High-throughput Genome Sequencing of Bacterial Strains

DNA was isolated from single-colony overnight cultures of each strain using DNAzol (Chomczynski et al. 1997 (link)). High-throughput DNA sequencing was performed on Illumina GA IIx 75 bp paired-end platform (∼200 bp insert size) at BGI-Shenzhen (BGI) and the Genome Research Center (GRC), University of Hong Kong. Sequence libraries were prepared using Illumina kits with standard protocol. Raw sequencing reads were deposited to National Center for Biotechnology Information (NCBI) Sequence Read Archive (accession ID: SRA057077). The reads from each strain were mapped to the reference QB928 genome (Yu et al. 2012 (link)) using SHRiMP 2.1.1 (David et al. 2011 (link)) (-p opp-in -E -Q –single-best-mapping –half-paired). Gene annotations were originated from B. subtilis str.168 (Barbe et al. 2009 (link)), with refinements described previously (Yu et al. 2012 (link)). Sequencing depths of the different genomes are shown in supplementary table S1, Supplementary Material online.