Comparison of RNA-Seq and real-time RT-PCR analyses. Expression profiles of (A) transcription factor FAMA, (B) Trichoderma-induced osmotin 2 (OSM2), (C) serine/threonine kinase receptor (STKR), (D) hypothetical protein (HP), (E) WRKY transcription factor of cluster 2 (WRKY-C2), (F) WRKY transcription factor 1 (WRKY1), (G) chalcone synthase 3 (CHS3), (H) auxin response factor (ARF), (I) constans-like protein (COL), (J) mitogen-activated protein kinase (MAPK), (K) protein phosphatase 2C (PP2C), (L) polyphenol oxidase (PPO), (M) chlorophyll a-b binding protein (CAB), (N) acidic endochitinase 3 (Chit3), (O) Trichoderma-induced osmotin 1 (OSM1), (P) AP2-like ethylene-responsive transcription factor (AP2), (Q) invertase (INV1), (R) receptor-like serine/threonine-protein kinase (RLK), (S) universal stress A-like protein (UspA), (T) ABC transporter C family member (ABC-C), (U) sucrose synthase (SS), (V) ethylene-responsive transcription factor (ERF), (W) LRR receptor-like serine/threonine-protein kinase (LK), and (X) WRKY transcription factor of cluster 10 (WRKY-C10). Blue dotted lines represent expression levels (FPKM) as assessed by RNA-Seq analysis and reported as means and standard errors of three biological replicates for each treatment: control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Histograms represent the relative expression levels (fold-change relative to the expression in control plants) as assessed by real-time RT-PCR and reported as means and standard errors of three biological replicates for each treatment.