Fig. 2
a The Volcano plot showing the significant and differentially expressed genes (Pcal < 0.05). The Y axis denotes the mean expression value of log 10 (p-value) whereas the X axis displays the log2 Fold change value. The highlighted genes are significantly expressed at a default adjusted p-value cut-off of 0.05 (red; denotes upregulated, blue; denotes downregulated). Log FC indicates the log of the change in gene expression in T. harzianum T34 primed treatments compared to the un-inoculated control. Log counts are the log of the read counts mapping to each gene. Volcano plots show the LogFC vs. the – log10 FDR (False discovery rate), points with more fold change and higher –log10 FDR are more reliable. b PCA analysis plot for tomato un-inoculated control (C1, C2, and C3) and the treatment Trichoderma-tomato interaction (treatment) (T1, T2, and T3). c PCA heat map showing the pathway analysis of PCA rotation for the significant DEGs (pcal-value < 0.05). d The Box-plot showing the distribution showing the spread and centers of a data set. Measures of spread include the interquartile range and the mean of the data set. Measures of center include the mean or average and median (the middle of a data set). e Enriched GO annotation for the down-regulated DEGs (pcal-value < 0.05) showing the gene-specific pathways and number of significant genes (enrichment-specific to a particular pathway based on data from Ensemble plant and other databases. f Enriched GO annotation for the Up-regulated genes