Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus

文献类型： 外文期刊

第一作者： Liu, Yong-sheng

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

作者机构：

关键词： gene;ORF1a: encode papain-like cysteine protease;ORF1b: encode RNA dependent RNA polymerase;ORF2-6: encode envelop protein;ORF7: encode nucleocapsid protein;genetic variation;species evolution;mutational pressure

期刊名称：INFECTION GENETICS AND EVOLUTION （ 影响因子：3.342； 五年影响因子：3.188 ）

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收录情况： SCI

摘要： In this study, we calculated the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to implement a comparative analysis of codon usage pattern of open reading frames (ORFs) which belong to the two main genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By analysis of synonymous codon usage values in each ORF of PRRSV, the optimal codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in different ORFs of PRRSV were different and genetically conserved. Among them, ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main serotypes (EU and US). Due to mutational pressure, compositional constraint played an important role in shaping the synonymous codon usage pattern in different ORFs, and the synonymous codon usage diversity in ORFs was correlated with gene function. The degree of CUB for some particular amino acids under strong selection pressure probably served as a potential genetic marker for each ORF in PRRSV. However, gene length and translational selection in nature had no effect on the synonymous codon usage pattern in PRRSV. These conclusions could not only offer an insight into the synonymous codon usage pattern and differentiation of gene function, but also assist in understanding the discrepancy of evolution among ORFs in PRRSV

分类号： R1

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