Complete genome sequencing of Banana bract mosaic virus infecting cardamom revealed its closeness to banana infecting isolate from India

Abstract

The complete genome of Banana bract mosaic virus (BBrMV), a Potyvirus belonging to the family Potyviridae causing chlorotic streak disease of cardamom (Elettaria cardamomum) in India was determined for the first time from a naturally infected cardamom var. Njallani Green Gold through reverse transcription PCR using nine sets of primers designed to different overlapping regions of the genome. The complete genome has 9708 nucleotides excluding poly (A) tail and has the genome organization similar to that of BBrMV isolates infecting banana and flowering ginger (Alpinia purpurata). The virus has a single open reading frame of 9372 nucleotides that encodes for a polypeptide of 3124 amino acids which is later cleaved into ten matured proteins. The length and arrangements of different proteins in BBrMV-Cardamom was similar to other BBrMV isolates except for the P1 protein that showed a single amino acid deletion. Comparison with three available complete genome sequences revealed that, BBrMV-Cardamom isolate is more closer to BBrMV-Banana isolate from India (BBrMV-TRY) (96.7% identity) than to BBrMV- Banana isolate from Philippines and flowering ginger isolates from USA (94.5%). Analysis of polyprotein and their individual proteins also showed close identity of BBrMV-Cardamom and BBrMV-TRY. The phylogenetic analysis also suggested that BBrMV-Cardamom isolate is closely related to other BBrMV isolates