Molecular characterization of tobacco curly shoot virus infecting tomato (Solanum lycopersicum L.) in India

Tomato is an important vegetable crop cultivated through out India and leaf curl disease is the major constraint for production. The disease has previously been shown to be associated with begomoviruses and betasatellites. A distinct monopartite begomovirus was found associated with tomato plants showing sever leaf curl, interveinal chlorosis and stunting symptoms in polyhouse grown tomatoes in Pantnagar, Uttarakhand, India. The complete DNA-A component was amplified through rolling circle amplification (RCA) using Phi29 DNA polymerase and characterized. The DNA-A of the four isolates as comprised of 2,758 nucleotides, encoding six open reading frames (ORFs) with genome organization typical of an old world monopartite begomovirus. The begomovirus showed highest sequence identity of (89.3 to 95.8%) to tobacco curly shoot virus (TbCSV) and some other begomoviruses (59.6 to 88.1%) reported from India in tomato. Based on sequence comparison and phylogenetic analysis these isolates are strains of tobacco curly shoot virus. Recombinant analysis of the four isolates revealed that some of the isolates are recombinants of Ageratum enation virus (AEV) and tobacco curly shoot virus isolates. This is new begomovirus infecting tomato in addition to the known 16 begomoviruses occurring in India. Information on the distribution and prevalence of the different begomovirus species and recombinant forms comprising the disease complex is crucial in guiding tomato breeding programs in the search for stable and durable sources of resistance.