Sequence analyses of novel Potato virus YNTN and resistance-breaking PVYO isolates from Sweden

Abstract: Potato virus Y (PVY) is a devastating potato pathogen affecting potato (Solanum tuberosum) production worldwide. In the last few decades, novel PVY recombinant genotypes have been described to induce severe symptoms in numerous potato cultivars. This study aimed to determine complete and partial genome sequences of some Swedish PVY isolates with novel biological properties. The complete coding sequence of one resistance-breaking PVYO (O-MB) and three PVYNTN isolates were determined, along with six partial genomes. Isolate O-MB shared an amino acid identity of 99% with the PVYO and PVYZ strains and was in phylogenetic group PVYO/Z. O-MB differs from all studied isolates belonging to the PVYO and PVYZ strains by having a valine at position 90 in the HC-Pro protein, and from numerous PVYO and PVYZ isolates by having arginine at position 155 and glutamine at position 276 in the P3 protein. These amino acid residues may play a role in overcoming the resistance gene Nytbr in potato. In addition, the three Swedish PVYNTN isolates shared an amino acid identity of 99% with isolates of the variant PVYNTN (A) and were in phylogenetic group PVYNTN. Three of the partial genome sequences shared an amino acid identity of 99 – 100% with PVYNTN and PVYZ-NTN and were in phylogenetic group PVYNTN. These findings confirm the presence of the PVYNTN strain in Sweden. Two of the partial genome sequences shared an amino acid identity of 100% with the PVYN-W strain, and one sequence shared an amino acid identity of 99% with isolates of the PVYO, PVYZ and PVYN-W strains. These three partial genome sequences were in phylogenetic group PVYO/Z. Recombination analyses revealed that O-MB is a non-recombinant isolate, while the Swedish PVYNTN isolates have three recombinant junctions located within the HC-Pro/P3, VPg and CP cistrons, which is similar to numerous European isolates belonging to the variant PVYNTN (A). Interestingly, PVY defective RNA molecules (D-RNAs), i.e. PVY genomes with single-deletions of 1582 to 5149 nucleotide residues in length spanning the regions NIb to CP, CI to NIb, 6K2 to CP and CI to CP, were found for PVY for the first time. There were ten different patterns of PVY D-RNAs identified in this study. The D-RNA of NWO-KE1-2, which belongs to the PVYNTN strain, was found to have an in-frame single-deletion of 2907 nucleotide residues spanning CI/ to NIb region as well as a duplication of 383 nt located within the CI cistron. It is possible that these D-RNAs could play a role in PVY pathogenicity/virulence, adaption and/or evolution.