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 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 Shimizu, Shin-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

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.

Source: Nature
http://www.nature.com/nature/journal/v447/n7145/abs/nature05846.html

Posted by
Robert Karl Stonjek