Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)

doi:10.3389/fmars.2019.00782

CORC > 海洋研究所 > 中国科学院海洋研究所 > 海洋生态与环境科学重点实验室

	Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)
	Liu, Bing-Jian 2,3,4; Li, Yu-Long 1,2,4; Zhang, Bai-Dong 2,4; Liu, Jin-Xian 1,2,4
刊名	FRONTIERS IN MARINE SCIENCE
	2020-01-14
卷号	6 页码:11
关键词	population genomics genetic diversity restriction site-associated DNA sequencing single-nucleotide polymorphism discovery local adaptation
DOI	10.3389/fmars.2019.00782
通讯作者	Liu, Bing-Jian(bjetbj@163.com) ; Liu, Jin-Xian(jinxianliu@gmail.com)
英文摘要	The Japanese eel (Anguilla japonica) is a commercially important aquatic species in East Asia. The number of the Japanese eels has been dramatically declining over the last four decades, and it is now listed as an endangered species (International Union for Conservation of Nature [IUCN] 2014). To manage and conserve this endangered species, it is necessary to assess population genetic diversity, genetic structure, and identify regions of the genomes that are under selection. Here, we generated a catalog of novel single-nucleotide polymorphism (SNP) markers for the Japanese eel using restriction site-associated DNA (RAD) sequencing of 24 individuals from two geographic locations. The 73,557 identified SNPs were widely distributed across the draft genome of the Japanese eel. No genetic differentiation between the two populations was detected based on all loci or neutral loci. However, highly significant genetic differentiation was detected based on loci that appeared to be under selection. BLAST2GO annotations of the outlier SNPs yielded hits for 61 (72%) of 85 significant BLASTX matches. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified some of the putative targets of local selection, including genes in several important pathways such as calcium signaling pathway and intestinal immune network for IgA production. This SNP catalog will provide a valuable resource for future population genetic and genomic studies and allows for targeting specific genes and genomic regions under selection in the Japanese eel genome.
资助项目	National Natural Science Foundation of China (NSFC)[41676137] ; National Natural Science Foundation of China (NSFC)[41806156] ; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology[2017-2B05] ; Natural Science Foundation of Zhejiang Province[LY17C200010] ; Natural Science Foundation of Zhejiang Province[LY15D060004] ; Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes[2019J00048] ; Starting Research Fund from the Zhejiang Ocean University ; Open Foundation from Marine Sciences in the First-Class Subjects of Zhejiang Province
WOS研究方向	Environmental Sciences & Ecology ; Marine & Freshwater Biology
语种	英语
出版者	FRONTIERS MEDIA SA
WOS记录号	WOS:000507976200001
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/164472]
专题	海洋研究所_海洋生态与环境科学重点实验室
通讯作者	Liu, Bing-Jian; Liu, Jin-Xian
作者单位	1.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China 3.Zhejiang Ocean Univ, Natl Engn Lab Marine Germplasm Resources Explorat, Zhoushan, Peoples R China 4.Chinese Acad Sci, CAS Key Lab Marine Ecol & Environm Sci, Inst Oceanol, Qingdao, Peoples R China
推荐引用方式 GB/T 7714	Liu, Bing-Jian,Li, Yu-Long,Zhang, Bai-Dong,et al. Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)[J]. FRONTIERS IN MARINE SCIENCE,2020,6:11.
APA	Liu, Bing-Jian,Li, Yu-Long,Zhang, Bai-Dong,&Liu, Jin-Xian.(2020).Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica).FRONTIERS IN MARINE SCIENCE,6,11.
MLA	Liu, Bing-Jian,et al."Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)".FRONTIERS IN MARINE SCIENCE 6(2020):11.