Molecular characterization of a new begomovirus infecting Croton bonplandianum in India

Abstract

Weeds, those often-overlooked inhabitants of our ecosystems, play a remarkable role as hidden reservoirs and unconventional breeding grounds for novel viruses. Their significance, however, tends to be underestimated in the realm of biodiversity studies. Here we report the complete nucleotide sequence, phylogenetic analysis and recombination pattern of the begomovirus disease complex associated with new yellow vein diseases of Croton bonplandianum. During, survey conducted in August-2016, we have detected severe leaf curl and yellow vein symptoms on C. bonpandiaum at Trichy, Tamil Nadu, India. Total genomic DNA of infected leaf samples was isolated by using CTAB method and were subjected to PCR using begomovirus universal primers to confirm the presence of begomovirus. The samples were then used for Rolling Circle Amplification (RCA) followed by restriction digestion to yield ~ 2.7 Kb fragment unit length of begomoviruses. Full length fragments ligated with pUC19 vector was transformed to E. coli and the recombinant clones were confirmed by colony PCR and restriction digestion. The complete genome sequence obtained for the clone WK3 contained 2773bp and showed a highest nucleotide sequence identity of 89.62% and 89.26% with papaya leaf curl virus (PaLCuV) (MK087120) and bhendi yellow vein Bhubaneshwar virus (BYVBhV) (FJ589571) respectively. In phylogenetic analysis, WK3 sequence formed a separate clade with BYVBV. Recombination analysis indicated the putative evolution of newly characterized the begomovirus isolate WK3 through frequent recombination of parental sequences tomato leaf curl Iran virus (ToLCIRV) and BYVBhV in the background of CroYVMV. Based on the current ICTV criteria for the demarcation of begomoviruses species threshold (< 91%), this is identified as a member of new virus species for which the name “Croton yellow vein leaf curl virus” is proposed based on its symptom morphology.