Chili (Capsicum annuum L.) 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 of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton 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 Tajima D value 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 × 10^–4 substitutions site^–1 year^–1), CLCuMuV (1.49 × 10^–4 substitutions site^–1 year^–1), ToLCGV (7.47 × 10^–4 substitutions site^–1 year^–1), the genome of associated ChiLCB (4.20 × 10^–4 substitutions site^–1 year^–1) and CLCuMuA (1.49 × 10^–4 substitutions site^–1 year^–1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.

The structural model of begomovirus AC1 protein is useful for understanding biological function at molecular level and docking study. For this study we have used the ProSA program (Protein Structure Analysis) tool to establish the structure prediction and modeling of protein. This tool was used for refinement and validation of experimental protein structures. Potential problems of protein structures based on energy plots are easily seen by ProSA and are displayed in a three-dimensional manner. In the present study we have selected different AC1 proteins of begomovirus strains (YP_003288785, YP_002004579, and YP_003288773) for structural analysis and display of energy plots that highlight potential problems spotted in protein structures. The 3D models of Rep proteins with recognized errors can be effectively used for in silico docking study for development of potential ligand molecules against begomovirus infection.

Weeds are widely distributed throughout the world and have high environmental adaptability. Weeds are considered as a source of new viruses and reservoirs of unidentified economically important viruses but are often neglected during diversity studies. Many scientific reports have demonstrated that weeds serve as reservoir or alternative hosts for begomovirus (family Geminiviridae) survival and spread in the absence of the main crops. Thus, there is a pressing need for additional information on the diversity and distribution of begomoviruses associated weeds, which likely serve as virus reservoirs. This review thus presents a tip of the iceberg of the diversity of begomoviruses associated weeds in India and other parts of the world.