SMRT-seq of LabWT
Bacterial DNA methylation analysis was performed by SMRT (PacBio, USA) and high throughput DNA de novo sequencing (DNAlink, Republic of Korea). Detection of base modification and methylated motif was conducted by employing the SMRT analysis portal following genome assembly. Briefly, genomic DNA samples extracted from mid-exponential phase (OD600, ~0.5) of the WT strain and aamA mutant were used for the sequencing and methylation analysis. Each genomic DNA sample was sheared using Megaruptor (ver 3.0) to collect 10 Kb DNA fragments, and then purified using the SMRTbell clean-up bead system to remove small fragments (<10 kb). Each purified 10 kb DNA fragment (500 ng) was used as the sequencing library using the SMRTbell Express Template Preparation kit (ver. 3.0). To reveal the genome-wide base modifications and the identification of 6mA, 4mC, and 5mC residues in corresponding methylation (recognition) motifs, the SMRTbell library was sequenced on PacBio RS II System using SMRT Cell 8M (Pacific Biosciences) and Sequel Sequencing Kit 2.0 (Pacific Biosciences) on as previously described [34]. Reads were processed and mapped using BLASR mapper (ver. 12.0) and the Pacific Biosciences SMRT Analysis pipeline using the standard mapping protocol. Reads from the strains were mapped to Lab-WT reference whole genome sequence (accession numbers CP000521).