Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus

Abstract

Sugarcane bacilliform virus (SCBV) is a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since it occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among its 104 isolates from various germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel subgroups, viz., SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y, were proposed. Interestingly, SCBV-W isolate CBJ 46 showed highest variation in its nucleotide and protein sequence. Compared with the existing genomic database of SCBV and the findings from the present study, SCBV isolates from India exhibited greater diversity than that isolated from other regions. SCBV-U, SCBV-W and SCBV-X, potent recombinants with other eight recombinants discovered in this study indicated the plausible heterogeneity and genetic exchange occurred within SCBV species over time that might have led to the evolution of new variants. Neutrality tests indicated the existence of low-frequency polymorphism and selection pressure of < 1 pointed out at purifying selection of SCBV population. The current study regarding the genetic variation within SCBV species will aid in devising robust diagnostic tools for the detection of virus in quarantine laboratories and improving the knowledge of evolutionary changes in SCBV species.