马来西亚马鹿(Tor tambroides)基因组组装初稿及数据分析

Q1 Agricultural and Biological Sciences
Melinda Mei Lin Lau , Leonard Whye Kit Lim , Hung Hui Chung , Han Ming Gan
{"title":"马来西亚马鹿(Tor tambroides)基因组组装初稿及数据分析","authors":"Melinda Mei Lin Lau ,&nbsp;Leonard Whye Kit Lim ,&nbsp;Hung Hui Chung ,&nbsp;Han Ming Gan","doi":"10.1016/j.aaf.2022.05.002","DOIUrl":null,"url":null,"abstract":"<div><p>The Malaysian mahseer (<em>Tor tambroides</em>), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of <em>T. tambroides</em> with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.</p></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)\",\"authors\":\"Melinda Mei Lin Lau ,&nbsp;Leonard Whye Kit Lim ,&nbsp;Hung Hui Chung ,&nbsp;Han Ming Gan\",\"doi\":\"10.1016/j.aaf.2022.05.002\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>The Malaysian mahseer (<em>Tor tambroides</em>), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of <em>T. tambroides</em> with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.</p></div>\",\"PeriodicalId\":36894,\"journal\":{\"name\":\"Aquaculture and Fisheries\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2023-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Aquaculture and Fisheries\",\"FirstCategoryId\":\"1091\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2468550X22000818\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Aquaculture and Fisheries","FirstCategoryId":"1091","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2468550X22000818","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0

摘要

马来西亚马哈塞尔鱼(Tor tambroides)是世界上最珍贵的淡水鱼之一,主要供人类食用。到目前为止,该物种的有丝分裂基因组数据是可用的,但基因组信息仍然缺乏。我们首次在Illumina和Nanopore平台上对成鱼的全基因组进行了测序。杂交基因组组装从44726个重叠群中获得了1.23Gb的基因组序列,发现长度为44kb N50,BUSCO基因组完整性为87.6%。在基因组中检测和鉴定了四种类型的SSR,其AT丰度高于GC。预测的蛋白质序列已经在公共数据库中进行了功能注释,即GO、KEGG和COG。构建了一个最大似然系统发育树,包含52个放线翅目物种和一个作为外群的Sarcopterygii物种,首次深入了解了坦氏锥虫与其他鳍鱼的基于基因组的进化关系。这些数据对于促进种群基因组学、物种鉴定、形态变异和进化生物学的研究至关重要,这有助于保护该物种。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides)

The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.23 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 87.6%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 52 Actinopterygii species and one Sarcopterygii species as outgroup was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.

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
Aquaculture and Fisheries
Aquaculture and Fisheries Agricultural and Biological Sciences-Aquatic Science
CiteScore
7.50
自引率
0.00%
发文量
54
审稿时长
48 days
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信