Magattract hmw dna mini kit

The wDi gDNA was extracted using the MagAttract HMW DNA Mini kit (catalog number 67563, Qiagen) using manufacturer’s protocol with few modifications. The modifications were as follows: The bacterial pellet was resuspended in 180 µl ATL buffer [from DNeasy® Blood and Tissue Kit (catalog number 69506, Qiagen)] with 20 µl Proteinase K and incubated for 30 min at 56 °C. 15 μl MagAttract Suspension and 280 μl Buffer MB was added to the sample and mixed by pulse vortexing. The sample tubes were transferred to the tube holder of the Magnetic Rack (without the magnetic insert). The tube holder of the Magnetic Rack (without the magnetic insert) was placed onto the mixer and incubate at room temperature (15–25 °C) for 3 min at 1400 rpm. The magnetic insert was placed into the tube holder of the Magnetic Rack, wait (~ 1 min) until bead separation has been completed, and the supernatant was removed. The extracted gDNA was purified using the DNeasy PowerClean Cleanup kit (catalog number 1287750, Qiagen). gDNA was quantified using the Qubit 1 × dsDNA HS Assay kit (ThermoFisher Scientific) and DNA quality was assessed using the TapeStation Genomic DNA ScreenTape (Agilent Technologies).

Total genomic DNA of Xoo strains was isolated using MagAttract HMW DNA Mini Kit (QIAGEN). DNA samples were sequenced using a single molecule real-time (SMRT-Pacbio) platform, P4-C6 chemistry. For each strain, at least two SMRT cells were used, generating around 180× coverage per genome. De novo assembly was conducted using the hierarchical assembly pipeline (HGAP) implemented in Canu v.1.5 software^{33 (link)}. Raw PacBio reads were mapped against the resulting contigs using blasR aligner (https://github.com/PacificBiosciences/blasr) and corrections were conducted with the variant-caller software utilizing the arrow algorithm (https://github.com/PacificBiosciences/GenomicConsensus).
Genome annotation and gene prediction were conducted using the Prokka annotation pipeline^{34 (link)} and the NCBI Prokaryotic Genome Annotation (PGAP)^{35 (link)}. Genome sequences were deposited in the GenBank under BioProjects PRJNA497307 and PRJNA497605. Additional reported and publicly available genomes in GenBank were retrieved and used for comparisons (Supplementary Table 1).