Nucleotide evidence of Capsid Protein gene of potato virus Y from a Pakistani isolate.

Potato virus Y (PVY) is an emerging problem in main potato growing areas of Pakistan and new molecular tools are necessary for confirmation of PVY. Serological detection of PVY was achieved through Enzyme Linked Immunosorbant Assay (ELISA) and biologically authentication was accomplished on susceptible indicator host plants (Nicotiana tabacum cv. Samsun NN, N. rustica, N. benthamiana and Chenopodium album). Appropriate sense and antisense primers for Capsid Protein (CP) gene were used for molecular diagnosis of PVY in Polymerase Chain Reaction (PCR) and sequence of Pakistani isolate (JQ518267) exhibited 795 nucleotides with maximum composition of adenine followed by guanine, thymine or uracil and cytosine respectively. Physical and chemical properties of CP gene were computed and different bioinformatics tools clearly indicate that amplified gene is hydrophilic, non-allergen and highly conserved region. The final sequence was further compared with ordinary, common, necrotic and recombinant strains of PVY. The phylogenetic tree clearly indicates four different clusters and Pakistani isolate falls in first cluster exhibiting the high degree of nucleotide homology (99.98%) with previously reported isolates of Pakistan.