Nature 447, 714-719 (7 June 2007) | doi:10.1038/nature05846; Received 10 November 2006; Accepted 11 April 2007

The medaka draft genome and insights into vertebrate genome evolution

Masahiro Kasahara1,10, Kiyoshi Naruse2,10, Shin Sasaki1,10, Yoichiro Nakatani1,10, Wei Qu1, Budrul Ahsan1, Tomoyuki Yamada1, Yukinobu Nagayasu1, Koichiro Doi1, Yasuhiro Kasai1, Tomoko Jindo2, Daisuke Kobayashi2, Atsuko Shimada2, Atsushi Toyoda3, Yoko Kuroki3, Asao Fujiyama3,4, Takashi Sasaki5, Atsushi Shimizu5, Shuichi Asakawa5, Nobuyoshi Shimizu5, Shin-ichi Hashimoto6, Jun Yang6, Yongjun Lee6, Kouji Matsushima6, Sumio Sugano7, Mitsuru Sakaizumi8, Takanori Narita2,9, Kazuko Ohishi9, Shinobu Haga9, Fumiko Ohta9, Hisayo Nomoto9, Keiko Nogata9, Tomomi Morishita9, Tomoko Endo9, Tadasu Shin-I9, Hiroyuki Takeda2, Shinichi Morishita1 & Yuji Kohara9

  1. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
  2. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
  3. RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
  4. National Institute of Informatics, Tokyo 101-8430, Japan
  5. Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
  6. Department of Molecular Preventive Medicine, School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
  7. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
  8. Department of Environmental Science, Faculty of Science, Niigata University, Niigata 950-2181, Japan
  9. Center for Genetic Resource Information, National Institute of Genetics, Mishima 411-8540, Japan
  10. These authors contributed equally to this work.

Correspondence to: Hiroyuki Takeda2Shinichi Morishita1Yuji Kohara9 Correspondence and requests for materials should be addressed to Y.Kohara (Email: ykohara@lab.nig.ac.jp), S.M. (Email: moris@cb.k.u-tokyo.ac.jp) and H.T. (Email: htakeda@biol.s.u-tokyo.ac.jp).

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats1. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published2, 3, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination4, 5, 6 and developmental genetics7. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approx2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approx50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.


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