Molecular characterization of Indian Sugarcane streak mosaic virus isolates reveals recombination and negative selection in the P1 gene

• Published in: Gene 2014-11, Vol.552 (1), p.199-203
• Main Authors: Parameswari, B., Bagyalakshmi, K., Chinnaraja, C., Viswanathan, R.
• Format: Article
• Language: English
• Subjects: Cluster Analysis; Genetic Variation - genetics; Genome, Viral - genetics; India; Mosaic Viruses - genetics; Mutagenesis, Insertional - genetics; Negative selection; P1 gene; Phylogeny; Plant Diseases - virology; Polymorphism, Single Nucleotide - genetics; Recombination; Recombination, Genetic - genetics; RNA, Viral - genetics; Saccharum - virology; Sequence Analysis - methods; Sequence Deletion - genetics; Sugarcane streak mosaic virus (SCSMV); Viral Proteins - genetics
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.09.021

Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus is an important viral pathogen affecting sugarcane production in India. The P1 gene of ten Indian isolates was sequenced and compared with previously reported SCSMV isolates. Comparative sequence analysis revealed a high level of diversity in the P1 gene (83–98% nucleotide sequence identity; 87–100% amino acid sequence identity), and the Indian SCSMV isolates were found to be the most variable (up to 9% diversity at the amino acid level). Phylogenetic tree analysis showed clustering of 17 SCSMV isolates into two groups: group I included isolates from India (except SCSMV-TPT) and Pakistan, and group II consisted of isolates from Japan, Indonesia, Thailand and SCSMV-TPT. The results obtained from phylogenetic study were further supported by the different in silico analysis viz. SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. A significant proportion of recombination sites were observed at the N terminal region of P1 gene. Analysis of selection pressure indicated that the P1 gene of the Indian SCSMV isolates is under strong negative or purifying selection. It is likely that recombination identified in Indian SCSMV isolates, along with strong purifying selection, enhances the speed of elimination of deleterious mutations in the P1 gene. The evolutionary processes (recombination and selection pressure) together contributed to the observed genetic diversity and population structure of Indian SCSMV isolates. •P1 gene of SCSMV isolates exhibit genetic diversity, recombination and evolution.•Indian SCSMV population has 9% amino acid sequence variation.•SCSMV P1 gene has two evolutionary lineages, both detected in India.•Recombination in the virus genome favors removal of deleterious mutants.•Understanding evolutionary processes of P1 helps to design virus control strategies.