Micro-evolution of potato virus y through deep sequencing - testing the role of the host plant on the variability of the virus genome

Crutzen, François [UCL] Moreau, Virginie [UCL] Desoignies, Nicolas [UCL] Bragard, Claude [UCL]

Potato virus Y (PVY) is a major pathogen of potato crops worldwide. Genomic recombination events between viral strains gave rise to multiple PVY variants that are considered as different viral types. The potential impact of the host on the evolution and variation of the PVY genome is however still unknown. Our study aimed at assessing the possible influence of three potato varieties (Bintje, Kennebec and Lady Rosetta) or tobacco on the genome variability of a Belgian N-NTN strain of PVY. PVY-inoculated potatoes were left for 42 days in a controlled chamber before extraction of the total RNAs. For each PVY-infected potato variety, tobacco as well as the inoculum (original strain) and experimental controls (transcripts from plasmid clones), three targets were amplified by RT-PCR, two covering the coding sequence of the protein HcPro (Hc1 and Hc2) and one for the N-terminal coding sequence of the coat protein (CP). Amplicons were sent for 454 deep sequencing (Beckman Coulter Genomics, USA). More than 500.000 different sequences were generated, sorted and aligned using bioinformatics tools. The results analysis and implications in terms of understanding the PVY micro-evolution under different varietal contexts will be discussed.