Molecular characterization of Indian sugarcane streak mosaic virus isolate

Virus Genes. 2013 Feb;46(1):186-9. doi: 10.1007/s11262-012-0827-5. Epub 2012 Sep 26.

Abstract

Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, 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 9,786 nucleotides in length (excluding the poly (A) tail) and encoded a polyprotein of 3,131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity with SCSMV-PAK (93 % at nucleotide and 97 % at amino acid), and shared only 81 % nucleotide and 94 % amino acid identities with all the four SCSMV isolates (SCSMV-JP1, -JP2, -ID, and -THA). Phylogenetic tree analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups. SCSMV-IND and -AP isolates showed 18 % (nucleotide) divergence within the highly conserved 3' partial genome, suggesting a high level of genetic diversity among the Indian SCSMV isolates.

MeSH terms

  • Cluster Analysis
  • Genome, Viral*
  • India
  • Molecular Sequence Data
  • Phylogeny
  • Plant Diseases / virology*
  • Polyproteins / genetics
  • Potyviridae / genetics*
  • Potyviridae / isolation & purification
  • RNA, Viral / genetics*
  • Saccharum / virology*
  • Sequence Analysis, DNA*
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid

Substances

  • Polyproteins
  • RNA, Viral

Associated data

  • GENBANK/JN941985