Pacific Biosciences Releases Software Upgrade to Advance Bacterial DNA
Methylation Analysis and De Novo Genome Assembly Projects
Scientists Publish Complete Bacterial 'Methylomes' Using SMRT Sequencing
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
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
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
For Pacific Biosciences
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