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About the National Bio Resource Project Medaka Genome Project
Medaka genome

The medaka genome shown in this page was decoded by whole-genome shotgun sequencing of the Japanese medaka (Oryzias latipes) genomic DNA under "Genome Analyses", a subproject of the National Bio Resource Project by the Ministry of Education, Culture, Sports, Sciences and Technology in fiscal year 2002.

The medaka inbred strain, Hd-rR*, used in the analyses was a kind gift from Dr. Yuji Ishikawa of the National Institute of Radiological Sciences. The genomic DNA from this strain was prepared by Dr. Hiroyuki Takeda of the University of Tokyo.

Genome analyses were conducted by the National Institute of Genetics and Riken (Institute of Physical and Chemical Research).

The decoded genome was obtained by one million sequencing and 726 Mbp reads. This size is considered to be 0.9x sequence coverage of the whole medaka genome.

Hd-rR strain

*Hd-rR was established by Dr. Yasuko Hyodo-Taguchi (1990) of the National Institute of Radiological Sciences by inbreeding the original strain d-rR, which was established by Dr. Tokio Yamamoto (1953) of the Nagoya University. In both strains, the body of the male is orange-red and that of the female is white. Therefore, their genetic sex can be identified based on their body color from the hatching stage. They are considered to have originated from a medaka population in Southern Japan (Sakaizumi et al.,1983)

d-rR strain (upper, female; lower, male), photographing by Yoko Yamamoto


  • Hyodo-Taguchi, Y. (1990): Inbred strains of the medaka, Oryzias latipes. Fish Biol. J. Medaka 8: 11-14.

  • Sakaizumi, M., Moriwaki, K. and Egami, N. (1983): Allozymic variation and regional differentiation in wild populations of the fish Oryzias latipes. Copeia 1983: 311-318.

  • Yamamoto, T. (1953): Artificially induced sex-reversal in genotypic males of the medaka (Oryzias latipes). J. Exp. Zool. 123: 571-594.

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