Characterization of Sunn hemp begomovirus and its geographical origin based on in silico structural and functional analysis of recombinant coat protein

Sequence alignment of the 897 bp amplicon obtained from a diseased sunn hemp ( Crotalaria juncea L.) plant DNA revealed a complete 771 bp coat protein (CP) gene flanked by 3’ regions of the AV2 and AC3 genes. Southern hybridization using (α-32P) dCTP labeled (CP) gene probe of Indian tomato leaf curl virus (IToLCV) demonstrated the association of begomovirus with the leaf curl disease of sunn hemp. Phylogenetic data suggested that, the AV2, CP and AC3 genes have closest genetic relationship with begomovirus isolates from India, China and Bangladesh, respectively. In silico recombination analysis elucidated a 297 nucleotides hot spot (346 to 643 nucleotides) within AV2 overlapping region of CP gene, amenable to genetic rearrangements, with lineage from tomato leaf curl virus Bangalore (ToLCuVB) and Indian cassava mosaic virus-Ind (ICMV) as major and minor parents, respectively. Thus, it is concluded that the recombinant CP genes related to begomoviruses are evolved from the Indian isolates, causing broad host specificity and molecular diversity among the related begomoviruses across the geographical limits of Southeast Asia. Keywords: Begomovirus , sunn hemp, coat protein, recombination, phylogenetic analysis, in silico analysis