Comparative genomics of Pseudomonas aeruginosa rugose small colony variants
Genomic DNA (gDNA) was sheared using a Bioruptor UCD-200 (Diagenode) and end repaired using an End-It DNA end repair kit (Epicentre). Repaired fragments were subjected to A tailing using Taq DNA polymerase (Roche). Custom Y adaptors were used to barcode strain specific gDNA, and these were added by using T4 DNA ligase (New England Biolabs).  These custom adaptors contained defined sequences that were read as the first 13 bases. In addition to 9 unique bases, each barcode contained 4 identical bases at the 3 end to reduce variation in ligation efficiency (S3 Table). Libraries were size selected by using automated electrophoresis on a Pippen Prep system (Sage Science) and assessed for size range and concentration using a Qubit fluorometer (Invitrogen) and a Bioanalyzer (Agilent).