Genome sequence of the euryhaline Javafish Medaka, Oryzias javanicus: A small aquarium fish model for studies on adaptation to salinity

Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Olivier Bouchez, Cécile Donnadieu, Celia Barrachina, Laurent Journot, Mari Kawaguchi, Shigeki Yasumasu, Satoshi Ansai, Kiyoshi Naruse, Koji Inoue, Chuya Shinzato, Manfred Schartl, Yann Guiguen, Amaury Herpin

研究成果: Article査読

13 被引用数 (Scopus)


The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.

ジャーナルG3: Genes, Genomes, Genetics
出版ステータスPublished - 2020 3月 1

ASJC Scopus subject areas

  • 分子生物学
  • 遺伝学
  • 遺伝学(臨床)


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