Shi Xiaoli, Wang Xiyin, Li Zhe, Zhu Qihui, Tang Wen, Ge Song, Luo Jingchu
College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China.
Gene. 2006 Jul 19;376(2):199-206. doi: 10.1016/j.gene.2006.03.003. Epub 2006 Mar 18.
Understanding the correlation between synonymous substitution rate and GC content is essential to decipher the gene evolution. However, it has been controversial on their relationship. We analyzed the GC content and synonymous substitution rate in 1092 paralogues produced by two large-scale duplication events in the rice genome. According to the GC content at the third codon sites (GC3), the paralogues were classified into GC3-rich and GC3-poor genes. By referring to their outgroup sequences, we inferred the last common ancestor of sister paralogues and, consequently, calculated the average synonymous substitution rate for two gene classes. The results suggest that average synonymous substitution rate is lower in GC3-rich genes than that in GC3-poor genes, indicating that the synonymous substitution rate is negatively correlated with GC content in the rice genome. Through characterizing the synonymous nucleotide substitution pattern, we found a strong synonymous nucleotide substitution frequency bias from AT to GC in GC3-rich genes. This indicates possible limitations of commonly used methods developed to estimate the synonymous substitution rate. Their estimates might produce misleading results on correlation between the synonymous substitution rate and GC content.
了解同义替换率与GC含量之间的相关性对于解读基因进化至关重要。然而，它们之间的关系一直存在争议。我们分析了水稻基因组中两次大规模复制事件产生的1092个旁系同源基因的GC含量和同义替换率。根据第三密码子位点的GC含量（GC3），将旁系同源基因分为富含GC3的基因和GC3含量低的基因。通过参考它们的外类群序列，我们推断出姐妹旁系同源基因的最后共同祖先，从而计算出两类基因的平均同义替换率。结果表明，富含GC3的基因的平均同义替换率低于GC3含量低的基因，这表明水稻基因组中的同义替换率与GC含量呈负相关。通过表征同义核苷酸替换模式，我们发现在富含GC3的基因中，同义核苷酸替换频率存在从AT到GC的强烈偏向。这表明用于估计同义替换率的常用方法可能存在局限性。它们的估计可能会在同义替换率与GC含量之间的相关性上产生误导性结果。
