Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as "pestification." Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests,

1 7 1 8 1 9 3 1agricultural-type pathogen in wild forests. We detected a SNP predicting the ability of the 3 2 fungus to parasitize the different host populations, which induced an early stop codon in a 3 3 gene coding for a small secreted protein in the agricultural-type fungal population, thus 3 4 representing a putative avirulence gene which function loss would enable to parasitize 3 5 cultivated apples. Pathogenicity tests in fact revealed the pestification of V. inaequalis, with 3 6 higher virulence of the agricultural-type population on both wild and domesticated trees. Our 3 7 findings highlight the threat posed by cultivating a crop near its center of origin, with the 3 8invasion of a pestified pathogen on wild plants and introgression in the wild-type pathogen.

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