Medaka: a promising model animal for comparative population genomics.
Medaka: a promising model animal for comparative population genomics.
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DOI：
10.1186/1756-0500-2-88
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发表时间：
2009-05-10
影响因子：
1.8
通讯作者：
Mitani, Hiroshi
中科院分区：
文献类型：
--
作者：
Matsumoto, Yoshifumi;Oota, Hiroki;Mitani, Hiroshi
背景：物种内基因组多样性在人类身上得到了最好的研究。国际单体型图计划揭示了人类中大量的单核苷酸多态性（SNP），其中许多显示了人类进化过程中正向选择的信号。然而，在大多数情况下，由于人类遗传学研究固有的困难，等位基因之间的功能差异仍未得到实验验证。因此，拥有一个具有以下特征的脊椎动物模型将非常有用：（1）物种内遗传多样性高，（2）已经开发出多种基因操作方案，以及（3）完整测序的基因组。青鳉 (Oryzias latipes) 及其同属物种（广泛分布于东亚和东南亚的小型淡水硬骨鱼）符合这些标准。 结果：利用来自 27 个当地种群的青鳉物种，我们对 11 个在青鳉和人类之间具有明显直系同源的基因进行了非同义 SNP 的简单筛选。我们发现青鳉单核苷酸多态性（SNP），已知人类直系同源物中的相同位点在 HapMap 群体中具有高度差异性。重要的是，其中一些 SNP 显示出正选择信号。 结论：这些结果表明，青鳉是一个很有前途的模型系统，可用于比较群体基因组学，探索等位基因分化的功能和适应性意义。
BACKGROUND: Within-species genome diversity has been best studied in humans. The international HapMap project has revealed a tremendous amount of single-nucleotide polymorphisms (SNPs) among humans, many of which show signals of positive selection during human evolution. In most of the cases, however, functional differences between the alleles remain experimentally unverified due to the inherent difficulty of human genetic studies. It would therefore be highly useful to have a vertebrate model with the following characteristics: (1) high within-species genetic diversity, (2) a variety of gene-manipulation protocols already developed, and (3) a completely sequenced genome. Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria.FINDINGS: Using Oryzias species from 27 local populations, we conducted a simple screening of nonsynonymous SNPs for 11 genes with apparent orthology between medaka and humans. We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations. Importantly, some of these SNPs show signals of positive selection.CONCLUSION: These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations.