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Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)
Liu, Bing-Jian1,2,3; Li, Yu-Long1,3,4; Zhang, Bai-Dong1,3; Liu, Jin-Xian1,3,4
2020-01-14
发表期刊FRONTIERS IN MARINE SCIENCE
卷号6页码:11
通讯作者Liu, Bing-Jian(bjetbj@163.com) ; Liu, Jin-Xian(jinxianliu@gmail.com)
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.
关键词population genomics genetic diversity restriction site-associated DNA sequencing single-nucleotide polymorphism discovery local adaptation
DOI10.3389/fmars.2019.00782
收录类别SCI
语种英语
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 ; 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
WOS类目Environmental Sciences ; Marine & Freshwater Biology
WOS记录号WOS:000507976200001
出版者FRONTIERS MEDIA SA
引用统计
被引频次:1[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.qdio.ac.cn/handle/337002/164473
专题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, CAS Key Lab Marine Ecol & Environm Sci, Inst Oceanol, Qingdao, Peoples R China
2.Zhejiang Ocean Univ, Natl Engn Lab Marine Germplasm Resources Explorat, Zhoushan, Peoples R China
3.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China
4.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, 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;  中国科学院海洋大科学研究中心
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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.
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