Pseudogene repair driven by selection pressure applied in experimental evolution. 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.