Illumina reads for Pantoea agglomerans CB1
High molecular weight genomic DNA was extracted (Miller et al. 1988) with the following modifications: the pre-lysozyme lysis buffer was 1M Tris pH 7.5, 0.5M EDTA pH 8.0, 5M NaCl, lysozyme digestion was performed at 48C for 1h, DNA resuspension was in 10 mM Tris pH 7.5, RNAse treatment was followed by two additional washes. DNA quantity was assessed using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, U.S.A.). DNA integrity was assessed by agarose gel electrophoresis.  For short-read sequencing, the DNA library was prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina with the NEBNext Multiplex Oligos (New England Biolabs, USA). AMPure XP beads (Beckman Coulter, USA) were used for DNA size-selection and purification. The DNA library was quantified by Qubit 3.0 fluorometer, and library quality was assessed using the Fragment Analyzer 2100 system (Advanced Analytical Technologies, Inc., U.S.A.). The DNA library was sequenced on a MiSeq platform (Illumina, USA).