Pseudogene repair driven by selection pressure applied in experimental evolution

We performed evolution of ?menF?entC strain of Escherichia coli K12 MG1655 to study how the system adapt to the loss of siderophore biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring. Overall design: Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation. ALE is the acronym for adaptive laboratory evolution. ALE_39.91, ALE_29.82 and ALE_30.83 are the independent biological replicates of ?menF?entC which are evolved in our laboratory to study how the strains adapt to the loss of the menF and entC genes. Similarly, ALE_36.86, ALE_37.25 and ALE_38.28 are the independent biological replicates of ?menF?entC?ubiC which are evolved in our laboratory to study how the strains adapt to the loss of the menF, entC and ubiC genes.