Coat protein gene based-molecular characterization of tomato mosaic virus (Tomv) infecting tomato (Solanum lycopersicum L.)

The Tobamovirus genus of Tomato mosaic virus (ToMV) is one of the most destructive diseases and causes very high yield loss in Tomato. The present investigation aimed to characterize the ToMV infecting to tomato from different regions of Maharashtra. The characterization of ToMV samples was achieved using coat protein gene based characterization. The coat protein gene specific amplification of 479 bp fragment was detected in the ToMV infected samples. The coat protein gene (479 bp) of representative ToMV isolates i. e. ToMV Pune-1, ToMV Parbhani-1, ToMV Latur-2, and ToMV Solapur-1 was sequenced. BLASTn analysis of four isolated ToMV showing the highest similarity i.e., 99.74% with other strains of ToMV. In BLASTp analysis, protein sequences showed 98.74% similarity with other coat protein gene sequences of the tomato mosaic virus available in the NCBI database. Among four isolates of ToMV coat protein gene sequences the ToMV Latur-2 and ToMV Solapur-1 sequences showed the highest similarity at nucleotide as well as protein sequence level. The ToMV isolated were 14 Tobamoviruses CP gene sequences were analysed phylogenetically clustered in to three group based on nucleotide and protein sequences. Tomato mottle mosaic virus (ToMMV) is found closely related to ToMV and grouped in the same cluster in nucleotide and protein sequences. The tobacco latent virus was out-grouped. The Percent identity within the coat protein gene of ToMV isolates varied from 89 to 100% at the nucleotide level and at 82 to 100% at the protein level. Whereas percent identity among the ToMV and other related Tobamoviruses ranges from 46 to 78% at nucleotide and 12 to 74% at the protein sequence level. Thus variation, mutation and evolution in the sequence of the coat protein gene is an important mechanism of virus adaptation and may lead to the development of new species.