Fig. 3

Changes in gene expression at steady states. a Scatter plots of gene expression at steady states under the regular temperature. The gene expression of the ancestor strain at regular temperature (Anc_r) is plotted against gene expression of the evolved strains at regular temperature (41B_r, 43B_r and 45L_r), which represents a comparison of genotypes (genome mutations). Correlation coefficients are indicated. b Scatter plots of gene expression at steady states under the evolution-stimulating temperatures. The gene expression patterns of the evolved strains at regular (41B_r, 43B_r and 45L_r) and evolutionary-stimulating (41B_e, 43B_e and 45L_e) temperatures are plotted individually, representing a comparison of the growth temperatures. Correlation coefficients are indicated. c Heat maps of enriched gene groups of differentiated expression. The results of GSEA based on gene category are shown. The left and right panels represent comparisons of genotypes and growth temperatures, respectively, corresponding to (a) and (b) panels, respectively. The statistical significance (FDR q value) is indicated in the heat map. Vivid colors represent high significance in the directions of either up-regulated (yellow) or down-regulated (blue) genes. The strains are indicated. The labeled black bars (C1–C4) located at the right of the heat maps indicate the manually categorized clusters showing distinguished changing patterns