title: The medaka draft genome and insights into vertebrate genome evolution.
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 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.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kasahara
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Naruse
authors.forename: Shin
authors.initials: S
authors.lastname: Sasaki
authors.forename: Yoichiro
authors.initials: Y
authors.lastname: Nakatani
authors.forename: Wei
authors.initials: W
authors.lastname: Qu
authors.forename: Budrul
authors.initials: B
authors.lastname: Ahsan
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Yamada
authors.forename: Yukinobu
authors.initials: Y
authors.lastname: Nagayasu
authors.forename: Koichiro
authors.initials: K
authors.lastname: Doi
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Kasai
authors.forename: Tomoko
authors.initials: T
authors.lastname: Jindo
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kobayashi
authors.forename: Atsuko
authors.initials: A
authors.lastname: Shimada
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Takashi
authors.initials: T
authors.lastname: Sasaki
authors.forename: Atsushi
authors.initials: A
authors.lastname: Shimizu
authors.forename: Shuichi
authors.initials: S
authors.lastname: Asakawa
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Shimizu
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Hashimoto
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Lee
authors.forename: Kouji
authors.initials: K
authors.lastname: Matsushima
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Sakaizumi
authors.forename: Takanori
authors.initials: T
authors.lastname: Narita
authors.forename: Kazuko
authors.initials: K
authors.lastname: Ohishi
authors.forename: Shinobu
authors.initials: S
authors.lastname: Haga
authors.forename: Fumiko
authors.initials: F
authors.lastname: Ohta
authors.forename: Hisayo
authors.initials: H
authors.lastname: Nomoto
authors.forename: Keiko
authors.initials: K
authors.lastname: Nogata
authors.forename: Tomomi
authors.initials: T
authors.lastname: Morishita
authors.forename: Tomoko
authors.initials: T
authors.lastname: Endo
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Takeda
authors.forename: Shinichi
authors.initials: S
authors.lastname: Morishita
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kohara
mesh_terms: D000818:Animals; D002681:China; D002875:Chromosomes / Q000235:genetics; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics; D016678:Genome / Q000235:genetics*; D023281:Genomics; D006801:Humans; D007564:Japan; D009990:Oryzias / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013624:Taiwan; D013997:Time Factors
chemical_list: D029941:Fish Proteins