PDF(Pubmed)
Abstract：
Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.
摘要：
编码序列进化受自然选择和中性进化力的影响。在许多物种中,突变偏倚的影响，密码子使用和GC偏倚基因转换（gBGC）对基因序列进化的影响尚未详细说明。因此，有必要量化这些力量如何塑造替代模式，以了解自然选择的强度和方向。这里,我们使用比较基因组学研究了蝴蝶和飞蛾（鳞翅目）基因序列进化的碱基组成和密码子使用偏差之间的关联，包括对一个物种的潜在模式和过程的深入分析，LeptideaSinapis.数据显示，在第三个密码子位置存在明显的G/C到A/T取代偏好，不同蝴蝶谱系之间的强度有一定差异。然而,替代偏差低于先前估计的突变率比预期，部分是由于gBGC的影响。我们发现在大多数物种中，A/T结尾密码子的比例过高，但是密码子使用偏倚的程度与第三密码子位置的GC含量之间存在正相关。此外,与一般编码序列相比，芥子乳杆菌中的tRNA基因群体在第三个密码子位置显示出更高的GC含量，并且A/T末端密码子的过度表达较少。同义取代和密码子使用偏倚之间存在反比关系,表明在同义位点上的选择。我们得出的结论是，鳞翅目的进化率受到潜在的G/C->A/T突变偏倚和部分抵消固定偏倚之间复杂相互作用的影响，主要由整体纯化选择赋予，gBGC和密码子使用的选择。
