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PacBio Sequencing to Support 100K Genome Project

NEW YORK (GenomeWeb News) – Pacific Biosciences said today that researchers at the University of California, Davis, will use the PacBio RS sequencer to support the 100K Genome Project, a multi-partner effort to sequence the genomes of 100,000 foodborne pathogens.

PacBio said that researchers at UC Davis and other members of the consortium will use its Single Molecule, Real-Time technology to sequence the genomes from at least 1,000 foodborne pathogen samples and to elucidate their epigenomes, including bacteria such as Salmonella, Campylobacter, Escherichia coli, Vibrio, and Listeria.

The company said it will provide technical guidance, training, and support for these activities.

The 100K Genome Project was launched last year by UC Davis, Agilent Technologies, and the US Food and Drug Administration to use genome sequencing and analysis to create a publicly available genetic database of microbes that cause disease and to address concerns about food safety. In December, OpGen also signed on as a partner in the project.

PacBio said the long reads that its SMRT sequencing generates have been shown to be effective for microbial genomic and epigenomic analysis in recent publications, including those regarding the genetic analysis of Haitian cholera and German E. coli outbreaks.

"Through the combination of long reads, high consensus accuracy, and the lack of sequencing bias to GC content or sequence contexts, SMRT sequencing harbors the necessary requirements to construct finished genomes in an unbiased, hypothesis-free manner," PacBio CSO Jonas Korlach said in a statement.

"SMRT technology will enable production of complete genomes that will contribute great value toward databases for biological insight, new biomarker discovery, and reference genomes for food pathogen detection," added UC Davis Professor Bart Weimer, director of the 100K Genome Project.

"A project of this scale is needed since microbial genome variations, including structural variations, the acquisition and loss of mobile elements, and phages or plasmids, are very difficult or impossible to detect without a de novo sequencing and genome assembly approach, yet they have a significant impact on food safety," Weimer explained.