Sulfitobacter D7 genomic DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA was prepared for sequencing using the Nextera XT kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. After processing, libraries were assessed for size using an Agilent TapeStation 2000 automated electrophoresis device (Agilent Technologies, Santa Clara, CA) and for concentration by a Qubit fluorometer (Thermo Fisher Scientific Inc., Waltham, MA). Libraries were pooled in equimolar ratio and sequenced using an Illumina NextSeq 500 sequencer, with paired-end 2 × 150 base reads. Library preparation and sequencing were performed at the DNA Services Facility, University of Illinois at Chicago. Standard Pacific Biosciences large insert library preparation was performed. DNA was fragmented to approximately 20 kb using Covaris g-TUBEs. Fragmented DNA was enzymatically repaired and ligated to a PacBio adapter to form the SMRTbell template. Templates larger than 10 kb were BluePippin (Sage Science) size selected, depending on library yield and size. Templates were annealed to sequencing primer, bound to polymerase, and then bound to PacBio MagBeads and SMRTcell sequenced. Sequencing was performed at the Great Lakes Genomics Center at the University of Wisconsin–Milwaukee. De novo assembly was performed using the SPAdes assembler (61) on both raw Illumina and PacBio reads, with multiple k-mers specified as “-k 31,51,71,91”. Coverage levels were assessed by mapping raw Illumina reads back to the contigs with Bowtie2 (62) and computing the coverage as the number of reads aligning per contig times the length of each read divided by the length of the contig. We assessed the relationship between coverage and cumulative assembly length over coverage-sorted contigs and took 33% of the coverage level at half the total assembly length as a coverage threshold. Contigs with coverage less than this value or with a length shorter than 500 base pairs were removed. The sequence of Sulfitobacter D7 has been deposited in GenBank (accession numbers CP20694 to CP20699, BioProject PRJNA378866).

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