Molecular detection and characterization of phytoplasma in association with begomovirus in eggplant

The samples from eggplants showing mixed symptoms of little leaf and mosaic were collected from two districts (Mirzapur and Varanasi) of Uttar Pradesh, India. The total nucleic acid extracted from these samples was amplified by PCR using universal 16S rRNA primers specific to phytoplasma and primers specific to DNA-A-like sequence of begomovirus. A total of eighteen eggplant samples showing the symptoms of little leaf and mosaic tested positive for the presence of both begomovirus and phytoplasma. The phytoplasma associated with the mixed symptoms of mosaic and little leaf in the eggplant samples was identified as a member belonging to Clover proliferation group (16SrVI) (nucleotide sequence identity of 97.5-97.8%). The characterized begomovirus from the eggplant samples was identified as a strain of previously described bipartite begomovirus tomato leaf curl Palampur virus (ToLCPalV) (92.5-94.1% nucleotide sequence identity), which is known to infect cucurbits and solanaceous crops in India and Ireland. Further, putative recombination events were detected within the 16S rRNA gene F2n/R2 fragment of phytoplasma and DNA-A of strain of ToLCPalV. Most of the sequence variations observed within the phytoplasma were due to intra and interspecific recombination events between eggplant little leaf-16SrVI-D, Ca. P. asteris-16SrI and Ca. P. pruni-16SrIII. Similarly, most of the DNA fragments of newly characterized strain of ToLCPalV appear to have been derived from tomato leaf curl New Delhi virus (ToLCNDV), squash leaf curl China virus (SLCCNV) and ToLCPalV like ancestors. This perhaps is the first evidence of mixed infection of both phytoplasma-begomovirus in eggplant in India.