Identification and characterization of Sw5a, Ty1/Ty3, and Pelota gene in chilli plant against Chilli Leaf Curl Disease

Chili leaf curl virus disease (ChiLCVD), caused by begomoviruses, significantly hinders chili (Capsicum annuum L.) production globally. Begomoviruses manipulate protein interactions to undermine host defense mechanisms. This study focused on three key resistance genes, namely Sw5a, Ty1/Ty3, and a Pelota-like gene, which are involved in defending against the Chilli leaf curl virus (ChiLCV). These genes were identified in chili plants through their interactions with ChiLCV in tomato plants, retrieved, and subjected to BLAST analysis against C. annuum genomes. A comprehensive characterization included analyses of conserved motifs and domains, protein-protein interactions, and phylogenetic relationships in both chili and tomato plants. Additionally, molecular docking and molecular dynamics simulations were performed on the Pelota protein with plant-derived compounds from Nirgundi (Vitex negundo), which were identified through GC-MS analysis. Seven conserved motifs were identified across homologous proteins, highlighting domains such as the aRF1/eRF1/PelA superfamily, NB-ARC, RdRP, and RX-CC-like domains. The Pelota protein was found to interact directly with RDRP, suggesting its crucial role in resistance. Phylogenetic analysis revealed that all protein sequences clustered within the same evolutionary branch for both chili and tomato. Among the 48 ligands tested, oleanolic acid displayed the highest binding energy (-6.3 kcal/mol), followed by vitrofloal-E and acetyl oleanolic acid. These findings emphasize the potential of V. negundo compounds to enhance resistance in the non-mutated Pelota protein, mimicking natural resistance mechanisms. This study advances our understanding of molecular resistance pathways in ChiLCV and highlights the therapeutic potential of natural plant compounds as sustainable solutions to mitigate ChiLCVD.