Molecular characterization and genome organization of temperature insensitive necrosis inducing strain of BCMV infecting common bean in India

Abstract

BCMV strain NL-1n differing from already reported BCMV strains has been encountered on common bean in the entire North-Western Himalayan region. Unlike other strains of BCMV, this strain induced mosaic symptoms in cultivars possessing recessive “i” alleles and temperature insensitive necrosis (below and above 30 °C) on differential cv. Jubila carrying the dominant allele “I″. Despite the importance of the crop and the virus there is lack of genome information about any strain of this virus in the Indian subcontinent. In this study, complete genome sequence of NL-1n was determined to understand its relationship with other BCMV strains. The genome was 10,081 nucleotides long containing an open reading frame of 3222 amino acids that encoded a single polyprotein of approximately 365.99 kDa which is cleaved into ten proteins typical of Potyvirus. Pair wise comparison and phylogenetic analysis revealed that BCMV-NL-1n is more closely related to BCMV-NL-1 though clustered along with other strains and isolates of BCMV. Recombination analysis also revealed BCMV-NL-1n to be a recombinant showing two unique events. Based on these features, we propose to designate NL-1n as a recombinant of NL-1 and RU-1 strains. This is the first report of a BCMV strain inducing temperature-insensitive local necrosis on I gene carrying differential cv. Jubila as well as its complete genome sequence from India.