Illumina HiSeq 4000 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. Libraries for whole-genome sequencing were then constructed using the Nextera XT DNA Library Preparation Kit (Illumina) with 1 ng genomic DNA input, 5 min tagmentation at 55�C and 12 PCR cycles, and sequenced on an Illumina HiSeq 4000.