NextSeq 500 paired end sequencing
Genomic DNA was extracted from cell pellets using the NucleoSpin Microbial DNA Mini kit (Macherey-Nagel) with minor changes: 1 �L of RNase Cocktail Enzyme Mix (Invitrogen) was added before lysis on a FastPrep-24 5G (MP Biomedicals; 2 cycles with 20 s each at 6 m/s) and incubated for 5 min at room temperature to remove residual RNA before proceeding with the manufacturer's protocol. 100 ng of genomic DNA were sheared with a Covaris S2 system (50 �L sample volume, duty cycle 10%, intensity 5.0, 40 s). Libraries for whole-genome sequencing were then constructed using the KAPA HyperPrep DNA Kit (Roche) according to the manufacturer�s protocol with NEXTFLEX UDI adapters (Bioo Scientific), a 0.8x and 0.6x bead-based clean-up and 4 PCR cycles, and sequenced on an Illumina NextSeq 500.