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Background   Campylobacter species  are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to  Campylobacter jejuni,  about 5 % of  Campylobacter coli  strains exhibit susceptibility to restriction endonuclease digestion by  Dpn I cutting specifically 5’-G m ATC-3’ motifs. This indicates significant differences in DNA methylation between both microbial species.  The goal of the study was to analyze the methylome of a  C. coli  strain susceptible to  Dpn I digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like  C. jejuni  and  Helicobacter pylori .    Results  Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the  Dpn I susceptible strain  C. coli  BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to  C. coli  clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %.    Conclusions  Only five dominant methylation motifs have been identified in  C. jejuni , which have been associated with known RM-systems.  C. coli  BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with  Dpn I prescreening RM-system IIP, methylation of GATC motifs was detected in  C. coli  BfR-CA-9557. A homologous IIP RM-system has been described for  H. pylori . The remaining methylation motifs are specific for  C. coli  BfR-CA-9557 and have been neither detected in  C. jejuni  nor in  H. pylori .  The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in  C. coli .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2317-3) contains supplementary material, which is available to authorized users.

SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs