Genetic diversity and evidence of recombination in the coat protein gene of Onion yellow dwarf virus

The coat protein (CP) coding region of seven Polish Onion yellow dwarf virus (OYDV) isolates was sequenced. It was 771 bp long in all the seven isolates, and encoded a protein of 257 amino acids. Comparative nucleotide sequence analysis revealed diversity of 3 % among the Polish isolates and of 20 % among all garlic isolates worldwide. The comparison of CP sequences of 15 OYDV onion isolates, retrieved from GenBank, revealed an identity of 88-100 and 94-100 % at nt and aa level, respectively. Phylogenetic analysis clustered Polish OYDV isolates in the Subgroup I with isolates from Italy, Argentina and Japan. GARD and SBP algorithms in Datamonkey server and RDP program were employed to detect recombination events in the genome. Recombination analysis provided strong evidence for recombination events in 12 of the sequences analyzed. As regards selection inference, six algorithms (SLAC, FEL, IFEL, REL, MEME and PARRIS) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of OYDV capsid. The ratio of nonsynonymous and synonymous polymorphic sites indicated that purifying selection has acted to eliminate deleterious mutations in coding sites. This is the first report of recombination in OYDV isolates.