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Characterization of the porcine epidemic diarrhea virus codon usage bias

文献类型： 外文期刊

作者： Chen, Ye 1 ; Shi, Yuzhen 1 ; Deng, Hongjuan 1 ; Gu, Ting 1 ; Xu, Jian 1 ; Ou, Jinxin 1 ; Jiang, Zhiguo 1 ; Jiao, Yiren 2 ; Z 1 ;

作者机构： 1.South China Agr Univ, Coll Anim Sci, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Guangzhou 510642, Guangdong, Peoples R China

2.South China Agr Univ, Coll Anim Sci, Guangdong Prov Key Lab Agroanim Genom & Mol Breed

关键词： Codon usage bias;Porcine epidemic diarrhea virus;Mutation bias;Natural selection

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： Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree. (C) 2014 Elsevier B.V. All rights reserved.

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