Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
Vet Res Commun. 2010 Apr;34(4):393-404. doi: 10.1007/s11259-010-9359-4. Epub 2010 Apr 28.
In this study, we calculate the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to carry out a comparative analysis of codon usage pattern for open reading frames (ORFs) among 85 samples which belong to all seven serotypes of foot-and-mouth disease virus (FMDV). Although the degree of CUB for ORFs is a relatively slight, there is a significant variation for CUB among different serotypes, which is mainly determined by codon usage pattern depending on RSCU. By comparison with RSCU values for all samples, although RSCU values fail to show the relationship of specific-lineage serotype, there are two main genetic populations existing in FMDV, namely (i) serotypes Asia 1, A, C & O; (ii) serotypes SAT 1, 2 & 3. This interesting characteristic may be formed by the mechanism of RNA virus recombination. The analysis of quantitative & qualitative evaluation based on CUB indicates interesting characteristic of codon usage, which suggests that more FMDV genome diversity may exist in specific-lineage serotypes rather than exist randomly. Furthermore, the relationship between amino acids and codon usage pattern indicates that mutation pressure rather than translational selection in nature is the important determinant of the codon usage bias observed. Our work might give some sight into some characteristics of FMDV ORF and some evolutionary information of this virus.
在这项研究中，我们计算了相对同义密码子使用（RSCU）值和密码子使用偏性（CUB）值，以对属于口蹄疫病毒（FMDV）所有 7 个血清型的 85 个样本的开放阅读框（ORF）的密码子使用模式进行比较分析。尽管 ORF 的 CUB 程度相对较低，但不同血清型之间的 CUB 存在显著差异，这主要取决于取决于 RSCU 的密码子使用模式。与所有样本的 RSCU 值相比，尽管 RSCU 值未能显示特定谱系血清型的关系，但 FMDV 中存在两个主要的遗传群体，即（i）血清型 Asia 1、A、C 和 O；（ii）血清型 SAT 1、2 和 3。这一有趣的特征可能是由 RNA 病毒重组的机制形成的。基于 CUB 的定量和定性评估分析表明了密码子使用的有趣特征，这表明特定谱系血清型中可能存在更多的 FMDV 基因组多样性，而不是随机存在。此外，氨基酸和密码子使用模式之间的关系表明，在自然界中，突变压力而不是翻译选择是观察到的密码子使用偏性的重要决定因素。我们的工作可能会为了解 FMDV ORF 的一些特征和该病毒的一些进化信息提供一些线索。
