Cloning and Characterization of Rep Gene of the Strain of Tomato Leaf Curl New Delhi Virus (G: Begomovirus, F: Geminiviridae) Infecting Ridge Gourd in Karnataka and in silico Analysis of Rep Protein

Abstract

Ridge gourd [Luffa acutangula (Roxb.) L.,] is one of the important vegetable crop affected by various diseases particularly viral disease tomato leaf curl New Delhi virus (ToLCNDV). The ridge gourd plants with leaf curling and yellowing symptoms were collected and used in for the amplification of the of the Rep gene. Cloning, sequencing and bioinformatics analysis of the Rep gene was carried out.  The results revealed the association of this virus isolate with the different host of Cucurbitaceae family. Pairwise identity derived implemented by BLAST identified that the replicator initiator protein gene (Rep) of the bipartite virus showed  maximum 96.90% sequence identity to the corresponding Rep gene of ridge gourd tomato leaf curl New Delhi virus isolate RG3 in ridge gourd - complete genome from Madikari, Karnataka (accession no KT426905). This also showed 97.90% sequence similarities with tomato leaf curl New Delhi virus strain CH7 of Chrysanthemum. Phylogenetic dendrogram of the Rep gene depicted that it grouped with ToLCNDV of different Indian isolates of ridge gourd and with ToLCNDV of potato from Pakistan (LN908936), and with tomato from Bangladesh (KM383738.1) showing 93.12% and 92.94% sequence similarity respectively. This study provides association of the Rep gene infected ridge gourd pants with Cucurbitaceae family crops and other related crops. This will helps in carrying further research in the management of ToLCNDV diseases using different biotechnological applications.