The medaka draft genome and insights into vertebrate genome evolution

By M. Kasahara, K. Naruse, Shin Sasaki, Yoichiro Nakatani, W. Qu, Budrul Ahsan, Tomoyuki Yamada, Yukinobu Nagayasu, K. Doi, Y. Kasai and 28 more. Nature, 2007

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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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/39e30ef192819f7c3b61d3f69d844e54a46da679

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Citations in the corpus

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. (2007, background): “To test if they are really remaining blocks of the gnathostome protochromosomes, their syntenies in the medaka genome (Kasahara et al. 2007) were investigated (for details, see the Supplemental Document).”
Genome duplication in amphibians and fish: an extended synthesis (2011, methodology): “Draft genome sequences are available for Fugu (or Takifugu Aparicio et al., 2002) and Medaka (Kasahara et al., 2007) and have been used to identify paleopolyploid events and the proto-karyotype of vertebrates (Panopoulou et al., 2003; Jaillon et al., 2004; Dehal & Boore, 2005; Panopoulou & Poustka, ”
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss (2011, background): “Given the small total divergence time between maize and sorghum and the fact that tetraploidy can temporarily increase the frequency of genome rearrangements (19), the sorghum genome was treated as representative of the genome organization of both diploid genomes present in the initial tetraploid an”