Institutional Repository of Key Laboratory of Marine Ecology & Environmental Sciences, CAS
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 |
DOI | 10.3389/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 | |
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 |
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. |
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