Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes.
Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes.
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DOI：
10.1186/1471-2148-11-312
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发表时间：
2011-10-22
影响因子：
3.4
通讯作者：
Kawamura S
中科院分区：
文献类型：
--
作者：
Hiwatashi T;Mikami A;Katsumura T;Suryobroto B;Perwitasari-Farajallah D;Malaivijitnond S;Siriaroonrat B;Oota H;Goto S;Kawamura S
常规的三色视觉是卡卡林动物（人类、类人猿和旧大陆猴子）的特征。这是由排列在X染色体上的L和M视蛋白基因和常染色体上的S视蛋白基因实现的。据报道，在非人类卡他宁中，影响色觉表型的遗传变异在L和M视蛋白基因中都不存在或罕见，尽管有证据表明基因转换使这两个基因均质化。然而，卡氏鼠的内含子和外显子的核苷酸变异只对人类和黑猩猩的L视蛋白基因进行了详细的研究。在本研究中，我们检测了长臂猿（Catarrhini, Hylobatidae） L和M视蛋白基因的核苷酸变异。具体来说，我们集中研究了3.6~3.9 kb的区域，该区域包括位于中心位置的外显子3到外显子5，该区域编码了基因光谱调节功能的氨基酸位点。在3属（hyloates、Nomascus和Symphalangus）的152个个体中，均有L和M视蛋白基因，无L/M杂交基因。对94个个体进行详细的DNA测序，各物种外显子中L和M视蛋白基因的核苷酸差异显著高于内含子的差异。内含子的inter-LM分化与intra-L/M多态性的比值显著低于同义位点。利用外显子序列重建系统发育树，发现L/M基因重复出现在卡他龙的共同祖先中，而利用内含子序列重建系统发育树时，基因重复出现在不同物种中多次。使用GENECONV程序，我们还检测到L和M视蛋白基因之间的基因转换大部分发生在内含子区域。这些结果表明长臂猿内含子中L和M视蛋白基因之间基因转换的历史积累。我们的研究进一步支持了L和M视蛋白基因转换的均质化作用，以及在非人类卡他宁中，针对这种均质化在中心外显子上的纯化选择，以维持L和M视蛋白之间的光谱差异。
Routine trichromatic color vision is a characteristic feature of catarrhines (humans, apes and Old World monkeys). This is enabled by L and M opsin genes arrayed on the X chromosome and an autosomal S opsin gene. In non-human catarrhines, genetic variation affecting the color vision phenotype is reported to be absent or rare in both L and M opsin genes, despite the suggestion that gene conversion has homogenized the two genes. However, nucleotide variation of both introns and exons among catarrhines has only been examined in detail for the L opsin gene of humans and chimpanzees. In the present study, we examined the nucleotide variation of gibbon (Catarrhini, Hylobatidae) L and M opsin genes. Specifically, we focused on the 3.6~3.9-kb region that encompasses the centrally located exon 3 through exon 5, which encode the amino acid sites functional for the spectral tuning of the genes. Among 152 individuals representing three genera (Hylobates, Nomascus and Symphalangus), all had both L and M opsin genes and no L/M hybrid genes. Among 94 individuals subjected to the detailed DNA sequencing, the nucleotide divergence between L and M opsin genes in the exons was significantly higher than the divergence in introns in each species. The ratio of the inter-LM divergence to the intra-L/M polymorphism was significantly lower in the introns than that in synonymous sites. When we reconstructed the phylogenetic tree using the exon sequences, the L/M gene duplication was placed in the common ancestor of catarrhines, whereas when intron sequences were used, the gene duplications appeared multiple times in different species. Using the GENECONV program, we also detected that tracts of gene conversions between L and M opsin genes occurred mostly within the intron regions. These results indicate the historical accumulation of gene conversions between L and M opsin genes in the introns in gibbons. Our study provides further support for the homogenizing role of gene conversion between the L and M opsin genes and for the purifying selection against such homogenization in the central exons to maintain the spectral difference between L and M opsins in non-human catarrhines.
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