Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus

文献类型： 外文期刊

第一作者： Zhou, Jian-hua

作者： Zhou, Jian-hua;Zhang, Jie;Ding, Yao-zhong;Chen, Hao-tai;Ma, Li-na;Liu, Yong-sheng

作者机构：

关键词： Codon usage bias;Foot-and-mouth disease virus;Intertypic recombination;Phylogenetic incongruence

期刊名称：BIOSYSTEMS （ 影响因子：1.973； 五年影响因子：2.063 ）

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收录情况： SCI

摘要： The mechanism of utilization of alternative two AUGs in foot-and-mouth disease virus (FMDV) is still unknown to date. In this study, the characteristics of codon usage bias (CUB) of the region between the two AUGs (the region-La) and of the same-sized region behind the second AUG (the region-Lb) in 94 different FMDV RNA sequences were analyzed using relative synonymous codon usage (RSCU) values. The results indicated that many codons with negative CUB were preferentially used in the region-La. There were two conserved residues (Thr and Cys) on the 4th and 6th residue positions of the region-La. The conserved residues had a general tendency to choose synonymous codons with negative CUB. Although most positions in the region-La did not contain conserved residues, many positions tended to use codons with negative CUB in this region. Among these codons, the majority belonged to the amino acids containing synonymous codons with clearly positive and negative CUB, including Asp, Val, Ile, Leu, Thr, Ala, Ser, Asn and Arg. The presence of many codons with negative CUB in the region-La might impair the efficiency of the first AUG selection. The phylogenetic incongruence of the region-La and the region-Lb implied that intertypic recombination played an important role in the evolution of FMDV. Furthermore, due to the existence of more positions with positive CUB and more widespread phylogenetic incongruence in the region-Lb than the region-La, a probable relationship between the degree of CUB and the evolution of the two target regions was revealed.

分类号： Q

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