Fig. 5

Clustering of differentially expressed genes (DEGs) based on the metabolic function in E. coli. For this, logarithmic fold change (logFC) medians of DEGs with the same metabolic function were plotted against the number of DEGs within this group. Fold changes were calculated by dividing values of the later generation population (LGP) by values of the early generation population (EGP). LGPs correspond to populations with 60–65 evolved generations, while EGPs correspond to populations with 7–10 evolved generations. E. coli strains W3110 (A, C, E) and MDS42 (B, D, F) transformed with one of three plasmids engineered for L-cysteine production (pCYS: A, B; pCYS_i: C, D; pCYS_m: E, F) were analysed. A p-value cut-off < 0.05 was selected. Genes with unknown function as well as clusters mapped with only one gene were disregarded here, but can be found in Additional file 1: Tables S6-S11. A: 81 genes in total (57 genes within 12 cluster, 20 genes with unknown function and 4 single gene clusters). B: 34 genes in total (34 genes within 5 cluster, 6 genes with unknown function and 2 single gene clusters). C: 65 genes in total (47 genes within 8 cluster, 10 genes with unknown function and 8 single gene clusters). D: 23 genes within 2 cluster. E: 105 genes in total (70 genes within 12 cluster, 17 genes with unknown function and 18 single gene clusters. F: 14 genes in total (6 genes within 3 cluster, 4 genes with unknown function and 4 single gene clusters)