Tomato leaf curl Karnataka virus from Bangalore, India, Appears to be a Recombinant Begomovirus

The genome of Tomato leaf curl virus (ToLCV) from Bangalore, India, a whitefly-transmitted geminivirus, was cloned (pIND9) and sequenced. The circular DNA of 2,759 nucleotides (U38239) is organized similarly to that of other begomoviruses with monopartite genomes. Comparison of the nucleotide sequence of pIND9 with other tomato-associated begomoviruses from India (Tomato leaf curl Bangalore virus [ToLCBV, Z48182]) and Tomato leaf curl New Delhi virus-Severe (ToLCNdV-Svr, U15015) showed moderate DNA sequence identities (82 to 87%) between capsid protein (CP) genes but low identities (66 to 67%) for the intergenic regions and the replication-associated protein (Rep) genes (75 to 81% identity). Phylogenetic trees generated with nucleotide sequences of the Rep and CP genes of 26 begomoviruses indicated that this ToLCV is distinct from other begomoviruses and that it may be a recombinant virus derived from at least three different viral lineages. Tomatoes (Lycopersicon esculentum) inoculated with the cloned DNA monomer of ToLCV (pIND9) via particle bombardment developed leaf curling and yellowing symptoms. The virus was transmitted by Bemisia tabaci biotype B from tomatoes infected via particle bombardment to healthy tomatoes and by sap inoculation from infected tomatoes to tomato, Nicotiana benthamiana and N. tabacum. This ToLCV is a distinct member of the genus Begomovirus from India that differs from the previously characterized Tomato leaf curl Sadasivanagar virus isolate Bangalore 1 (L12739), ToLCBV (Z48182), ToLCBV isolate Bangalore 4 (AF165098), and the bipartite ToLCNdV (U15015, U15016). Thus, this ToLCV is named Tomato leaf curl Karnataka virus (ToLCKV).