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

doi:10.1017/S0025315423000504

	A first genome survey sequencing of alvinocaridid shrimp Shinkaicaris leurokolos in deep-sea hydrothermal vent environment
	Wang, Aiyang1,2,3,4 ; Cheng, Jiao 1,2,3; Xin, Qian 4,5; Sha, Zhongli1,2,3,4 ; Hui, Min 1,2,3
	2023-09-06
发表期刊	JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM
ISSN	0025-3154
卷号	103 页码:8
通讯作者	Sha, Zhongli(shazl@qdio.ac.cn) ; Hui, Min(minhui@qdio.ac.cn)
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.
关键词	genome survey hydrothermal vent microsatellite DNA mitogenome Shinkaicaris leurokolos
DOI	10.1017/S0025315423000504
收录类别	SCI
语种	英语
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
WOS类目	Marine & Freshwater Biology
WOS记录号	WOS:001062231000001
出版者	CAMBRIDGE UNIV PRESS
WOS关键词	INSIGHTS ; ADAPTATION ; DECAPODA ; CARIDEA ; CRUSTACEA ; PROVIDES
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/182931
专题	海洋生物分类与系统演化实验室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.Laoshan Lab, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 4.Univ Chinese Acad Sci, Shenyang 100049, Peoples R China 5.Qingdao Univ, Affiliated Hosp 2, Affiliated Qingdao Cent Hosp, Med Coll, Qingdao 266042, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
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.