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Plant nitrogen (N) fertilization is known to affect disease; however, the underlying mechanisms remain mostly unknown. We investigated the impact of N supply on the  Arabidopsis thaliana–Botrytis cinerea  interaction.  A. thaliana  plants grown in low nitrate were more tolerant to all wild‐type  B. cinerea  strains tested. We determined leaf nitrate concentrations and showed that they had a limited impact on  B. cinerea  growth in vitro. For the first time, we performed a dual RNA‐Seq of infected leaves of plants grown with different nitrate concentrations. Transcriptome analysis showed that plant and fungal transcriptomes were marginally affected by plant nitrate supply. Indeed, only a limited set of plant (182) and fungal (22) genes displayed expression profiles altered by nitrate supply. The expression of selected genes was confirmed by quantitative reverse transcription PCR at 6 hr postinfection (hpi) and analysed at a later time point (24 hpi). We selected three of the 22  B. cinerea  genes identified for further analysis.  B. cinerea  mutants affected in these genes were less aggressive than the wild‐type strain. We also showed that plants grown in ammonium were more tolerant to  B. cinerea . Furthermore, expression of the selected  B. cinerea  genes in planta was altered when plants were grown with ammonium instead of nitrate, demonstrating an impact of the nature of N supplied to plants on the interaction. Identification of  B. cinerea  genes expressed differentially in planta according to plant N supply unveils two novel virulence functions required for full virulence in  A. thaliana : a secondary metabolite (SM) and an acidic protease (AP).

Plant nitrogen supply affects the Botrytis cinerea infection process and modulates known and novel virulence factors