Bacterial Genome Sequencing Protocol

DNA was extracted from overnight liquid LB cultures grown at 37°C with the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich, Johannesburg, South Africa). The UCMB5007 and UCMB5044 genomes were sequenced using paired-end library preparation and an Illumina HiSeq 2000 at Macrogen Inc. (Republic of Korea). SMRT sequencing was carried out on a PacBio RSII machine (1 SMRT cell per strain) at the FGCZ, Zurich, Switzerland. Size selection was performed using the BluePippin system (SAGE Science, United States) as described before (Omasits et al., 2017 (link)) and resulted in fragments with an average subread length of 8–10 kb. Two 2 × 300 bp Illumina paired end libraries were prepared per strain using the Nextera XT DNA kit and sequenced on a MiSeq at Agroscope (Wädenswil, Switzerland). The At1 genome was sequenced with PacBio RSII CCS technology at Inqaba Biotec Ltd. (Pretoria, South Africa). DNA quality was evaluated spectrophotometrically at 260 and 280 nm light absorbance with a NanoDrop 1000 spectrometer (Thermofisher, South Africa). All raw DNA and RNA reads generated for this project by Illumina and PacBio sequencers are available from NCBI SRA database records accessible through the BioProject Web-sites. BioProject accession numbers are indicated in Table 1.