气候变化领域集成服务门户(CCPortal): The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology

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DOI	10.1016/j.marpolbul.2020.111118
	The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology
	Lee B.-Y.; Park J.C.; Kim M.-S.; Choi B.-S.; Kim D.-H.; Lim J.-S.; Yum S.; Hwang U.-K.; Nah G.J.; Lee J.-S.
发表日期	2020
ISSN	0025326X
卷号	154
英文摘要	The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate change effects in the ocean. In this study, we sequenced and assembled the genome of O. javanicus using the Oxford Nanopore technique and anchored the scaffolds to the 24 genetic linkage map of a sister species Oryzias melastigma. The assembled genome consisted of 773 scaffolds including 24 LG-based scaffolds, and the estimated genome length was 846.3 Mb (N50 = 19.3 Mb), containing 24,498 genes. As detoxification processes are crucial in aquatic organisms, antioxidant-related genes including glutathione S-transferases, superoxide dismutase, catalase, and glutathione peroxidase were identified in this study. In the genome of O. javanicus, a total of 21 GSTs, 4 SODs, 1 CAT, and 7 GPxs were identified and showed high similarities between sister species O. melastigma and Oryzias latipes. In addition, despite having 8 classes of cytosolic GSTs family, medaka showed no presence of GST pi and sigma classes, which are predominantly found in carp and salmon, but not in neoteleostei. This study adds another set to genome-library of Oryzias spp. and is a useful resource for better understanding of the molecular ecotoxicology. © 2020
英文关键词	Antioxidants; Glutathione S-transferases; Marine molecular ecotoxicology; Transposable elements
语种	英语
scopus关键词	Aquatic organisms; Climate change; Detoxification; Enzymes; Peptides; Scaffolds; Water pollution; Detoxification process; Ecotoxicological; Genome libraries; Global climate changes; Glutathione peroxidase; Glutathione S-transferases; Oryzias melastigma; Super oxide dismutase; Genes; catalase; glutathione peroxidase; glutathione transferase; molecular scaffold; superoxide dismutase; catalase; brackish water; climate change; climate effect; ecotoxicology; fish; genome; marine pollution; pollution effect; aquatic species; Article; carp; cytosol; detoxification; ecotoxicology; enzyme analysis; fish genetics; gene library; gene mapping; gene sequence; genetic linkage; male; marine environment; nonhuman; Oryzias; Oryzias javanicus; Oryzias latipes; Oryzias melastigma; protein family; salmonine; teleost; animal; ecotoxicology; genetics; genome; Oryzias; Cyprinidae; Neoteleostei; Oryzias; Oryzias javanicus; Oryzias latipes; Oryzias melastigma; Oryziinae; Animals; Aquatic Organisms; Catalase; Ecotoxicology; Genome; Oryzias
来源期刊	Marine Pollution Bulletin
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/149007
作者单位	Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea; Phyzen Genomics Institute, Seoul, 08787, South Korea; NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea; Risk Assessment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje, 53201, South Korea; Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon, 46083, South Korea
推荐引用方式 GB/T 7714	Lee B.-Y.,Park J.C.,Kim M.-S.,et al. The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology[J],2020,154.
APA	Lee B.-Y..,Park J.C..,Kim M.-S..,Choi B.-S..,Kim D.-H..,...&Lee J.-S..(2020).The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology.Marine Pollution Bulletin,154.
MLA	Lee B.-Y.,et al."The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology".Marine Pollution Bulletin 154(2020).