Abstract
Sugarcane bacilliform virus (SCBV), a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since the virus occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among the virus isolates from 104 isolates infecting germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel genotypes are being proposed: SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y. SCBV-W: CBJ 46, due to the divergence in the nucleotide and protein sequence with existing isolates, established itself as a novel candidate in SCBV species. In comparison with the existing database of SCBV and conclusion from the present study, SCBV isolates from India exhibited maximum diversity in comparison with other regions. SCBV-U, SCBV-W, SCBV-X which turned out as potent recombinants along with other six recombinants in the study, directs at the plausible heterogeneity and genetic exchange happened within SCBV species over time which lead to the evolution of new variants. Neutrality tests indicate the existence of low-frequency polymorphism and Selection pressure of < 1 pointed out at purifying selection. Codon usage bias acted as an efficient tool for identifying patterns in SCBV, in which non-randomness in mutational events might lead to the over expression of codon AGA. The current study on characterization and evidence of nucleotidal variation within SCBV species will lead to devising robust diagnostics of the virus in quarantine and improving the knowledge on the evolutionary changes in SCBV species.
Dynamics of genetic diversity among Indian Sugarcane bacilliform virus species and implications of associated recombination events in the virus