1. LR LS SR SS RR RS Cluster T7 Cluster T6 Cluster T4 Cluster T1
Additional File 2: Log fold change hierarchical clustering of P. gregata treatment response.
The treatment hierarchical clustering heat map was created with 3,788 significant (FDR < 0.001) unique DE genes responding to treatment, resistant response to P. gregata treatment, and susceptible response to P. gregata treatment. The columns differentiate the treatments (leaves resistant (LR), leaves susceptible (LS), stems resistant (SR), stems susceptible (SS), roots resistant (RR, and roots susceptible (RS)). The rows group genes by similar expression pattern, resulting in seven expression clusters. Colors indicate gene expression values based on log fold change mapped to a color gradient from low (blue) to high (yellow) expression.

2. Rbs3 Infected Sus Mock Cluster STG2 Cluster STG1 A. Cluster RTG2 Rbs3
Additional File 10: Hierarchical clustering of treatment x genotype response in stems and roots.
The hierarchical clustering heat map was created with significant (FDR < 0.001) DE genes responding to the treatment x genotype interaction in stems (A) and roots (B). Hclust was used to cluster genes with similar expression patterns based on Z-score. The Z-score was calculated by comparing expression of the gene in a sample (in log2 counts per million, cpm) to the mean of all samples for the gene, divided by the standard deviation of the gene across all samples. The columns differentiate the four treatments within each tissue (resistant-infected, resistant-mock, susceptible-infected, and susceptible-mock). The rows group genes by similar expression pattern, resulting in two expression clusters for each tissue delineated by colored bars on the Y-axis. Colors indicate Z-score values. A Z-score less than zero indicates lower expression than the mean, and a Z-score greater than zero indicates greater expression than the mean. DE genes for the genotype by treatment interaction for all tissues are listed in Additional File 8. For visualization purposes, the heat maps are not to scale.