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

Author

K. Bagyalakshmi, Rasappa Viswanathan, B. Parameswari, and C. Chinnaraja

Subjects
Sequence analysis, India, Single-nucleotide polymorphism, Genome, Viral, Biology, Polymorphism, Single Nucleotide, Viral Proteins, Negative selection, Mosaic Viruses, Genetics, Cluster Analysis, Indel, Gene, Phylogeny, Plant Diseases, Sequence Deletion, Recombination, Genetic, Genetic diversity, Phylogenetic tree, Nucleic acid sequence, Genetic Variation, General Medicine, Saccharum, Mutagenesis, Insertional, RNA, Viral, Sequence Analysis
Abstract

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.

Published
2014
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2. Molecular characterization of Indian Sugarcane streak mosaic virus isolates reveals recombination and negative selection in the P1 gene.

Author

Parameswari B, Bagyalakshmi K, Chinnaraja C, and Viswanathan R

Subjects
Cluster Analysis, Genetic Variation genetics, India, Mutagenesis, Insertional genetics, Phylogeny, Plant Diseases virology, Polymorphism, Single Nucleotide genetics, RNA, Viral genetics, Sequence Analysis methods, Sequence Deletion genetics, Genome, Viral genetics, Mosaic Viruses genetics, Recombination, Genetic genetics, Saccharum virology, Viral Proteins genetics
Abstract

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., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Published
2014
Full Text
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