Botrytis cinerea expression profile and metabolism differs between noble and grey rot of grapes

Botrytis cinerea, the pathogen causing grey rot (GR) with important economic losses in fruit crops, can also cause noble rot (NR) of grape berries under certain environmental conditions, leading to metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in biochemical processes in these harmful vs. beneficial berry rot types are still scarcely understood. We generated and analyzed transcriptomic data from healthy (H), NR and GR grape berries collected in the Tokaj wine region in Hungary. Our study shows that B. cinerea is most active in NR, followed by GR and H berries. In addition, expression profiles differed qualitatively between NR and GR, and to a smaller extent between months. Several functional genes expressed during NR were linked to well-known physico-chemical changes in botrytized grape berries, including berry skin degradation and the formation of metabolites favorable for botrytized wine production. In addition, we found that B. cinerea appeared to express genes involved in the biosynthesis of antimicrobials during NR, but not in GR, which likely contributes to the dominance of this fungus during NR.