Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus

Abstract

Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72-97% nt sequence identity; 83-99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.

Population structure of Banana bract mosaic virus reveals recombination and negative selection in the helper component protease (HC-Pro) gene

“…Similar to our study, potential recombinants were detected in HC-Pro gene of PVY [22], SCSMV [1] and Turnip mosaic virus (TuMV) [14]. Zhang et al [26] showed that the hot spot of recombination sites were located at 5 0 and 3 0 termini of HC-Pro gene of TVBMV.…”

“…The three neutrality test statistics were significantly negative (P [ 0.05), suggesting a strong negative or purifying selection indicating the occurrence of recent BBrMV population expansion. The recombination, together with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene of potyviruses [1,9]. Finally, this study showed the level of genetic variation, phylogenetic relationship, recombination and operation of selection among the different isolates of BBrMV with respect to HCPro gene.…”

“…The aa of HCPro that were under positive selection were located in domain 1, which is responsible for aphid transmission, RNA binding, and genome amplification [16]. Though SCSMV isolates had high nt diversity, none of codons of HC-Pro gene of the isolates were reported to be under positive selection [1]. The significance of this positive selection in BBrMV isolates on the codon at position 74 and 79 needs further investigation.…”

“…Our previous study showed that CP gene sequence analysis grouped the isolate TN16 as a distinct variant whereas in this study the HC-Pro gene of the same isolate showed 94-97 % similarity with all the other isolates. Bagyalakshmi et al [1] reported a high level of diversity of 3-28 % at nt and 1-17 % at aa level in the HC-Pro gene of Sugarcane streak mosaic virus (SCSMV) and this wider variation was due to the use of diverse virus isolates from the world sugarcane germplasm collection. The HC-Pro gene sequences of 25 Potato virus Y (PVY) isolates characterized were 81.6-99.7 and 89.4-100 % identical at nt and aa levels, respectively [22].…”

Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand

“…More isolates of SCSMV and their complete genome sequences were reported from China (Li et al, 2011) and India (Parameswari, Bagyalakshmi, Viswanathan, & Chinnaraja, 2013). The study on genetic variability of SCSMV has been investigated using the analysis of CP (He et al, 2013), P1 (He et al, 2013) and HC-Pro (Bagyalakshmi et al, 2012) coding regions. The comparison of these genes revealed high variation among different SCSMV isolates resulting from recombination (Bagyalakshmi et al, 2012;He et al, 2013).…”