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SMRT Sequencing Selected by 100K Pathogen Genome Project to Finish Genomes

Thursday, January 17, 2013

A recently announced
partnership with the University of California, Davis (UC Davis) highlights the
benefits of one of the key applications for Single Molecule, Real-Time (SMRT®)
 Sequencing: rapid and complete finishing
of pathogen genomes.
As part of the project, Pacific Biosciences’ SMRT technology
will be used for the 100KPathogen Genome Project 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.
Speaking to GenomeWeb,
Bart Weimer, Professor and Director of the 100K Genome Project, commented that
building these pan-genomes will be important because it will help in better
“identifying organisms that are inside of an outbreak. As an outbreak
occurs, we’ll know at a detailed level, [if] this new isolate is part of the
existing outbreak or outside of it.”
Also commenting for the GW article, Marc Allard, an FDA research microbiologist and the
research area coordinator of comparative genomics at FDA’s Center for Food
Safety and Applied Nutrition, said that having closed genomes is important for
“providing a single complete picture of the genetic makeup of a
pathogen,” and that the FDA would be using the PacBio® RS to “rapidly close bacterial
genomes.”
“SMRT Sequencing has been shown to be a powerful
technology for the comprehensive determination of microbial genomes and
epigenomes,” said Dr. Jonas Korlach, Chief Scientific Officer of Pacific
Biosciences, in the press release. “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.”
“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 Dr. Weimer in the press release. “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,” he continued.
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.
We are looking forward to providing technical guidance and
training to support these activities, and interfacing closely with the involved
laboratories to assist in the efficient construction of these pipelines. The
data will be submitted to the NationalCenter for Biotechnology Information
Stay tuned for more!

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