Analysis of synonymous codon usage in foot-and-mouth disease virus |
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Authors: | Jian-Hua Zhou Jie Zhang Hao-Tai Chen Li-Na Ma Yong-Sheng Liu |
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Institution: | (1) 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, 730046, China |
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Abstract: | 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. |
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