猪圆环病毒的基因密码子偏好性分析

Analysis of codon usage bias in porcine circovirus gene

为了解不同型猪圆环病毒(PCV)(PCV1、PCV2、PCV3)的密码子使用特点及其主要影响因素,本研究通过生物信息学方法对3个型PCVs的rep和cap两个基因序列的密码子偏好性进行综合分析。结果显示3个型PCVs间、rep与cap两个基因间、PCVs与宿主间的密码子偏好性均存在明显差异。密码子适应指数(CAI)分析预示3个型PCVs的两个基因在宿主细胞中表达水平低。同义密码子的相对使用频率(RSCU)分析表明PCV1与PCV2具有相似的同义密码子使用模式,而PCV3与PCV1、PCV2存在明显差异,3个型PCVs与宿主的密码子偏好性也存在明显差异。rep基因偏好使用U或G结尾的同义密码子,cap基因偏好使用C结尾的同义密码子。通过中性绘图分析和ENC绘图分析显示,PCV的密码子使用模式受自然选择压力影响大,受突变压力的影响小。本研究为阐明PCV的分子进化规律及病毒对宿主翻译系统的适应性提供重要的实验依据。

Based on pathogenicity and antigenicity, porcine circovirus （PCV） is divided into three types： PCV1, PCV2, and PCV3. To investigate codon usage pattern and main influence factor, the codon usage bias of rep and cap genes in three types of PCVs were analyzed with bioinformatic soflwares. There were significant differences in the codon usage bias among the three types of PCVs and between PCVs and host. Codon adaptation index analysis predicted that the two PCV genes from three types had low expression levels in host cells. The analysis on relative synonymous codon usage suggested PCV1 had similar synonymous codon usage patterns with PCV2, while PCV3 was apparently different from PCV1 and PCV2. There were significant differences in codon usage bias between the three PCVs and host. rep gene preferred to use U or G-end synonymous codon, whereas cap gene prefered to use C-end synonymous codon. Neutrality plot and ENC plot analysis showed compared to mutation pressure, natural selection played a substantial role in codon usage pattern of PCV. This study provided experimental evidences for elucidating of the molecular evolution rules of PCV and the viral adaptability to the host translation system.