DNA-seq of Enterococcus faecalis OG1RF: Experimental evolution
Isolated genomic DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA). Library preparation was performed using NexteraXT library kit (Illuma, California, USA) per manufacturers recommendations. Final library quantity was measured by KAPA SYBR FAST qPCR with QuantStudio  5 System (Applied Biosystems, California, USA), and library quality evaluated by TapeStation HSD1000 ScreenTape (Agilent Technologies, CA, USA). Illumina 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads (20M in each direction) per sample.