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

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.

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

“…The ENC-plot, PR2, neutrality plot and regression analyses between the ARO and GRAVY values and ENC, GC, GC3S, and the first two principle axes values significantly showed that BBWV-2 is influenced by natural selection and mutation pressure to variable degrees. Consistent with PVM [ 23 ], both the ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV-2.…”

“…Normally, RNA viruses have low codon usage bias to perform efficient replication in the host by lowering the competition with the host genes [ 55 , 65 , 66 , 67 , 68 ]. Previous reports showed low codon usage bias from several plant viruses such as CTV, PRSV, PVM, RSV and SCMV [ 19 , 20 , 21 , 22 , 23 , 24 ]. In our study, a lower codon usage pattern of the BBWV2 genome (the ENC values higher than 35) was also found, indicating a low degree of preference.…”

“…The evolution and dynamics of infectious diseases are influenced by host–parasite interactions [ 69 , 70 , 71 ]. For viruses, several reports showed that codon usage patterns have a significant effect on the viruses’ host-specific adaption [ 23 , 55 , 67 , 68 ]. In this study, our CAI analysis showed that both BBWV-2 genes have codon usage preferences that are closer to pepper than to other hosts.…”

“…CUB in viruses is expected to affect their survival, fitness, evolution, adaption, and avoidance of host cell responses [ 7 , 13 ]. Until now, only several reports have described the influence of codon usage in the evolution of plant viruses, such as begomoviruses [ 18 ], citrus tristeza virus (CTV) [ 19 ], rice black-streaked dwarf virus (RBSDV) [ 20 ], rice strape virus (RSV) [ 21 ], papaya ringspot virus (PRSV) [ 22 ], potato virus M (PVM) [ 23 ], and sugarcane mosaic virus (SCMV) [ 24 ].…”

Genetic Adaptations, Biases, and Evolutionary Analysis of Canine Distemper Virus Asia-4 Lineage in a Fatal Outbreak of Wild-Caught Civets in Thailand

“…An RSCU value greater than 1.0 indicates a positive codon usage bias, whereas a value less than 1.0 represents a negative codon usage bias. Furthermore, RSCU values >1.6 indicate overrepresented codons, while values <0.6 suggest underrepresented codons, as described previously [50]. The RSCU values were implemented and calculated using MEGA 7.0.…”