A series of recent peer-reviewed scientific publications highlights
the growing use of Single Molecule, Real-Time (SMRT®) Sequencing to
annotate plant and animal genomes. These reports from the genomics
community show that PacBio sequencing consistently detects more
genes, alternative splicing events, and other important elements
compared with competing sequencing platforms. Characterizing these
elements is essential for a deeper understanding of these organisms
as well as for breeding efforts to improve crops and livestock.
Genome annotation using short-read technology (RNA-seq) is
challenging because individual reads are too short to span entire
gene transcripts, which can be multiple kilobases long. As a
result, scientists must stitch together many short reads using
error-prone assembly processes. Alternative splicing, in which the
same gene expresses functionally different transcripts, is
particularly difficult to detect with short reads because segments
of those transcripts are often conflated during assembly. SMRT
Sequencing produces significantly longer reads, achieving mean
lengths of 10-18 kb, allowing scientists to generate full-length
transcripts or isoforms without introducing errors from assembly
algorithms. For transcriptome analysis, this is known as the
Iso-Seq™ method because it produces full-length isoform
sequences.
“Scientists are embracing the Iso-Seq method to produce a more
complete genetic view of everything from important crops, such as
wheat and barley, to livestock, including chickens,” said Kevin
Corcoran, Senior Vice President of Market Development for Pacific
Biosciences. “The beauty of this approach is that SMRT Sequencing
provides a lot of novel information about gene content even for
organisms that lack a reference assembly or have incredibly complex
genomes. With our latest instrument, the Sequel System, we
anticipate that more groups will adopt SMRT Sequencing as a fast
and affordable means of generating the most comprehensive
transcriptomes possible.”
“In our analysis of gene activity in chickens, SMRT Sequencing
allowed us to overcome challenges that had limited our view of
genes in this bird for years,” said David Burt, Professor at the
University of Queensland, Genomics Initiative, who serves on the
steering committee for the Functional Annotation of Animal Genomes
(FAANG) Project. “A major advance over previous methods was the
accurate characterization of all alternative splice transcripts -
from start to end - allowing us to define all transcription start
sites. More importantly, for the first time we were able to define
accurate long non-coding RNAs. Based on this success, we anticipate
implementing the Iso-Seq method for transcriptomic studies of many
livestock species across the FAANG consortium as the surest path to
fully characterizing the gene content in these animals.”
Recent Iso-Seq publications include:
Normalized long read RNA sequencing in chicken reveals
transcriptome complexity similar to human, BMC GenomicsPrincipal
investigator David Burt and his team studied embryonic and brain
tissue from chickens, finding 70% more genes than were previously
known to exist in this animal.
An improved assembly and annotation of the allohexaploid wheat
genome identifies complete families of agronomic genes and provides
genomic evidence for chromosomal translocations, Genome
Research
Led by Matthew Clark, this project analyzed gene content in
Chinese Spring bread wheat. PacBio data revealed more than 6,600
genes missed by other technologies, and corrected more than 8,100
gene models that were inaccurate in previous annotations.
A chromosome conformation capture ordered sequence of the barley
genome, Nature
Principal investigator Nils Stein and collaborators used SMRT
Sequencing and other tools to characterize the transcriptome of
barley. Their analysis revealed about 40,000 high-confidence
genes.
Alternative splicing profile and sex-preferential gene
expression in the female and male Pacific abalone Haliotis
discus hannai, Gene
Senior author Young Chang Sohn and team reported a detailed
analysis of gene content in abalone, finding that transcriptome
patterns differed substantially between males and females. More
than 500 genes in females and nearly 400 genes in males had
multiple isoforms, i.e., evidence of alternative splicing.
Single-cell mRNA isoform diversity in the mouse brain, BMC
Genomics
Scientists Kasper Karlsson and Sten Linnarsson
report unexpected alternative splicing diversity in mouse brain
tissue, with many cells expressing unique isoforms.
For more information, please visit
http://www.pacb.com/research-focus/plant-animal-sciences/.
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®) Sequencing 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, quality or
performance of, or benefits of using, products or technologies, 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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