Diversity and distribution of begomoviruses infecting tomato in India

Leaf curl begomoviruses cause serious yield losses to Indian tomato crops. Total DNAs were extracted from leaves of 69 tomato plants and 34 weeds or neighbouring crops collected from all the major tomato producing areas of India. Eighty-one of the 103 samples were positive by PCRs using begomovirus genus-specific primers. Coat protein (CP) genes from 29 samples were PCR amplified, cloned and sequenced. Phylogenetic analyses of the CP sequences revealed five different tomato leaf curl begomovirus (TLCB) clusters each < 88% identity to the others. Four clusters represented known Indian TLCBs, whereas one cluster contained sequences originating from Haryana State with most identity (89%) to the provisional Begomovirus species Croton yellow vein mosaic virus. Sixty-five begomovirus positive samples were characterised further by PCR with DNA-beta, DNA-B, four Indian TLCB species, PALIc1960/PARIv722 (universal begomovirus primers), and by sequencing. The majority of samples represented monopartite TLCBs associated with DNA-beta components. All four known TLCBs appeared to be present throughout India. TLCBs were also present in chilli, cowpea, okra and tobacco crops, as well as in some common weeds. Papaya leaf curl virus and Pepper leaf curl Bangladesh virus sequences were detected in tomato. Mixed begomovirus infections, a prerequisite for recombination, were evident in 13 samples.