Download Cold Spring Harbor Laboratory Scientists Produce High

June 24, 2016
Cold Spring Harbor Laboratory Scientists Produce High-Quality Maize Transcriptome with
PacBio SMRT Sequencing
Findings of novel genes and corrections of previous mis-annotations published in Nature
Communications
MENLO PARK, Calif., June 24, 2016 (GLOBE NEWSWIRE) -- 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 misannotated 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 fulllength 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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