The medaka draft genome and insights into vertebrate genome evolution

Masahiro Kasahara, Kiyoshi Naruse, Shin Sasaki, Yoichiro Nakatani, Wei Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, Koichiro Doi, Yasuhiro Kasai, Tomoko Jindo, Daisuke Kobayashi, Atsuko Shimada, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi ShimizuShin Ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Shinichi Morishita, Yuji Kohara

Research output: Contribution to journalArticle

654 Citations (Scopus)

Abstract

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 ∼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 ∼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.

Original languageEnglish
Pages (from-to)714-719
Number of pages6
JournalNature
Volume447
Issue number7145
DOIs
Publication statusPublished - 2007 Jun 7

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Oryzias
Vertebrates
Genome
Tetraodontiformes
Single Nucleotide Polymorphism
Zebrafish
Fresh Water
Sex Determination Processes
Ecotoxicology
Genes
Far East
Karyotype
Population
Ovum
Ecosystem
Carcinogenesis
Fishes
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan, B., ... Kohara, Y. (2007). The medaka draft genome and insights into vertebrate genome evolution. Nature, 447(7145), 714-719. https://doi.org/10.1038/nature05846

The medaka draft genome and insights into vertebrate genome evolution. / Kasahara, Masahiro; Naruse, Kiyoshi; Sasaki, Shin; Nakatani, Yoichiro; Qu, Wei; Ahsan, Budrul; Yamada, Tomoyuki; Nagayasu, Yukinobu; Doi, Koichiro; Kasai, Yasuhiro; Jindo, Tomoko; Kobayashi, Daisuke; Shimada, Atsuko; Toyoda, Atsushi; Kuroki, Yoko; Fujiyama, Asao; Sasaki, Takashi; Shimizu, Atsushi; Asakawa, Shuichi; Shimizu, Nobuyoshi; Hashimoto, Shin Ichi; Yang, Jun; Lee, Yongjun; Matsushima, Kouji; Sugano, Sumio; Sakaizumi, Mitsuru; Narita, Takanori; Ohishi, Kazuko; Haga, Shinobu; Ohta, Fumiko; Nomoto, Hisayo; Nogata, Keiko; Morishita, Tomomi; Endo, Tomoko; Shin-I, Tadasu; Takeda, Hiroyuki; Morishita, Shinichi; Kohara, Yuji.

In: Nature, Vol. 447, No. 7145, 07.06.2007, p. 714-719.

Research output: Contribution to journalArticle

Kasahara, M, Naruse, K, Sasaki, S, Nakatani, Y, Qu, W, Ahsan, B, Yamada, T, Nagayasu, Y, Doi, K, Kasai, Y, Jindo, T, Kobayashi, D, Shimada, A, Toyoda, A, Kuroki, Y, Fujiyama, A, Sasaki, T, Shimizu, A, Asakawa, S, Shimizu, N, Hashimoto, SI, Yang, J, Lee, Y, Matsushima, K, Sugano, S, Sakaizumi, M, Narita, T, Ohishi, K, Haga, S, Ohta, F, Nomoto, H, Nogata, K, Morishita, T, Endo, T, Shin-I, T, Takeda, H, Morishita, S & Kohara, Y 2007, 'The medaka draft genome and insights into vertebrate genome evolution', Nature, vol. 447, no. 7145, pp. 714-719. https://doi.org/10.1038/nature05846
Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B et al. The medaka draft genome and insights into vertebrate genome evolution. Nature. 2007 Jun 7;447(7145):714-719. https://doi.org/10.1038/nature05846
Kasahara, Masahiro ; Naruse, Kiyoshi ; Sasaki, Shin ; Nakatani, Yoichiro ; Qu, Wei ; Ahsan, Budrul ; Yamada, Tomoyuki ; Nagayasu, Yukinobu ; Doi, Koichiro ; Kasai, Yasuhiro ; Jindo, Tomoko ; Kobayashi, Daisuke ; Shimada, Atsuko ; Toyoda, Atsushi ; Kuroki, Yoko ; Fujiyama, Asao ; Sasaki, Takashi ; Shimizu, Atsushi ; Asakawa, Shuichi ; Shimizu, Nobuyoshi ; Hashimoto, Shin Ichi ; Yang, Jun ; Lee, Yongjun ; Matsushima, Kouji ; Sugano, Sumio ; Sakaizumi, Mitsuru ; Narita, Takanori ; Ohishi, Kazuko ; Haga, Shinobu ; Ohta, Fumiko ; Nomoto, Hisayo ; Nogata, Keiko ; Morishita, Tomomi ; Endo, Tomoko ; Shin-I, Tadasu ; Takeda, Hiroyuki ; Morishita, Shinichi ; Kohara, Yuji. / The medaka draft genome and insights into vertebrate genome evolution. In: Nature. 2007 ; Vol. 447, No. 7145. pp. 714-719.
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