Genome sequencing of E. coli after adaptation to antibiotics
gDNA libraries were generated according to the manufacturers protocols using the Ion Xpress Plus gDNA Fragment Library Preparations (Thermo Fisher Scientific). Bar-coded libraries were prepared according to the Ion Plus fragment library kit (Thermo Fisher Scientific) and the Ion Xpress DNA bar-coding kit (Thermo Fisher Scientific) according to the 200-base-read Ion Proton libraries instructions of the manufacturer. The size distribution and yield of the barcoded libraries were assessed using the 2200 TapeStation System with Agilent High Sensitivity D1000 ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef System using the Ion PI Hi-Q Chef Kit (Thermo Fisher Scientific). Sequencing was performed on an Ion Proton System using a Ion PI v3 chip (Thermo Fisher Scientific) according to the instructions of the manufacturer.