Recombination events in PVY genomes
Potato virus Y (PVY) is one of the main pathogen that reduces tobacco crop yields worldwide. Different strains of PVY are associated with differing degrees of pathogenicity, of which the most common and economically important are known to be recombinant. Recombination is prevalent in viruses and its impact on the virulence of disease may be considerable. In order to detect recombination events, genomic sequences of 15 PVY isolates derived from Poland, Germany and Croatia were compared to 82 available genomic sequences of the PVY. Reshuffle in genomic sequences were observed in 95 isolates. The number of recombination sites of these isolates ranged from two to nine. Only in the case of two isolates belonging to the PVYC strain there was no recombination event. Isolates belonging to the PVYO strain always had two recombination sites. Most PVYNW isolates had three or four recombination sites rarely six or seven. Most of recombination sites were found within isolates belonging to the PVYNTN strain. One isolate possessed even nine recombination sites, typically 5-7. Among the fifteen tested isolates, all of them both PVYNW and PVYNTN, had a recombined fragment of genome derived from New Zealand isolate. Within PVYNTN isolates this fragment covered the whole of the 5' end of the genome, including P1, HC-Pro, and small part of P3 gene, whereas within PVYNW isolates this fragment was smaller and comprised about half of the P1 and the whole HC-Pro gene. An exception is the IUNG 14 isolate, which despite belonging to PVYNW strain, possessed fragment derived from New Zealand, such as in PVYNTN isolates. Moreover, within PVYNW isolates was found recombinant fragment near the 5' end of the genome derived from SASA 110 isolate (strain O). In addition, all PVYNTN isolates had genome fragment derived from N 605 isolate. This fragment covered NIa-Pro, NIb and almost entire VPg and coat protein gene.