Supplementary Data 1 - 20

Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) <i>Papiliotrema terrestris</i>, the pathogen <i>Penicillium expansum</i>, and the host <i>Malus domestica</i>. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissues, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to <i>P. expansum</i> analysis, 1017 DEGs are upregulated when grown in apple tissues, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host <i>M. domestica</i> finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with <i>P. expansum</i>. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.<br>