Suzuki Yoshiyuki
Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Nagoya-shi, Aichi-ken 467-8501, Japan.
Genes Genet Syst. 2011;86(2):123-9. doi: 10.1266/ggs.86.123.
In the analysis of protein-coding nucleotide sequences, the ratio of the number of nonsynonymous substitutions to that of synonymous substitutions (d(N)/d(S)) is used as an indicator for the direction and magnitude of natural selection operating at the amino acid sequence level. The d(S) and d(N) values are estimated based on the comparison of homologous codons, which are often identified by converting (reverse-translating) aligned amino acid sequences into codon sequences. In this method, however, homologous codons may be mis-identified when frame-shifts occurred or amino acid sequences were mis-aligned, which may lead to overestimation of the d(N)/d(S) ratio. Here the effect of reverse-translating aligned amino acid sequences on the estimation of d(N)/d(S) ratio was examined through a large-scale analysis of protein-coding nucleotide sequences from vertebrate species. Apparently, 1-9% of codon sites that were identified as homologous with reverse-translation contained non-homologous codons, where the d(N)/d(S) ratio was unduly high. By correcting the d(N)/d(S) ratio for these codon sites, it was inferred that the ratio was 5-43% overestimated with reverse-translation. These results suggest that caution should be exerted in the study of natural selection using the d(N)/d(S) ratio by reverse-translating aligned amino acid sequences.
在蛋白质编码核苷酸序列分析中，非同义替换数与同义替换数的比率（d(N)/d(S)）被用作在氨基酸序列水平上自然选择的方向和强度的指标。d(S)和d(N)值是基于同源密码子的比较来估计的，同源密码子通常通过将比对的氨基酸序列转换（反向翻译）为密码子序列来识别。然而，在这种方法中，当发生移码或氨基酸序列比对错误时，同源密码子可能会被错误识别，这可能导致d(N)/d(S)比率的高估。在这里，通过对脊椎动物物种的蛋白质编码核苷酸序列进行大规模分析，研究了将比对的氨基酸序列反向翻译对d(N)/d(S)比率估计的影响。显然，通过反向翻译被鉴定为同源的密码子位点中有1-9%包含非同源密码子，其中d(N)/d(S)比率过高。通过校正这些密码子位点的d(N)/d(S)比率，可以推断出反向翻译会使该比率高估5-43%。这些结果表明，在使用反向翻译比对的氨基酸序列的d(N)/d(S)比率研究自然选择时应谨慎。
