A. Pairwise similarity between strains based on the genome-wide gene expression levels (log2(TPM+1)). The similarity was simply estimated by using Pearson correlation coefficient. X-axis and y-axis represent different strains. The similarity was assessed by Pearson correlation coefficient between strains. Hierarchical clustering was further applied at the strain level. The exact comparison pairs (the x-axis and y-axis values) and their corresponding coefficient value (the z-axis value) can be obtained by hovering the mouse on top of the heatmap.