Identification of Two Novel Recombinant Types of Potato Virus Y from Solanum tuberosum Plants in Southern Region of Russia.

Abstract

Potato virus Y (PVY, genus Potyvirus, family Potyviridae) is one of the most devastating and economically important potato pathogens. Members of the Potyviridae family demonstrate high recombination rates. In nature, 5 major parental variants of PVY were identified with at least 35 recombinants. In this study we report two novel PVY recombinants discovered in the sprouts of potato tubers produced in field conditions in Astrakhan region of Russia in 2021 using high-throughput sequencing and de novo genome assembly. These recombinants, which were named Ast-A-I and Ast-A-II, have previously unknown arrangements of genome sections derived from PVYO and PVYN with a novel recombination junction at the position 7850 nt of the PVY genome, in the middle part of the RNA-dependent RNA polymerase (NIb) gene, with PVYO-type sequence at the 5'-end of this junction and PVYN-type at the 3'-end. Other recombinant junctions in the novel PVY variants were previously found in PVYNTNa and PVYNTNb. This includes those at the positions 2390 and 9200 (PVYN at the 5'-end and PVYO at the 3'-end) which were present in both novel recombinants, and at the position 500 (PVYO at the 5'-end and PVYN at the 3'-end) which present in Ast-A-II. The presence of PVY variants with novel recombinant point is verified by Sanger sequencing. Phylogenetic analysis of genomic RNA showed that the sequences of these recombinants form a separate branch which do not cluster with previously described PVY strains.