Molecular characterization of Indian Sugarcane streak mosaic virus isolate

Abstract

Sugarcane streak mosaic virus (SCSMV), an unassigned member of the family Potyviridae is an important viral pathogen affecting sugarcane cultivation in India. The complete nucleotide sequence of a SCSMV isolate from India (SCSMV-IND) was determined. The linear, assembled, single stranded positive sense RNA genome of SCSMV-IND was 9786 nucleotides in length (excluding the poly (A) tail) and it comprises a large open reading frame encoding polyprotein of 3131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity at nucleotide (93%) and amino acid (97%) levels with SCSMV-PAK and shared 81% and 94% nucleotide and amino acid identities respectively with all the three SCSMV isolates (SCSMV-JP1, -JP2 and -ID). Phylogenetic analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups: group I includes isolates from India (SCSMV-IND) and Pakistan (SCSMV-PAK), group II consists of isolates from Japan (SCSMV-JP1 and -JP2) and Indonesia (SCSMV-ID). SCSMV-IND and -AP isolates originating from the same geographical region (India) showed 18% divergence at nucleotide level within the highly conserved 3 half genome indicated existence of diversity among SCSMV isolates from India. Recombination analysis revealed one potentially significant intra-specific recombination in SCSMV-PAK. This work provided the first opportunity to establish the whole genome and polyprotein variability between SCSMV isolates from India and other Asian countries.