Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.
Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.
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DOI：
10.1534/g3.114.014860
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发表时间：
2014-10-17
期刊：
影响因子：
--
通讯作者：
Schaeffer SW
中科院分区：
文献类型：
--
作者：
Fuller ZL;Haynes GD;Zhu D;Batterton M;Chao H;Dugan S;Javaid M;Jayaseelan JC;Lee S;Li M;Ongeri F;Qi S;Han Y;Doddapaneni H;Richards S;Schaeffer SW
人们对研究稳定选择对全基因组性状（如密码子使用偏好）的作用重新产生了兴趣。密码子偏好，当同义密码子以不相等的频率使用时，发生在多种分类群中。标准的进化模型解释了密码子偏好的维持是通过遗传漂变、突变和弱纯化选择的平衡来实现的。在重组受抑制的区域，选择的效力预计会降低。与果蝇中的观察相反，最近的一些研究未能检测到重组率之间的关系，选择作用于同义位点的强度，以及根据这些标准模型预测的密码子偏倚的大小。在此，我们研究了在2798蛋白质编码位点的密码子偏好的第三染色体上的D。pseudobscura使用47个个体的全基因组序列，代表了五种常见的第三染色体基因排列。使用超过100万个分离位点构建了精细规模的重组图谱。正如预期的那样，重组被证明是显着抑制染色体排列之间，允许直接检查重组，选择和密码子偏好之间的关系。与其他果蝇物种一样，我们观察到一个强烈的突变偏好远离最常用的密码子。我们发现同义和非同义多态性的比率在不同的氨基酸之间是可变的。然而，我们没有观察到密码子偏好性的降低或重组抑制区域的选择强度的降低。相反，我们发现弱稳定选择和突变偏好之间的相互作用可能在D.伪暗
There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.
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