Molecular Variability in the replicase gene of viruses causing tomato leaf curl disease in India

Abstract

Tomato Leaf Curl Virus (ToLCV) - infected samples collected from four different ecological zones of India: Northern zone, NewDelhi (IARI) [ToLCNDV - IARI]; Central zone, Jabalpur [ToLCV - Jb], Raipur [ToLCV - Rp] and Southern zone, Dharwad [ToLCV - Dh] were maintained by whitefly transmission into tomato cv Pusa Early Dwarf. Replicase gene coding for replication initiator protein (Rep) was amplified by PCR using gene specific primers, yielding an amplicon of 1086 bp for all the isolates. Sequence analysis of the rep amplicons of all the Indian isolates of ToLCV causing the disease clearly shows the presence oftwo subgroups irrespective of their geographical evolution. Isolates belonging to subgroup I comprising of tomato leaf curl virus - New Delhi (ToLCV - NDe) having bipartite genome are conserved within themselves and showed 94 - 9 5% nucleotide sequence homology. Second subgroup comprising of tomato leaf curl virus - Bangalore (ToLCBV) having monopartite genome and conserved among themselves, but showed only 73 - 75 % homology with the subgroup I. In phylogenetic tree analysis, ToLCV - NDe appeared in a different cluster than ToLCV - Ban. All the four isolates used in this study fall in ToLCV - NDe group based on their replicase gene sequences. The specificity determinant located at N terminal suggests ToLCV - NDe and ToLCV-Rp as mild isolates.