Genetic diversity and recombination in Potato Virus Y.

摘要

Genetic diversity and abundance of RNA viruses are due to three major forces: mutation, recombination and reassortment. The evolution of these viruses has been studied both experimentally and through sequence analysis. Massive numbers of virus genome sequences and bioinformatics tools give us a chance to explore evolutionary mechanisms through whole genome analysis.;Potato virus Y (PVY) is a positive-strand RNA virus in the Potyvirus genus. It is one of the most damaging plant pathogens, causing significant yield and quality losses in four main crops: potato, tomato, tobacco and pepper. Because of multiple documented mutations and frequent recombination, it is a particularly attractive model to study mechanisms of general RNA virus evolution. Various PVY strains can be distinguished by symptoms in different host plants, serology and with reverse transcript polymerase chain reaction (RT-PCR) tools, and newly emerged strains can also be identified. In this study, we characterized two new PVY strains, L26 and O5, whose properties changed because of mutations. L26 lost its ability to induce tobacco veinal necrosis because of one mutation in the HC-Pro gene, where Asp-205 in the PVYNTN strain mutated to Gly-205; O5 gained a new serological property because of a single mutation in the capsid protein, where Arg-98 in the PVYO strain mutated to Gln-98. This change allowed O5 to react positively with a PVYN-specific monoclonal antibody, IFS, and to be misidentified as a PVYN strain.;The evolutionary mechanisms driving the emergence of PVY recombinants are not clear. We investigated the influence of two factors, RNA secondary structure and AU-rich regions, based on the replicase-mediated template-switching model. Using the FORS-D value and the AU content distributions along PVY genomes, only a few recombination junctions were located in lower negative FORS-D and/or higher AU content regions. Most recombination junctions had more negative FORS-D values upstream and/or higher AU content downstream. We concluded that these two factors are not the main forces to drive recombination in PVY, although they may fit the template-switching model in specific recombination regions.;Taken together, we have successfully applied bioinformatics and laboratory experiments to determine recombinant structure and characterize specific mutations of PVY, and to understand the evolution of RNA viruses.