Expressed and differentially expressed genes before and after F. verticillioides inoculation. (A) Venn diagrams of total and F. verticillioides-inoculated genes. Venn diagrams illustrating the relationships between total expressed (expr) genes and differentially expressed genes (DEGs) after F. verticillioides inoculation in the two maize genotypes CO354 and CO441. (B) Clustering and heat maps of differentially expressed genes grouped into 4 clusters based on the expression profiles. Modulated genes are distinguished in genes differentially regulated between CO354 and CO441 genotypes before F. verticillioides inoculation (Cluster I), genes modulated by F. verticillioides common to both genotypes (Cluster II), genes specific to CO441 and CO354 lines (Cluster III and IV, respectively). The colour scale indicates the FPKM expression values (darker red indicate higher level expression values, light red indicates lower gene expression values). The heat map and clustering of FPKM expression values were generated with custom scripts using Euclidean distance measure with average linkage.