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Scientists publish unique genomic discoveries with single molecule, real-time sequencing

November 12, 2015

A new paper released in Nature today reported the virtually complete draft genome of Oropetium thomaeum, a grass species that can regrow after exposed to 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 Donald Danforth Plant Science Center researchers, senior author Todd Mockler, Ph.D., associate member, Geraldine and Robert Virgil Distinguished Investigator, lead authors post-doctoral associate Robert VanBuren, Ph.D., and Doug Bryant, Ph.D. and other collaborators. The resulting assembly has an accuracy of 99.99995% and includes telomere and centromere sequences, long terminal repeat retrotransposons, tandem duplicated genes, and other difficult-to-assemble 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 extreme drought tolerance for potential application in crop improvement.

"We submitted the idea to sequence the resurrection grass, Oropetium thomaeum to PacBio because it has the smallest known genome among the grasses. Having the genomic data of a highly drought tolerant species is really powerful in facilitating crop improvement, and providing a valuable resource for the plant comparative genomics community. Information gained from this collaboration is an important step in the effort to sustainably improve the ability of important food and energy crops to survive in drought conditions without reducing the harvest," said Mockler.

This hearty grass is a resurrection plant due to its ability to survive in desert like conditions even though it looks lifeless but still has less than a third of its original water content. The tiny C4 grass, which grows on rock outcrops in parts of Africa and India, is closely related to major food, feed and bioenergy crops and has the ability to be revived with a small amount of water and resume growth. The Oropetium genome sequence will help lead to understanding of novel drought tolerance mechanisms for efficient and productive agricultural land use.

"Our customers often tell us that SMRT Sequencing helps them make completely new discoveries in the organisms they study," said Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. "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."
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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. http://www.genomebiology.com/2015/16/1/184

About The Donald Danforth Plant Science Center

Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research, education and outreach aim to have impact at the nexus of food security and the environment, and position the St. Louis region as a world center for plant science. The Center's work is funded through competitive grants from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation, and the Bill & Melinda Gates Foundation.

To keep up to date with Danforth Center's current operations and areas of research, please visit, http://www.danforthcenter.org, featuring information on Center scientists, news, and the "Roots & Shoots" blog. Follow us on Twitter at @DanforthCenter.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (NASDAQ:PACB) offers the PacBio® RS II Sequencing System and Sequel™ System 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. The PacBio Sequencing Systems, including consumables and software, provides a simple, fast, end-to-end workflow for SMRT Sequencing. More information is available at http://www.pacb.com.

Donald Danforth Plant Science Center

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