Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts
Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts
复制标题
马铃薯病毒 M 的同义密码子使用偏差分析及其对宿主的适应。
DOI：
10.3390/v11080752
复制
发表时间：
2019-08-01
期刊：
影响因子：
4.7
通讯作者：
Liang, Xinyan
中科院分区：
文献类型：
--
作者：
He, Zhen;Gan, Haifeng;Liang, Xinyan
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.
