Positive correlations between the genomic and environmental contributions. Firstly, scatter plot of the expression levels of 3710 common genes in MDS42 and MG1655 is shown (A, top panel). A total of 159 genes with differential expression in MDS42 caused by genome reduction (DEGs_gr) are highlighted, including 83 with increased expression (in orange) and 76 with reduced expression (in purple), respectively. The expression levels of these 159 genes (DEGs_gr) in MG1655 under the regular and heat shock conditions (MG1655 vs. MG1655_heatshock) are additionally compared (A, bottom panel). Secondly, scatter plot of the expression levels of 3710 common genes in MG1655 in the presence or absence of heat shock treatment is shown (B, top panel). A total of 95 genes with differential expression due to heat shock (DEGs_hs) in MG1655 are highlighted, including 64 upregulated (in yellow) and 31 downregulated (in cyan) genes, respectively. The expression levels of these 95 genes (DEGs_hs) in both MG1655 and MDS42 under regular conditions (MG1655 vs. MDS42) are also compared (B, bottom panel). Finally, positive correlations between the genetic and environmental contributions to the transcriptional changes of total 3710 common genes are shown (C). The genetic contribution refers to the changes in gene expression caused by genome reduction, i.e., the subtraction of the expression level in MG1655 from the expression level in MDS42. The environmental contribution refers to the changes in gene expression due to heat shock in MG1655, i.e., the subtraction of the expression level in MG1655 from the expression level in MG1655_heatshock. The expression level is determined as log10 (mRNA concentration), with the unit of pM. The Pearson’s correlation coefficients are indicated.