State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-Sen University, Guangzhou 510275, China.
Mol Biol Evol. 2011 Jan;28(1):771-80. doi: 10.1093/molbev/msq251. Epub 2010 Sep 20.
Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression and contribute to an understanding of substitution patterns observed at synonymous sites. They can also be informative about the distinctive evolutionary properties of sex chromosomes such as genetic degeneration of the Y chromosome, dosage compensation, and hemizygosity of the X chromosome in males, which can affect the selection on codon usage. Here, we study CUB in Silene latifolia, a species of interest for studying the early stages of sex chromosome evolution. We have obtained a large expressed sequence tag data set containing more than 1,608 sequence fragments by 454 sequencing. Using three different methods, we conservatively define 21 preferred codons. Interestingly, the preferred codons in S. latifolia are almost identical to those in Arabidopsis thaliana, despite their long divergence time (we estimate average nonsynonymous site divergence to be 0.216, and synonymous sites are saturated). The agreement suggests that the nature of selection on codon usage has not changed significantly during the long evolutionary time separating the two species. As in many other organisms, the frequency of preferred codons is negatively correlated with protein length. For the 43 genes with both exon and intron sequences, we find a positive correlation between gene expression levels and GC content at third codon positions, but a strong negative correlation between expression and intron GC content, suggesting that the CUB we detect in S. latifolia is more likely to be due to natural selection than to mutational bias. Using polymorphism data, we detect evidence of ongoing natural selection on CUB, but we find little support for effects of biased gene conversion. An analysis of ten sex-linked genes reveals that the X chromosome has experienced significantly more unpreferred to preferred than preferred to unpreferred substitutions, suggesting that it may be evolving higher CUB. In contrast, numbers of substitutions between preferred and unpreferred codons are similar in both directions in the Y-linked genes, contrary to the expectation of genetic degeneration.
密码子使用偏性（CUB）模式提供了有关基因表达诱导的同义密码子选择的有用信息，并有助于理解同义位点观察到的替代模式。它们还可以提供有关性染色体独特进化特性的信息，例如 Y 染色体的遗传退化、X 染色体的剂量补偿和雄性的半合性，这些特性会影响密码子使用的选择。在这里，我们研究了 Silene latifolia 中的 CUB，这是一种研究性染色体进化早期阶段的物种。我们通过 454 测序获得了一个包含超过 1608 个序列片段的大型表达序列标签数据集。使用三种不同的方法，我们保守地定义了 21 个首选密码子。有趣的是，尽管 Silene latifolia 和 Arabidopsis thaliana 的分化时间很长（我们估计平均非同义位点的分化率为 0.216，而同义位点已经饱和），但 Silene latifolia 的首选密码子几乎与 Arabidopsis thaliana 的相同。这种一致性表明，在两个物种分离的漫长进化时间里，密码子使用选择的性质没有发生显著变化。与许多其他生物体一样，首选密码子的频率与蛋白质长度呈负相关。对于具有外显子和内含子序列的 43 个基因，我们发现基因表达水平与第三密码子位置的 GC 含量呈正相关，但与内含子 GC 含量呈强负相关，这表明我们在 Silene latifolia 中检测到的 CUB 更可能是由于自然选择而不是突变偏差。使用多态性数据，我们检测到 CUB 上正在进行自然选择的证据，但我们几乎没有发现偏向基因转换影响的证据。对十个性连锁基因的分析表明，X 染色体经历了更多的非首选到首选取代，而不是首选到非首选取代，这表明它可能正在进化更高的 CUB。相比之下，在 Y 连锁基因中，首选和非首选密码子之间的替换数量在两个方向上都相似，这与遗传退化的预期相反。
