Genome Organization and Molecular Characterization of P1 Suppressor from Indian Sugarcane Streak Mosaic Virus isolates

Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, family Potyviridae, is an important viral pathogen affecting sugarcane cultivation in India. For the first time in India, the complete nucleotide sequence of an SCSMV isolate (SCSMV-IND) was determined from seven overlapping cDNA clones. The linear, assembled, single-stranded positive-sense RNA genome of SCSMV-IND was 9,786 nucleotides (nt) in length (excluding the poly (A) tail) and encoded a polyprotein of 3,131 amino acid (aa) residues. The genome of SCSMV-IND shared high degree of sequence identity with Pakistan isolate (93 % at nt and 97 % at aa), and shared only 81 % nt and 94 % aa identities with other SCSMV isolates from Japan, Indonesia and Thailand. Phylogenetic tree analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups. Further studies are in progress to establish variability in the genomes of different strains in the country. Recently the P1 gene was identified as a potent RNA silencing suppressor of the members of the genus Poacevirus and the knowledge of P1 suppressor gene sequences will be useful to develop RNAi based transgenic sugarcane in India. Hence, we sequenced the P1 gene of ten Indian SCSMV isolates and compared the sequence diversity and the phylogenetic relationship with known SCSMV isolates. Comparative sequence analysis revealed a high level of diversity in the P1 gene (83–98% nt sequence identity; 87–100% aa sequence identity), and the Indian SCSMV isolates were found to be the most variable (up to 9% diversity at the aa level). Phylogenetic tree analysis showed clustering of 17 SCSMV isolates into two groups. The conserved domain in the predicted P1 protein was explored using ALL-IN-ONE SEQ-ANALYZER and NCBIs conserved domain database (CDD). The sequence of SCSMV viral P1 Protein was compared with respect to both inter and intra-species across different members of the family Potyviridae. This study revealed that all the 10 Indian SCSMV isolates have a LXKA motif (67–70 aa) and a putative zinc finger motif (C86–C89–H103–C106) in the N-terminal half of its P1 protein, which implicates the role of P1 in suppression of gene silencing as it has been reported in the tritimoviruses. Our studies are in progress to express the P1 gene in RNA silencing vector to establish its silencing activity in model tobacco lines.