, Charles Plessy\",\"doi\":\"10.1093/gbe/evae182\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.\",\"PeriodicalId\":12779,\"journal\":{\"name\":\"Genome Biology and Evolution\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.2000,\"publicationDate\":\"2024-09-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384890/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gbe/evae182\",\"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/evae182","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

Oikopleura dioica 是一种广泛分布于全球海洋水域的浮游鳞栉水母（Appendicularia class）。我们采用单分子 PacBio Hi-Fi 方法对从日本冲绳采集的一只雄性个体的基因组进行了测序，并用 NOVOLoci 进行了组装。有丝分裂基因组长 39,268 bp，其中有一个约 22,000 bp 的大型控制区。我们对蛋白 atp6、cob、cox1、cox2、cox3、nad1、nad4 和 nad5 进行了注释，还发现了一个与任何已知基因都不匹配的开放阅读框。这项研究标志着首次完整地组装了附肢动物的有丝分裂基因组，并揭示了A和T同源聚合体累计占其长度的近一半。该参考序列将成为环境 DNA 和系统发育研究的宝贵财富。

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

Tracing Homopolymers in Oikopleura dioica's Mitogenome.

Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4, and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.

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.