Grapevine genes differentially expressed during Trichoderma harzianum T39-induced resistance to Plasmopara viticola.(A) Venn diagram summarising the distribution of 7,024 differentially expressed genes in control (C), T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.) and P. viticola-inoculated T39-treated (T39+P.v.) plants. Differentially expressed genes were identified by the DESeq package with a false discovery rate (FDR) of 5% and a fold-change greater than two in at least one pairwise comparison. (B) Grouping of differentially expressed genes into 10 clusters based on the expression profiles. Genes modulated by T39 were distinguished as those with comparable expression levels before and after P. viticola inoculation in T39-treated plants (cluster 1), genes initially modulated by T39 and further modulated by P. viticola inoculation in T39-treated plants (cluster 2), and genes affected exclusively by T39 (cluster 3). Genes modulated by P. viticola with comparable expression levels in control and T39-treated plants were classified as those with (cluster 4) and without (cluster 5) direct modulation by T39. Genes modulated by P. viticola with greater modulation (> 1.5-fold) in T39-treated than in control plants (ISR-primed genes) where classified as those with (cluster 6) and without (cluster 7) modulation by T39 treatment. Genes modulated by P. viticola exclusively in control plants were classified as those with (cluster 8) and without (cluster 9) modulation by T39, whereas genes modulated by P. viticola exclusively in T39-treated plants were grouped in cluster 10 (ISR-responsive specific genes).