Garth Ehrlich from the Center for Genomic Sciences at Allegheny Singer Research Institute reports on new studies of pneumococcal epigenetics. Streptococcus pneumonia, which causes more than 1.6 million deaths annually, has a highly plastic genome. Methylation analysis with SMRT Sequencing found a novel modification in addition to the expected epigenetic changes.
Peter Evans from the US FDA shares insights on whole-genome sequencing for bacteria of importance to public health. Comparing data across PacBio, 454, and MiSeq sequencers, he says having closed genomes, long reads, and methylation patterns are critical for gleaning comprehensive information about a microbe.
Sebastian Suerbaum from Hannover Medical School shows that genome-wide methylation patterns in Helicobacter pylori are highly complex and diverge significantly between strains of the microbe. He presents a full-methylome analysis of two H. pylori strains, finding 32 total methylated motifs with just seven shared between strains. Of the 32 motifs, 11 were new discoveries.
UC Davis’s Bart Weimer describes foodborne pathogens and their proclivity for rapid genome rearrangement. The 100K Pathogen Genome Project he leads is using PacBio long-read sequencing to close genomes and analyze methylation; Weimer reports that his team has already discovered new epigenetic modifications in Salmonella and Listeria with the technology.
How does the PacBio sequencer produce epigenetic data? CSO Jonas Korlach describes how the technology works, which DNA modifications can be detected, and gives examples of kinetic signatures for various modifications and their associated target motifs.
Brian Anton from New England BioLabs presents data on methylation analysis using SMRT Sequencing. He describes both restriction-modification systems and orphan methylases, noting that the number of methylases characterized has more than tripled since the introduction of SMRT Sequencing. The presentation includes a phylogenetic analysis of methyltransferase genes
Epigenetics expert Michael Jennings from Griffith University first posited the phasevarion, or the phase variable regulon mechanism in host-adapted pathogens. This mechanism switches expression of multiple genes in a coordinated fashion and has significant implications on pathogen virulence. In his talk, Jennings describes the phasevarion and his use of whole methylome data to rapidly identify methylation targets.
In this presentation, Greg Harhay from the USDA offers data on pathogens involved in bovine respiratory disease complex, known as “shipping fever.” His team used PacBio sequencing to analyze several isolates from two different pathogens, looking at their DNA sequence and methylation patterns.