Improved Reference Genome for Aedes
aegypti, Carrier of Zika Virus and Other Public Health Threats,
Published in Nature
Pacific Biosciences of California Inc., (Nasdaq:PACB), the leading
provider of high-quality sequencing of genomes, transcriptomes and
epigenomes, today announced that an international team of
scientists have published the highest quality genome assembly to
date of the Aedes aegypti mosquito genome using its Single
Molecule, Real-Time (SMRT®) technology. The peer-reviewed paper
appears online today in the journal Nature.
Analysis of the Ae. aegypti mosquito genome could help
scientists combat the pest and the infectious diseases it spreads,
including Zika, dengue, chikungunya, and yellow fever. Generation
of a high-quality reference genome for this species is critically
important for exploring the genomic basis of insecticide
resistance, disease transmission, blood-feeding host preference,
and development of novel repellents.
“The high-quality genome assembly and annotation described here
will enable major advances in mosquito biology and has already
allowed us to carry out a number of experiments that were
previously impossible,” the authors write. The effort was led by
Leslie B. Vosshall and colleagues at Rockefeller University, along
with researchers at several other institutions. The sequencing was
performed by Pacific Biosciences at the company’s headquarters in
California.
Previous efforts to sequence the 1.3 gigabase, highly repetitive
Ae. aegypti genome suffered from shorter segment sequences that had
to be pieced together, resulting in more than 30,000 gaps. Using
SMRT Sequencing data, the team produced an assembly that is highly
contiguous, representing a 93 percent decrease in the number of
contigs.
Dr. Vosshall commented: “A lot of the most important questions
in mosquito biology are being attacked with molecular biology and
genetics. Without a properly assembled genome, it is extremely
difficult to make any progress because we lack information about
the total number of genes and their arrangement on chromosomes. The
new genome assembly – powered by extremely high-quality PacBio
data—has already transformed the field. Because the mosquito genome
is highly repetitive, only long-read sequencing produces the
high-quality data necessary to bridge the ‘oceans’ of repetitive
DNA to find the ‘islands’ of meaningful DNA containing genes and
gene-related sequences.”
“The completion of this mosquito genome provides an enormous
contribution to future global health efforts and may address the
devastating diseases carried by this species, such as the Zika
virus,” said Jonas Korlach, Chief Scientific Officer of Pacific
Biosciences. “SMRT Sequencing has been employed extensively in the
study of infectious disease, particularly for the smaller genomes
of viral and microbial pathogens. Recent performance improvements
in the technology have also made it more cost effective to resolve
the larger, more complex genomes of host species, providing a more
complete picture of disease lifecycle. The methods used in this
reference genome assembly create a path for producing high-quality
reference assemblies for other challenging species.”
As the field of genomics evolves, there is a growing awareness
in the scientific community of the importance of long-read
sequencing data. The ability to read DNA in long, uninterrupted
segments provides researchers with a more complete and accurate
picture of gene elements and their positioning. PacBio
sequencing offers the most comprehensive view of genomes —
including the full spectrum of genetic variation — of any
sequencing technology on the market today by providing very long
average read lengths, very high consensus accuracy, and uniform
coverage. SMRT Sequencing technology consistently produces some of
the longest average read lengths available in the industry,
averaging greater than 20,000 base pairs, with some reads more than
60,000 base pairs.
More than seventy scientists collaborated to create this new
assembly, AaegL5, which has already revealed some of what
biologists have been missing. For instance, one gene crucial for
sex determination—the Nix gene—was entirely missing from previous
Ae. aegypti assemblies. Being able to locate where this gene and
the corresponding male-determining factor (M-factor) appear on the
chromosome is important for scientists who wish to breed and
release males into the wild as a strategy to bias the population
towards males rather than disease-transmitting females over
multiple generations.
The new genome has also provided critical clues into how the
insects sense a vast array of chemical cues, such as the carbon
dioxide and human body odor that attracts female mosquitoes.
Another important find was the location of markers that
differentiated mosquitoes capable of transmitting certain viruses,
like dengue. Other discoveries enabled by the new assembly could
provide insight into insecticide resistance, as well as identify
potential new candidate insecticides. By tracing ion channels, for
example, the team identified a type of insecticide widely used in
agricultural and veterinary applications that could be re-purposed
to kill mosquito larvae.
The genome was assembled into contigs using PacBio’s
FALCON-Unzip assembler, followed by scaffolding to the three Ae.
aegypti chromosomes end-to-end using Hi-C technology. The
researchers also generated a dramatically improved gene set
annotation (AaegL5.0) using the NCBI RefSeq pipeline.
An infographic about how genome references like this mosquito
accelerate science is available here. More information about the
benefits of PacBio sequencing for plant and animal sciences is
available here.
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 methods, products or technologies for
particular applications, studies or projects, the expected benefits
of sequencing projects, 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 Litchfield415.793.6468nicole@bioscribe.com
Investors:Trevin Rard650.521.8450ir@pacificbiosciences.com
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