Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites inCapsicum annumFrom India

Chili (Capsicum annuumL.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A ofChili leaf curl virus(ChiLCV), CS-1 is considered to be a new distinct species ofTomato leaf curl Gujrat virus(ToLCGV) whereas RV-1 as a new strain ofCotton leaf curl Multan virus(CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and TajimaDvalue of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 x 10(-4)substitutions site(-1)year(-1)), CLCuMuV (1.49 x 10(-4)substitutions site(-1)year(-1)), ToLCGV (7.47 x 10(-4)substitutions site(-1)year(-1)), the genome of associated ChiLCB (4.20 x 10(-4)substitutions site(-1)year(-1)) and CLCuMuA (1.49 x 10(-4)substitutions site(-1)year(-1)). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms inN. benthamianaand chili, suggesting prerequisite association for typical disease development.