Cold Spring Harbor Laboratory Scientists Produce High-Quality Maize Transcriptome with PacBio SMRT Sequencing
June 24 2016 - 7:30AM
Improvements in maize breeding are required to feed a growing
population and will depend on a more complete understanding of
global gene expression in the plant. In a new publication from Cold
Spring Harbor Laboratory (CSHL), scientists produced the largest
collection of full-length transcripts for the maize genome and a
significantly improved genome annotation using Single Molecule,
Real-Time (SMRT®) Sequencing and the Iso-Seq™ analysis method from
Pacific Biosciences. The work appears online today in Nature
Communications.
Led by CSHL scientists Doreen Ware, who is also
affiliated with the USDA Agricultural Research Service, and Bo
Wang, the team embarked on the project to leverage the advantages
that SMRT Sequencing and the Iso-Seq method offer for transcriptome
analysis in plants. The Iso-Seq protocol allows scientists to
generate long reads covering full-length gene transcripts,
providing a more accurate view of gene structure, gene expression,
and important mechanisms such as alternative gene splicing.
Iso-Seq analysis of SMRT Sequencing data more than
doubled the number of isoforms, corrected numerous previously
mis-annotated gene models, and identified many novel genes and long
non-coding RNAs. Additionally, the team showed that long reads are
even more important than expected for transcriptome studies. The
average transcript length in this project — almost 3 kb — is much
longer than that from the previous maize annotation, highlighting a
strong bias limitation in previous approaches.
“Although data from short-read sequencing have
accumulated over recent years, they do not provide full-length
sequence for each RNA, limiting their utility for defining
alternatively spliced forms,” Wang et al. write. “In some cases,
short-read sequencing generates low-quality transcripts, leading to
incorrect annotations.”
“We congratulate the scientists at Cold Spring
Harbor Laboratory for this very impressive work,” said Jonas
Korlach, Chief Scientific Officer of Pacific Biosciences. “Maize is
an incredibly difficult genome to work with, and therefore really
benefits from the advantages of SMRT Sequencing and the Iso-Seq
method through their ability to produce highly accurate full-length
transcripts without the need for post-sequence assembly.”
More information is available in this blog post,
and in the paper, “Unveiling the complexity of the maize
transcriptome by single-molecule long-read sequencing.”
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 is the only DNA sequencing technology that
provides 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.
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