Pacific Biosciences Releases Software Upgrade to Advance Bacterial DNA Methylation Analysis and De Novo Genome Assembly Projects
Monday, October 22, 2012
MENLO PARK, Calif., Oct. 22, 2012 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc. (Nasdaq:PACB), provider of the PacBio® RS High Resolution Genetic Analyzer, today announced it has expanded the capabilities of its system through a major software upgrade, providing customers more tools for performing DNA base modification analysis and de novo genome assembly. Scientists from New England BioLabs (NEB) and Pacific Biosciences demonstrated the power of the new software in a paper this month titled “The Methylomes of Six Bacteria” in Nucleic Acids Research.
DNA base modifications are important to the understanding of biological processes such as gene expression, host-pathogen interactions, DNA damage, and DNA repair. Traditionally, it has been difficult for scientists to study the many types of base modifications that occur in nature. Most studies to date have focused solely on cytosine methylation using indirect detection methods. PacBio’s Single Molecule, Real-Time (SMRT®) sequencing inherently detects modified bases because they are measured according to the kinetics of DNA base incorporation during the sequencing process. No other technology on the market provides this capability.
With the release of the new SMRT Analysis 1.3.3 software upgrade, customers can automatically detect the most common types of bacterial methylation, namely: N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and Tet-converted 5-methylcytosine (5-mC), and perform methyltransferase (MTase) recognition motif analysis. In addition, the new software integrates the Celera® Assembler, which was recently optimized for PacBio sequence data, to facilitate de novo genome assembly.1
In the NAR paper, PacBio and NEB used the PacBio RS with the SMRT Analysis software to sequence six bacteria and analyze the methylation and MTase recognition motifs in those bacteria. In every case a number of new N6-methyladenine and N4-methylcytosine methylation patterns were discovered and the MTases responsible for those methylation patterns were assigned. The researchers concluded that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active but also revealing their recognition sequences.
Richard Roberts, Ph.D., Chief Scientific Officer, New England BioLabs and senior author on the paper, commented: “DNA methylation is widespread in bacteria where it can protect against restriction enzymes and also regulate gene expression. Until the advent of SMRT sequencing it was not possible to examine the complete methylome of any bacterium. Now it has become simple and we are awash in fascinating new data. Understanding the biological significance of these methylation patterns represents a welcome new challenge for microbiologists.”
Jonas Korlach, Ph.D., Chief Scientific Officer of Pacific Biosciences, commented: “We are committed to continuing to unlock more of the inherent advantages of our SMRT sequencing technology for our customers worldwide, and are proud to offer customers unique capabilities to perform methylome analysis. These continued enhancements expand the utility of our system and make it a great solution for more researchers, including microbiologists.”
For more information about Pacific Biosciences, please visit www.pacb.com.
1 See “Hybrid error correction and de novo assembly of single-molecule sequencing reads” by Koren et al. in Nature Biotechnology, July 2012.
About Pacific Biosciences
Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the PacBio® RS 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.
For Pacific Biosciences
Source: Pacific Biosciences of California, Inc.
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