-transparent.png){kind=logo}
The medaka draft genome and insights into vertebrate genome evolution. 2007
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.
Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, 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 determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 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 approximately 50 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.
Related Publications
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
December 2005,
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
December 2002,
Science (New York, N.Y.),
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
January 2005,
Genome biology,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
March 2008,
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
October 2019,
Ecology and evolution,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
June 2008,
Development, growth & differentiation,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
February 2018,
Nature genetics,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
May 2018,
Nature genetics,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
November 2018,
Nature genetics,
Masahiro Kasahara, and
Kiyoshi Naruse, and
Shin Sasaki, and
Yoichiro Nakatani, and
Wei Qu, and
Budrul Ahsan, and
Tomoyuki Yamada, and
Yukinobu Nagayasu, and
Koichiro Doi, and
Yasuhiro Kasai, and
Tomoko Jindo, and
Daisuke Kobayashi, and
Atsuko Shimada, and
Atsushi Toyoda, and
Yoko Kuroki, and
Asao Fujiyama, and
Takashi Sasaki, and
Atsushi Shimizu, and
Shuichi Asakawa, and
Nobuyoshi Shimizu, and
Shin-Ichi Hashimoto, and
Jun Yang, and
Yongjun Lee, and
Kouji Matsushima, and
Sumio Sugano, and
Mitsuru Sakaizumi, and
Takanori Narita, and
Kazuko Ohishi, and
Shinobu Haga, and
Fumiko Ohta, and
Hisayo Nomoto, and
Keiko Nogata, and
Tomomi Morishita, and
Tomoko Endo, and
Tadasu Shin-I, and
Hiroyuki Takeda, and
Shinichi Morishita, and
Yuji Kohara
February 2018,
Nature communications,
