PACIFIC BIOSCIENCES OF CALIFORNIA, INC. Pacific Biosciences of California, Inc. and the University of California, Davis announced a partnership for the 100K Pathogen Genome Project. As part of the project, Pacific Biosciences' Single Molecule, Real-Time (SMRT(R)) technology will be used to sequence the genomes from at least 1,000 foodborne pathogen samples to completion, and to elucidate their epigenomes. These bacteria represent major illness-causing pathogens, including Salmonella, Campylobacter, E. coli, Vibrio, and Listeria.
The 100K Genome Project was founded by the U.S. Food & Drug Administration, Agilent Technologies, and the laboratory of Dr. Bart Weimer at UC Davis to create a consortium of partners from around the world that will sequence 100,000 foodborne pathogens using next-generation sequencing. This initiative addresses a significant shortage of bacterial pathogen information for use in designing molecular diagnostics, creates a resource to expand its understanding of infection mechanisms, and constructs a public repository for new insights into bacterial evolution by using large-scale genomics. Pacific Biosciences SMRT sequencing technology generates sequence reads an order of magnitude longer than other DNA sequencing technologies, thereby facilitating efficient de novo microbial genome assemblies.
Long reads are critical for resolving genetic complexity in the assembly and finishing of genomes. The kinetic information acquired during SMRT sequencing can be used to elucidate the epigenome of bacteria. Epigenetic DNA base modifications, such as methylation, play an important role in the phenotypic variation, adaptability and pathogenicity of many bacteria, but they have been difficult to study due to the lack of a sequencing method to detect them.
As part of the 100K Genome Project, the epigenomes of the pathogenic strains subjected to SMRT sequencing will be characterized, adding an important dataset to public database repositories. The partnership will entail the sequencing of at least 1,000 samples by the 100K consortium member labs with access to the PacBio RS instrumentation, including pipeline constructions for high-throughput pathogen sequencing, de novo genome assemblies, epigenome determination, and data curation and deposition. Pacific Biosciences will provide technical guidance and training to support these activities, and interface closely with the involved laboratories to assist in the efficient construction of these pipelines.
