Pacific Biosciences of California, Inc. (Nasdaq:PACB), the leading
provider of high-quality sequencing of genomes, transcriptomes and
epigenomes, today announced that a multi-institutional consortium
of maize researchers is using the Sequel® System to create a
26-line pangenome reference collection.
Led by faculty investigator R. Kelly Dawe, Distinguished
Research Professor at the University of Georgia, the $2.8 million
National Science Foundation-funded Plant Genome Research Project
will create comprehensive, high-quality assemblies of 25 inbreds
known as the NAM founder lines, the most extensively researched
maize lines that represent a broad cross section of modern maize
diversity, as well as an additional line containing abnormal
chromosome 10.
Leading maize researchers Matt Hufford, assistant professor at
Iowa State University, and Doreen Ware, a computational biologist
at USDA and Cold Spring Harbor Laboratory, will also participate in
the project. Ware's lab was involved in creating the first
reference genome for maize variety B73 in 2009, as well as an
improved version in 2017.
PacBio® Single Molecule, Real-Time (SMRT®) Sequencing and
BioNano Genomics optical mapping, which were essential in the
creation of the groundbreaking 2017 B73 maize reference, will be
used in the project.
Plant genomes are notoriously difficult to sequence, and maize
is particularly challenging because the vast majority of its 2.3 Gb
genome — a staggering 85 percent — is made up of highly repetitive
transposable elements that other types of sequencing can't address.
Understanding these regulatory and structural elements is crucial
to modern breeding efforts that aim to improve productivity across
marginal environments and under changing climate conditions.
Maize is also amazingly diverse. A study comparing genome
segments associated with kernel color from two inbred lines
revealed that 12 percent of the gene content was not shared –
that’s much more diversity within the species than between humans
and chimpanzees, which exhibit more than 98 percent sequence
similarity. The new project will create multiple reference genomes
to reflect this diversity.
“By relying on a single type specimen as the sequence reference
for most of the genetic information in maize, we may be missing
much of the highly valuable natural variation in maize,” Dr. Ware
said.
"SMRT Sequencing will be essential as the team assesses the role
of structural variation between the lines, such as presence-absence
variation and copy number variation, in the determination of
agronomic traits," she added.
“To go from a single reference to a broad perspective on the
entire genetic repertoire of genes and gene expression patterns
will be a major step forward in how we approach genome analysis in
crops,” said Dr. Dawe. “It’s something that has not happened for
any crop at this scale.”
Kevin Corcoran, Senior Vice President for Market Development at
Pacific Biosciences, commented: “Corn is one of the most important
crops in the world, and a significant species of study for
answering fundamental questions about how plants adapt to different
environments. Other important crop species could also benefit from
this approach, and commercial breeders are increasingly recognizing
the value of creating multiple reference genomes. We are excited
that our technology can contribute as scientists attempt to address
the challenges of a changing world.”
Industry leader Corteva Agriscience™, Agriculture Division of
DowDupont™ (formerly DuPont Pioneer) has helped with the NSF
pangenome project by carrying out the Bionano optical mapping phase
of the project. Corteva is also using highly-accurate PacBio
whole-genome sequencing to create its own extensive maize reference
collection, and projects to create multiple high-quality reference
genomes for other important crops have been announced by various
research institutions. These include: the Arizona Genomics
Institute, which is building reference genomes for 23 species of
rice; the HudsonAlpha Institute for Biotechnology, which is
creating several genomes for cotton, peanut and sorghum; the
University of California at Davis, which is amassing a collection
of genomes for wine grapes and other fruits; and Cornell
University, which is using SMRT Sequencing to detail several
varieties of coffee.
About Pacific Biosciences Pacific Biosciences
of California, Inc. (NASDAQ:PACB) offers sequencing systems to help
scientists resolve genetically complex problems. Based on its novel
Single Molecule, Real-Time (SMRT®) technology, Pacific Biosciences’
products enable: de novo genome assembly to finish genomes in order
to more fully identify, annotate and decipher genomic structures;
full-length transcript analysis to improve annotations in reference
genomes, characterize alternatively spliced isoforms in important
gene families, and find novel genes; targeted sequencing to more
comprehensively characterize genetic variations; and real-time
kinetic information for epigenome characterization. Pacific
Biosciences’ technology provides high accuracy, ultra-long reads,
uniform coverage, and the ability to simultaneously detect
epigenetic changes. PacBio® sequencing systems, including
consumables and software, provide a simple, fast, end-to-end
workflow for SMRT Sequencing. More information is available at
www.pacb.com.
Forward-Looking Statements All statements in
this press release that are not historical are forward-looking
statements, including, among other things, statements relating to
future availability, uses, accuracy, quality or performance of, or
benefits of using, products or technologies, the suitability or
utility of products or technologies for particular applications,
studies or projects, the expected benefits of the Plant Genome
Research Project, and other future events. You should not place
undue reliance on forward-looking statements because they involve
known and unknown risks, uncertainties, changes in circumstances
and other factors that are, in some cases, beyond Pacific
Biosciences’ control and could cause actual results to differ
materially from the information expressed or implied by
forward-looking statements made in this press release. Factors that
could materially affect actual results can be found in Pacific
Biosciences’ most recent filings with the Securities and Exchange
Commission, including Pacific Biosciences’ most recent reports on
Forms 8-K, 10-K and 10-Q, and include those listed under the
caption “Risk Factors.”
Pacific Biosciences undertakes no obligation to revise or update
information in this press release to reflect events or
circumstances in the future, even if new information becomes
available.
Contacts Media: Nicole Litchfield 415.793.6468
nicole@bioscribe.com
Investors: Trevin Rard 650.521.8450
ir@pacificbiosciences.com
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