New Assembly Method Published for Rapid and Automated Genome Sequencing Using Long-Read, Single Molecule, Real-Time (SMRT(R)) Sequencing

MENLO PARK, Calif., May 6, 2013 (GLOBE NEWSWIRE) -- Researchers from Pacific Biosciences of California, Inc., (Nasdaq:PACB), the U.S. Joint Genome Institute and the University of Washington have published a new method for assembling high-quality genomes from Single Molecule, Real-Time (SMRT^®) DNA sequencing. Published in the May 5 edition of Nature Methodsⁱ, the paper by Chin et al. describes the hierarchical genome assembly process (HGAP) and demonstrates the method for efficient, automated de novo assembly from genomic DNA to a finished genome sequence for several microorganisms and a human bacterial artificial chromosome (BAC) clone. As part of the paper, the authors also describe a new consensus algorithm, Quiver, that achieves highly accurate de novo genome sequence results exceeding 99.999% (QV 50) accuracy.

Finished genomes are crucial for understanding microbes and advancing the field of microbiology.ⁱⁱ Previous attempts for obtaining the complete genome sequence of microbes in an automated, high-throughput manner have challenged researchers. For example, with second-generation sequencing methods, short read lengths inhibit the ability to resolve long repeats, resulting in unfinished, fragmented draft assemblies. Further, extreme sequence contexts, such as GC- or AT-rich regions, or palindromic sequences, lead to gaps in draft genome assemblies that cannot be covered using these second-generation methods. As a result, Sanger sequencing has typically been employed for finishing microbial genomes, but due to its laborious and low-throughput nature this process is slow and expensive.

More recently, hybrid-assembly approaches have been described in which long PacBio reads were used in combination with short-read data^iii,iv. Building on these advances, in this new paper the authors utilize just a single, long-insert shotgun DNA library in conjunction with SMRT Sequencing, thereby removing the need for additional sample preparation and sequencing data sets required for previously described hybrid strategies. A paper describing a similar strategy and assembly results by S. Koren, A. Phillippy, and colleagues from the National Biodefense Analysis and Countermeasures Center, Frederick, MD, and the United States Agriculture Department has been deposited in a pre-print archive.

"This approach can close the large gap that currently exists between 'draft' and high-quality 'finished' genomes," said Jonas Korlach, senior author on the paper and Chief Scientific Officer at Pacific Biosciences. "Further, the ability to automatically and cost-effectively assemble genomes independent of the availability of a reference sequence can be critical in the rapid characterization of new pathogen strains."

Evan Eichler, co-author on the paper, Howard Hughes Medical Investigator and Professor at the Department of Genome Sciences at the University of Washington, said, "I am excited by the ability of SMRT DNA Sequencing and HGAP for finishing complex regions of the human genome. This approach has demonstrated the potential to cost-effectively generate high-quality finished sequence from large-insert clones of these regions, such as BACs. Short-read sequencing technologies simply cannot adequately access and assemble through these complex regions of genomes."

Pacific Biosciences recently launched the PacBio^® RS II – a new SMRT Sequencing system that provides the industry's highest consensus accuracy and longest reads with double the throughput from the previous version of the system. The PacBio RS II allows scientists to rapidly and cost-effectively generate finished genome assemblies, reveal and understand epigenomes, and characterize genomic variation. The PacBio RS II system, including consumables and software, provides a simple, fast, end-to-end sequencing workflow for applications such as infectious disease and microbiology, agriculture, and understanding rare diseases.

More information is available at www.pacb.com.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the PacBio^® RS II High Resolution Genetic Analyzer to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT^®) technology, the company's products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems. 

ⁱ Chin et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods doi 10.1038/nmeth.2474.

ⁱⁱ C. M. Fraser, et al., J Bacteriol 184 (23), 6403 (2002).

ⁱⁱⁱ Ribeiro et al. Finished bacterial genomes from shotgun sequence data, Genome Res. (2012)

^iv Koren, et al. Hybrid error correction and de novo assembly of single-molecule sequencing, Nature Biotechnology (2012)

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