Illumina MiSeq paired end sequencing
Genomic DNA was extracted using the NucleoSpin Microbial DNA Mini kit (Macherey-Nagel) according to the manufacturer's protocol using a FastPrep-24 5G for lysis (MP Biomedicals; 2 cycles with 20 s each at 6 m/s). After treatment with RNase Cocktail (Ambion) for 10 min at r.t., genomic DNA was again purified using the NucleoSpin Microbial DNA Mini kit (starting with step 3 of the manufacturer's protocol). DNA integrity and purity was examined by agarose gel electrophoresis, and DNA was quantified using a NanoDrop spectrophotometer. Libraries for whole-genome sequencing were constructed using the Illumina DNA Prep kit (Illumina) with 250 ng genomic DNA input and sequenced on an Illumina MiSeq.