Molecular characterization of banana bract mosaic virus from India reveals recombination and positive selection in the VPg gene

Abstract

Banana bract mosaic virus (BBrMV), a member of the genus Potyvirus, family Potyviridae, is an important viral pathogen affecting banana and plantains in India. The present study was undertaken to determine the genetic variation and molecular evolution of BBrMV infecting different cultivars of banana and plantain in the Indian subcontinent, based on the viral genome-linked protein (VPg) gene. Sequence identity of this gene from 29 BBrMV isolates showed a range of nucleotide (nt) and amino acid (aa) identity of 75–100% and 95–100%, respectively. Phylogenetic analysis based on nt revealed that except for two isolates (TN1 and TN2), all the other Indian isolates clustered together. Different functional motifs of the VPg gene previously reported were found to be conserved. A single possible recombination event was detected using a recombination detection programme. A codon-based selection analysis revealed that most of the codons in the VPg gene were under purifying selection except for those at position 46, 47, 71, 107, 149, 153, 156, 175, 176, and 178, which were under positive selection. Gene flow between different Indian populations of BBrMV from banana was relatively low. This is the first report on genetic diversity and evolution of the VPg gene of BBrMV. Since VPg is identified as a virulence determinant in resistance mediated by the eukariotic intiation factor 4E (eIF4E) in several plant-potyvirus interactions, any mutation in the VPg interacting domain may abolish the interaction with eIF4E or its isoforms in vitro and prevent viral infection in planta. Therefore, understanding the population structure of BBrMV based on VPg would potentially provide insight into the diversification and infection cycle of this virus.