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A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment

文献类型：期刊论文

作者Wang, Aiyang1,2,3,5; Cheng, Jiao1,2,5; Xin, Qian3,4; Sha, Zhongli1,2,3,5; Hui, Min1,2,5
刊名JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM
出版日期2023-09-06
卷号103页码:8
ISSN号0025-3154
关键词genome survey hydrothermal vent microsatellite DNA mitogenome Shinkaicaris leurokolos
DOI10.1017/S0025315423000504
通讯作者Sha, Zhongli(shazl@qdio.ac.cn) ; Hui, Min(minhui@qdio.ac.cn)
英文摘要The alvinocaridid shrimp Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, is an evolutionarily important deep-sea species in hydrothermal vents of north-western Pacific. A genome survey of S. leurokolos was carried out in order to provide a foundation for its whole-genome sequencing. A total of 599 Gb high-quality sequence data were obtained in the study, representing approximately 118x coverage of the S. leurokolos genome. According to the 17-mer distribution frequency, the estimated genome size was 5.08 Gb, and its heterozygosity ratio and percentage of repeated sequences were 2.85 and 87.03%, respectively, showing a complex genome. The final scaffold assembly accounted for a total size of 9.53 Gb (32,796,062 scaffolds, N50 = 597 bp). Repetitive elements nearly constituted 45% of the nuclear genome, among which the most ubiquitous were long interspersed nuclear elements, DNA transposons and long-terminal repeat elements. A total of 12,121,553 genomic simple sequence repeats were identified, with the most frequent repeat motif being di-nucleotide (70.27%), followed by tri-nucleotide and tetra-nucleotide. From the genome survey sequences, the mitochondrial genome of S. leurokolos was also constructed and 71 single nucleotide polymorphisms were identified by comparison with previous published reference. This is the first report of de novo whole-genome sequencing and assembly of S. leurokolos. These newly developed genomic data contribute to a better understanding of genomic characteristics of shrimps from deep-sea chemosynthetic ecosystems, and provides valuable resources for further molecular marker development.
WOS关键词INSIGHTS ; ADAPTATION ; DECAPODA ; CARIDEA ; CRUSTACEA ; PROVIDES
资助项目The samples were collected by RV KEXUE. The authors wish to thank the crews for their help during collection of samples.
WOS研究方向Marine & Freshwater Biology
语种英语
出版者CAMBRIDGE UNIV PRESS
WOS记录号WOS:001062231000001
源URL[http://ir.qdio.ac.cn/handle/337002/182930]  
专题海洋研究所_海洋生物分类与系统演化实验室
海洋研究所_实验海洋生物学重点实验室
通讯作者Sha, Zhongli; Hui, Min
作者单位1.Chinese Acad Sci, Inst Oceanol, Dept Marine Organism Taxon & Phylogeny, Qingdao 266071, Peoples R China
2.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
3.Univ Chinese Acad Sci, Shenyang 100049, Peoples R China
4.Qingdao Univ, Affiliated Hosp 2, Affiliated Qingdao Cent Hosp, Med Coll, Qingdao 266042, Peoples R China
5.Laoshan Lab, Qingdao 266237, Peoples R China
推荐引用方式
GB/T 7714		 Wang, Aiyang,Cheng, Jiao,Xin, Qian,et al. A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment[J]. JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM,2023,103:8.
APA Wang, Aiyang,Cheng, Jiao,Xin, Qian,Sha, Zhongli,&Hui, Min.(2023).A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment.JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM,103,8.
MLA Wang, Aiyang,et al."A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment".JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM 103(2023):8.

入库方式： OAI收割

来源：海洋研究所

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