Bacterial endophytes 1
Genomic DNA samples were fragmented using an enzymatic approach (NEB Ultra II FS kit). Resulting DNA fragments were size selected (200  700bp), using AMPure XP beads, the fragments were end repaired and Illumina specific adapter sequences were ligated to each fragment. Each sample was individually indexed, and a second size selection step was performed. Samples were then quantified, using a fluorometric method, diluted to a standard concentration (4nM) and then sequenced on Illuminas NextSeq platform, using a NextSeq mid out kit (300 cycle), following a standard protocol as described by the manufacturer. 400 Mb of data (2x150bp long paired-end reads) were produced for each sample.