April 16, 2014  |  General

Innovation Centre in Quebec Uses SMRT Sequencing for
Cost-Effective, Complete Microbial Genomes

At the McGill University and Génome Québec Innovation Centre, many projects conducted in the sequencing core facility fall under the umbrella of life sciences rather than biomedical research. To the scientists responsible for making the core facility operate as smoothly as possible, that makes a world of difference.

“When you’re in the life sciences in addition to human biomedical [research], you’re out there in the world of things that haven’t been sequenced before, or haven’t been sequenced particularly well,” says Ken Dewar, a principal investigator at the Innovation Centre.

To navigate this type of uncharted territory, scientists at the center rely on long-read sequencing from their PacBio® RS II platform to cost-effectively close microbial genomes, traverse repeat-heavy genomic regions, and perform full-length transcript sequencing. By leveraging the dramatically increased read lengths PacBio sequencing provides, they have driven down costs and improved completeness of their assemblies.

At the core facility, Alexandre Montpetit is dedicated to running the next-generation sequencing platforms. His primary affiliation is with Génome Québec, and he has an adjunct appointment at McGill. He and his colleagues have been champions of long-read sequencing for years, so when PacBio unveiled its platform with industry-leading read length, it was an obvious choice for the center to adopt the technology.

“We’ve always had a focus on sequencing things for the first time or assembling genomes for the first time, not for the thousand-and-first time,” Dewar says. “PacBio was a natural fit.”

At the center, SMRT Sequencing has been used in diverse research areas. Some examples include generation of high-quality assemblies in microbial sequencing, analysis of long, repetitive genomic regions, and sequencing of full-length human gene isoforms. Microbial sequencing encompasses a number of applications, including biotech industry efforts to improve microbial biofermentation and microbiome studies, from environmental remediation projects on Alberta tar sands to veterinary research on microbes present in cattle rumen.

In the two years they’ve been running the SMRT Sequencing platform, the Innovation Centre scientists have seen remarkable progress in what they have been able to achieve. Continued improvements in read lengths — partly due to new reagent kits from PacBio and partly due to more streamlined sample prep protocols developed at the center — have already made a major difference.

One major step was achieving complete bacterial sequencing and assembly in less than a day, a feat that may enable the core facility to serve as a rapid response center for organizations that study pathogen outbreaks and other urgent problems. In 2013, tests conducted with researchers at the Canadian Food Inspection Agency and other government agencies demonstrated that the Innovation Centre scientists could sequence a sample and fully assemble the genome and plasmid elements — all in 20 hours or less.

Indeed, the Innovation Centre team is routinely able to deliver affordable, high-quality, finished genomes. “A single bacterial genome, a library prep, and two SMRT Cells of sequencing — which is generally a little bit overkill — is less than $1,000,” Dewar says. “More and more often, we are getting a completely closed, finished-quality genome for that.”

High-quality assemblies aren’t just for bacteria. “We’ve shown recently that we can assemble a fungal genome of 20 or 30 megabases with four or eight SMRT Cells and get only 10 or 20 contigs — which often represents the number of chromosomes in the genome,” Montpetit says.

Read the full case study to learn more about how the Innovation Centre has deployed SMRT Sequencing, their shift from hybrid to PacBio-only assemblies, and how they differentiate their bioinformatics analysis service.

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