Molecular characterization of a new isolate of begomovirus affecting Croton bonplandianum in India.

Weeds, which are often-overlooked inhabitants of our ecosystems, play a remarkable role as hidden reservoirs and unconventional breeding grounds for novel viruses. Nevertheless, their importance is often underestimated in the field of biodiversity studies. Here, we report the complete nucleotide sequence, phylogenetic analysis and recombination pattern of a novel begomovirus associated with yellow vein diseases of Croton bonplandianum. During a survey conducted in August 2016, C. bonplandianum plants with severe leaf curl and yellow vein symptoms were identified at Trichy, Tamil Nadu, India. Total genomic DNA was isolated from symptomatic leaf samples by using the CTAB method, and begomovirus universal primers were used to confirm the presence of begomovirus via PCR. The samples were amplified using 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 were 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 2773 bp and showed a highest nucleotide sequence identity of 89.62% and 89.26% with papaya leaf curl virus (PaLCuV) (MK087120) and bhendi yellow vein Bhubaneswar virus (BYVBhV) (FJ589571), respectively. In phylogenetic analysis, WK3 sequence formed a separate clade with BYVBhV. Recombination analysis indicated the putative evolution of the newly characterized 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. [ABSTRACT FROM AUTHOR]