The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology SCIE SCOPUS

Cited 4 time in WEB OF SCIENCE Cited 5 time in Scopus
Title
The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology
Author(s)
Lee, Bo-Young; Park, Jun Chul; Kim, Min-Sub; Choi, Beom-Soon; Kim, Duck-Hyun; Lim, Jong-Sung; Yum, Seungshic; Hwang, Un-Ki; Nah, Gyoung Ju; Lee, Jae-Seong
KIOST Author(s)
Yum, Seung Shic(염승식)
Publication Year
2020-05
Abstract
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.
ISSN
0025-326X
URI
https://sciwatch.kiost.ac.kr/handle/2020.kiost/38673
DOI
10.1016/j.marpolbul.2020.111118
Bibliographic Citation
MARINE POLLUTION BULLETIN, v.154, 2020
Publisher
PERGAMON-ELSEVIER SCIENCE LTD
Subject
GLUTATHIONE-S-TRANSFERASE; GENE-EXPRESSION; COPPER CHAPERONE; FISH; ZEBRAFISH; EVOLUTION; TOXICITY; CLASSIFICATION; IDENTIFICATION; ENZYMES
Keywords
Transposable elements; Glutathione S-transferases; Marine molecular ecotoxicology; Antioxidants
Type
Article
Language
English
Document Type
Article
Publisher
PERGAMON-ELSEVIER SCIENCE LTD
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