putida_23974
Genomic DNA sequencing libraries were prepared following dx.doi.org/10.17504/protocols.io.pdmdi46 Briefly, samples were transferred into 96-well garnet bead plates and gDNA was extracted using the MagAttract PowerSoil DNA Kit (QIAGEN, Hilden, Germany) optimized for the KingFisher automated platform (ThermoFisher Scientific, Waltham, MA). Libraries were prepared using a miniaturized version of the Kapa HyperPlus Illumina-compatible library prep kit (Kapa Biosystems). DNA extracts were normalized to 5 ng total input per sample using an Echo 550 acoustic liquid handling robot (Labcyte Inc), and 1/10 scale enzymatic fragmentation, end-repair, and adapter-ligation reactions carried out using a Mosquito HV liquid-handling robot (TTP Labtech Inc). Sequencing adapters were based on the iTru proptocol (Glenn et al, 2016), in which short universal adapter stubs are ligated first and then sample-specific barcoded sequences added in a subsequent PCR step. Amplified and barcoded libraries were then quantified using a PicoGreen assay and pooled in approximately equimolar ratios before being sequenced