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Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

文献类型： 外文期刊

作者： Feng, Hua 1 ; Segales, Joaquim 2 ; Wang, Fangyu 1 ; Jin, Qianyue 1 ; Wang, Aiping 5 ; Zhang, Gaiping 1 ; Franzo, Giovanni 6 ;

作者机构： 1.Henan Acad Agr Sci, Henan Prov Key Lab Anim Immunol, Zhengzhou 450002, Peoples R China

2.OIE Collaborating Ctr Res & Control Emerging & Re, Cerdanyola Del Valle 08193, Spain

3.Campus Univ Autonoma Barcelona, Ctr Recerca Sanitat Anim CReSA IRTA UAB, UAB, Barcelona 08193, Spain

4.Univ Autonoma Barcelona, Fac Vet, Dept Sanitat & Anat Anim, Barcelona 08193, Spain

5.Zhengzhou Univ, Sch Life Sci, Zhengzhou 450001, Peoples R China

6.Univ Padua, Dept Anim Med Prod & Hlth MAPS, I-35020 Legnaro, Italy

关键词： porcine circovirus; codon usage pattern; natural selection; mutation pressure; viral host adaptability

期刊名称：VIRUSES-BASEL （ 影响因子：5.818； 五年影响因子：5.811 ）

ISSN：

年卷期： 2022 年 14 卷 1 期

页码：

收录情况： SCI

摘要： Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

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