Sequence variation of P1 gene in Potato virus Y isolated from Fujian Province

To understand the sequence variation and the putative protein structure of P1 gene in Potato virus Y (PVY) and to identify the sources of the variation, P1 gene in PVY isolated from Fujian Province was amplified by reverse-transcription polymerase chain reaction (RT-PCR) using a pair of degenerate primers designed from the conserved regions of published sequences. Sequence variation and putative protein structure were analyzed, and phylogenetic tree was reconstructed using Bayesian inference method. Expected fragments of 915 bp in size were amplified from 12 samples collected from Fujian Province by RT-PCR. The 12 sequences shared 73%-99% nucleotide identity with the reference sequences from GenBank. A strong recombination signal was identified at position 309 in sequences of isolates QK44, XT02, XT08 and LH05. Among the 12 sequences, 85 amino acid variants were detected, indicating high sequence variation in the P1 protein. However, positions 41-275 in the protein were highly conserved, especially in three active sites (H₁₉₂, D₂₀₁ and V₂₃₅). Phylogenetic analysis grouped the sequences into three clades, each with different Coiled-coil domains and 3D-structures, suggesting divergent phylogenetic relationship among the groups. The above results show P1 gene in PVY is highly variable but contains 3 conserved active sites (H₁₉₂, D₂₀₁, V₂₃₅) and the high genetic variation in the gene is primarily due to mutation and recombination.