Molecular variability in the cysteine rich protein of potato virus M

Tabasinejad, Fatemeh; Jafarpour, Behrooz; Zakiaghl, Mohammad; Siampour, Majid; Rowhani, Hamid; Mehrvar, Mohsen

doi:10.1007/s13337-015-0258-8

Cited by 3 publications

(2 citation statements)

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“…Low codon usage bias and higher genomic stability were observed from CTV, PRSV and RSV [60,61,62]. PVM, a carlavirus belonging to the family of Betaflexviridae , is an economically important pathogen of potato and pepino worldwide [3,4,5,6]. In the present study, comprehensive analyses of codon usage of PVM based on the CP and NABP coding sequences were performed.…”

Section: Discussionmentioning

confidence: 99%

“…PVM was first isolated from potato ( Solanum tuberosum ) in the United States in 1923 [1], and then isolated from pepino ( Solanum muricatum ), tomato and tobacco [2,3]. PVM is transmitted in a non-persistent manner by aphid and causes large economic losses of nightshade crops worldwide [2,3,4,5,6,7]. PVM contains a single stranded positive-sense RNA molecule that is approximately 8.5 kb in length and is enveloped by flexuous filamentous virions [8].…”

Section: Introductionmentioning

confidence: 99%

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

Gan

Liang

2019

Viruses

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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.

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