The medaka draft genome and insights into vertebrate genome evolution
The medaka draft genome and insights into vertebrate genome evolution
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DOI：
10.1038/nature05846
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发表时间：
2007-06-07
期刊：
影响因子：
64.8
通讯作者：
Kohara, Yuji
中科院分区：
文献类型：
--
作者：
Kasahara, Masahiro;Naruse, Kiyoshi;Kohara, Yuji
硬骨鱼占所有脊椎动物物种的一半以上，已经适应了各种海洋和淡水栖息地(1)。它们的基因组进化和多样化是理解脊椎动物进化的重要课题。虽然已经发表了两种河豚的基因组序列草图（2,3），但需要分析更多的鱼类基因组。在这里，我们报告了一种小型产卵淡水硬骨鱼medaka （Oryzias latipes）的高质量基因组序列草图。Medaka原产于东亚，是广泛生物学领域的优秀模型系统，包括生态毒理学、致癌作用、性别决定（4-6）和发育遗传学(7)。在不到斑马鱼基因组一半的medaka基因组（700兆碱基）中，我们使用基因表达标签信息的5'端序列分析预测了20,141个基因，其中包括2,900个新基因。结果表明，来自两个地区群体的两个自交系间的单核苷酸多态性（SNPs）平均为3.42%；这是在任何脊椎动物物种中所见的最高SNP率。基于密集SNP信息的分析显示，两个种群之间存在400万年的严格遗传分离，并表明不同的选择压力作用于特定的基因类别。与人类、河豚、斑马鱼和medaka基因组的四向比较显示，在硬骨鱼祖先的全基因组复制事件发生后，在非常短的时间内发生了8次主要的染色体间重排，大约为50 Myr，然后，有趣的是，medaka基因组将其祖先的核型保留了300 Myr以上。
Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats(1). Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published(2,3), 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(4-6) and developmental genetics(7). 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 similar to 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.