Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and subtropical 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.
Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) and chilli leaf curl betasatellite (ChiLCB). Phylogenetic analysis of complete genome (DNA-A) sequences of 132 ChiLCV isolates from five countries downloaded from NCBI database clustered into three major clades and showed high population diversity. The dN/dS ratio and Tajima D value of all viral DNA-A and associated betasatellite showed selective control on evolutionary relationships. Negative values of neutrality tests indicated purified selection and an excess of low-frequency polymorphism. Nucleotide diversity (π) for C4 and Rep genes was higher than other genes of ChiLCV with an average value of π = 18.37 × 10−2 and π = 17.52 × 10−2 respectively. A high number of mutations were detected in TrAP and Rep genes, while ChiLCB has a greater number of mutations than ChiLCA. In addition, significant recombination breakpoints were detected in all regions of ChiLCV genome, ChiLCB and, ChiLCA. Our findings indicate that ChiLCV has the potential for rapid evolution and adaptation to a range of geographic conditions and could be adopted to infect a wide range of crops, including diverse chilli cultivars.
Chili leaf curl virus (ChiLCV), a member of the Geminiviridae family (Genus: Begomovirus), is one of the most destructive plant viruses. Micro (mi) RNAs (miRNAs) are the endogenous non-coding small RNAs that play significant roles in plant growth and stress resistance by degrading targeted mRNA or repressing mRNA translation. Computational methods have identified numerous miRNAs in many plant species, whereas there is no report of chili miRNAs targeting essential genes of the ChiLCV genome and associated satellites. In this study, we have predicted chili-encoded miRNAs that could be used for silencing against chili leaf curl virus (Accession no. MF737343) infection. We predicted several potential mir-miRNAs, exhibited high complementarities with V1 coat protein and C1 (Rep) genes of ChiLCV. Other overlapping genes, such as V2, C2, and C3 were also targeted by mir-miRNAs.
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