Menlo Park, California, USA
November 11, 2015
New scientific publications demonstrate the increasing use of Single Molecule, Real-Time (SMRT®) Sequencing from Pacific Biosciences of California, Inc., (Nasdaq:PACB) to elucidate complex genomes and traits for plant and animal species. These papers show that SMRT Sequencing enables critical discoveries that cannot be found with other sequencing technologies, the company announced.
“These publications add to the mounting evidence demonstrating it is possible to produce very high-quality, complete genome assemblies for model and non-model organisms with SMRT Sequencing,” said Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. “These assemblies serve as invaluable long-term resources for the plant and animal research communities and are rapidly advancing our understanding of important biological mechanisms in complex organisms, even for organisms thought to be fully characterized already.”
A new paper released in Nature today reported the virtually complete draft genome of Oropetium thomaeum, a grass species that can regrow after extreme drought when water becomes available. The plant’s 245 Mb genome was analyzed with 72x coverage on the PacBio® RS II Sequencing System by scientists at the Donald Danforth Plant Science Center and collaborating institutions. The resulting assembly is > 99.999% accurate and includes telomere and centromere sequence, long terminal repeat retrotransposons, tandem duplicated genes, and other difficult-to-access genomic elements. This plant was sequenced through Pacific Biosciences’ “Most Interesting Genome in the World” grant program to help scientists determine the biological mechanisms behind its drought resistance for potential application in crop engineering.
A paper recently published in Proceedings of the National Academy of Sciences (PNAS) described the use of SMRT Sequencing to reveal a previously intractable region of the Y chromosome in Drosophila melanogaster. The authors discovered a new gene duplicated from a different chromosome that acquired a functional reproductive role in male fruit flies. The gene was found in a 55 kb region consisting of pseudogenes, transposable elements, and highly repetitive sequence — a stretch of the genome the authors had spent years trying to decode. “PacBio produced a seemingly error-free assembly of the FDY region, something that has eluded us for years of hard work,” they wrote.
In Genome Biology, another publication reported the use of the Iso-Seq™ method to produce full-length transcripts for the prediction and validation of gene models, as well as for genome annotation. Using the sugar beet as an example, the scientists validated more than 2,000 existing gene predictions and identified 665 novel gene structures. Gene model predictions based on Iso-Seq data resulted in a 17% improvement in genome annotation for sugar beet.
“Our customers often tell us that SMRT Sequencing helps them make completely new discoveries in the organisms they study,” said Dr. Korlach. “With the highest-quality genome assemblies, targeted sequencing for incredibly complex regions, and the ability to study full-length isoforms as well as epigenetics, PacBio technology portrays a truly comprehensive view of biology that no other sequencing technology can offer.”
Papers cited:
Robert VanBuren, Doug Bryant, et al. “Single-molecule sequencing of the desiccation tolerant grass Oropetium thomaeum.” Nature. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature15714.html
Bernardo Carvalho et al. “Birth of a new gene on the Y chromosome of Drosophila melanogaster.” PNAS: http://www.pnas.org/content/112/40/12450.full
Minoche, A.E., Dohm, J.C., Schneider, J., Holtgräwe, D., et al.
“Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.” Genome Biology. 16184.
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 DNA base modification identification to help characterize epigenetic regulation and DNA damage. Pacific Biosciences’ technology provides the industry’s highest consensus accuracy over the longest read lengths in combination with the ability to detect real-time kinetic information. 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.
Topics
Species
