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Background  The genome of the human gastric pathogen  Helicobacter pylori  encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian  H. pylori  clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).    Results  The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the  H. pylori  UM032 genome during normal growth was characterized by cloning.    Conclusion  Consistent with previously-studied  H. pylori  strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of  H. pylori .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1585-2) contains supplementary material, which is available to authorized users.

The complete methylome of Helicobacter pylori UM032