Evolutionary features of 8K (KDa) silencing suppressor protein of Potato mop-top virus

The cysteine-rich 8K protein of Potato mop-top virus (PMTV) suppresses host RNA silencing. In this study, evolutionary analysis of 8K sequences of PMTV isolates was studied on the basis of nucleotide and amino acid sequences. Twenty-one positively selected sites were identified in 8K coding regions. Recombination events were found in the 8K of PMTV isolates with a rate of 1.8. Totally 30 haplotypes were detected with haplotype diversity ranging from 0.8 to 1.0 and nucleotide diversity from 7.58 to 13.62. The positions 33 and 30 indicated the highly positive and negative selection (with the highest and the lowest dN-dS values), respectively. Tajima’s D test suggested that 8K is evolving with a strong positive selection for worldwide isolates. High frequency of segregating sites was identified along 204 positions of 8K. Moreover, in this study, we used Shannon entropy-based approach to evaluate the variability of each site of nucleotide and corresponding amino acid. Based on Shannon entropy method, 139 and 97 nucleotide sites had the highest entropy value, while 47 and 33 amino acid sites showed the most diversity along 8K sequences. Our findings suggest that 8K as an RNA silencing suppressor evolves rapidly. Taken together, its variability might play a big threat to infect other plants or overcome resistant cultivars.