PCR and Sanger sequencing was performed as previously described (Miller et al. 2014a (link)). Shotgun and paired-end (8–12 kb) 454 reads were obtained on a Roche 454 GS-FLX+ Genome Sequencer with Titanium chemistry using standard protocols. Illumina HiSeq reads were obtained from SeqWright (Houston, TX). SMRT sequencing was performed on the Pacific Biosciences (PacBio) RSII sequencing platform using 10 kb or 20 kb SMRTbell libraries, C2/C2 sequencing chemistry, and the 90-min data collection protocols. The SMRTbell libraries were prepared from 5 to 10 μg of bacterial genomic DNA, using the standard protocol from Pacific Biosciences (Menlo Park, CA, USA), and processed for sequencing as recommended by the supplier. A FASTQ file was generated from the PacBio reads using SMRTanalysis (ver. 2.1), and the reads were error-corrected using pacBioToCA with self-correction (Koren et al. 2013 (link)). The longest 20× of the corrected reads were assembled with Celera Assembler 8.1 (Koren et al. 2012 (link)). The resulting contigs were polished using Quiver (Chin et al. 2013 (link)).