IOCAS-IR  > 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-Jian1,2,3; Li, Yu-Long1,3,4; Zhang, Bai-Dong1,3; Liu, Jin-Xian1,3,4
2020-01-14
Source PublicationFRONTIERS IN MARINE SCIENCE
Volume6Pages:11
Corresponding AuthorLiu, Bing-Jian(bjetbj@163.com) ; Liu, Jin-Xian(jinxianliu@gmail.com)
AbstractThe 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.
Keywordpopulation genomics genetic diversity restriction site-associated DNA sequencing single-nucleotide polymorphism discovery local adaptation
DOI10.3389/fmars.2019.00782
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaEnvironmental Sciences & Ecology ; Marine & Freshwater Biology
WOS SubjectEnvironmental Sciences ; Marine & Freshwater Biology
WOS IDWOS:000507976200001
PublisherFRONTIERS MEDIA SA
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/164473
Collection海洋生态与环境科学重点实验室
Corresponding AuthorLiu, Bing-Jian; Liu, Jin-Xian
Affiliation1.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
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
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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