Genome-Wide Methylation Patterns in <i>Salmonella enterica</i> Subsp. <i>enterica</i> Serovars

<div><p>The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. <i>Salmonella</i> is an important foodborne pathogen, and methylation in <i>Salmonella</i> is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven <i>Salmonella enterica</i> isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N⁶-methyladenine (m6A) methylated motifs, one N⁴-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all <i>Salmonella</i> serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in <i>Salmonella</i>.</p>