title: Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus.
abstract: Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72-97% nt sequence identity; 83-99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.
authors.affiliation: Plant Pathology Section, Division of Crop Protection, Sugarcane Breeding Institute, ICAR, Coimbatore 641007, India.
authors.forename: K
authors.initials: K
authors.lastname: Bagyalakshmi
authors.forename: B
authors.initials: B
authors.lastname: Parameswari
authors.forename: C
authors.initials: C
authors.lastname: Chinnaraja
authors.forename: R
authors.initials: R
authors.lastname: Karuppaiah
authors.forename: V
authors.initials: V
authors.lastname: Ganesh Kumar
authors.forename: R
authors.initials: R
authors.lastname: Viswanathan
mesh_terms: D000595:Amino Acid Sequence; D001208:Asia; D001483:Base Sequence; D003546:Cysteine Endopeptidases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015967:Gene Expression Regulation, Viral / Q000502:physiology; D014644:Genetic Variation; D007194:India; D009154:Mutation; D010802:Phylogeny; D019176:Potyviridae / Q000145:classification / Q000235:genetics*; D016865:Reassortant Viruses / Q000235:genetics*; D011995:Recombination, Genetic; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D014764:Viral Proteins; D003546:Cysteine Endopeptidases; C072775:HC-Pro protein, potyvirus