title: Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.
abstract: The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica 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 Salmonella 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 Salmonella.
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Cary
authors: C
authors: Pirone-Davies
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Maria
authors: M
authors: Hoffmann
authors: New England Biolabs, Ipswich, Massachusetts, United States of America.
authors: Richard J
authors: RJ
authors: Roberts
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Tim
authors: T
authors: Muruvanda
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Ruth E
authors: RE
authors: Timme
authors: Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Errol
authors: E
authors: Strain
authors: Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Yan
authors: Y
authors: Luo
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Justin
authors: J
authors: Payne
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Khai
authors: K
authors: Luong
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Yi
authors: Y
authors: Song
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Yu-Chih
authors: YC
authors: Tsai
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Matthew
authors: M
authors: Boitano
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Tyson A
authors: TA
authors: Clark
authors: Pacific Biosciences, Menlo Park, California, United States of America.
authors: Jonas
authors: J
authors: Korlach
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Peter S
authors: PS
authors: Evans
authors: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America.
authors: Marc W
authors: MW
authors: Allard
mesh_terms: D001483:Base Sequence; D019175:DNA Methylation; D057890:Epigenomics; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D008780:Methyltransferases / Q000235:genetics; D059372:Nucleotide Motifs; D019779:Salmonella enterica / Q000235:genetics*
chemical_list: D008780:Methyltransferases