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Open AccessArticle

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
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Viruses 2019, 11(8), 752; https://doi.org/10.3390/v11080752
Received: 10 July 2019 / Revised: 12 August 2019 / Accepted: 13 August 2019 / Published: 14 August 2019
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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Abstract

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. View Full-Text
Keywords: Potato virus M; codon usage bias; pepino; natural selection; adaption evolution Potato virus M; codon usage bias; pepino; natural selection; adaption evolution
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He, Z.; Gan, H.; Liang, X. Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts. Viruses 2019, 11, 752.

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