Evolution of individual genes of Sugarcane mosaic virus

Sugarcane mosaic virus (SCMV) belongs to the Potyvirus genus and Potyviridae family of single-stranded RNA viruses. It is a disease of great economic importance, especially in sugarcane and maize in many parts of the world. SCMV has been understudied at both the genomic level with a greater emphasis put on the coat protein gene (CP) for molecular epidemiology. This was a computational study using publicly available sequences (NCBI GenBank) that sought to understand the evolutionary processes that shape SCMV molecular evolution such as phylogeny, recombination, selection pressure and nucleotide diversity by focusing on the individual genes of the polypeptide. Recombination was found to be a major driver of evolution with breakpoints found in P3, HC-Pro, C1, NIa-Pro, NIb, and CP. No statistically significant recombination was detected in the P1, 6K1, 6K2, and VPg genes most probably because of their relatively shorter length. After the removal of recombinants from the initial 82 full polyprotein-coding sequences, 57 sequences were used in phylogenetic analysis using a Bayesian MCMC framework implemented in BEAST2 with particular substitution models for each gene. All the ten genes gave similar low mean nucleotide substitution rates of between 3.35 x 10-3 (C1) to 4.29 x 10-3 (CP) and time to the most recent common ancestor (TMRCA) of 219 years (CP) to 264 years (P1). This would mean that the community’s over-reliance on the CP may produce results accurate for the whole genome, provided the researchers controlled for the effects of recombination, but that sufficient data exists for other genes as well, so there is no rational justification for excluding them from similar studies. The SCMV strains clustered into two distinct groups with sub-clustering well defined by their geographical isolation points, with sequences from Argentina closely grouping with Chinese strains. This observation may not be conclusive as most of the sequences studied were from China. Analysis of dN/dS shows significant negative selection in all the genes with P1 and CP registering relatively lower levels (SLAC: 0.192 for P1 and 0.153 for CP). A few sites in P1, HC-Pro, P3, NIa-VP, NIb, and CP appear to be under diversifying selection. P1 and CP also had the highest nucleotide diversity while the overlapping P3N-PIPO region had the least diversity relative to other regions of the polypeptide. The overlapping region is understandably highly conserved and presumably under strong purifying selection due to its double role in translation. This knowledge from this study enhances the understanding of SCMV evolution, highlights residues in several genes that may be affecting SCMV-crop interactions and will help in developing strategies for the control of the diseases in plants.M.S.Includes bibliographical referencesby Chris Njag