Scientists sequence drought tolerant grass using single molecule real-time sequencing
- Date:
- November 11, 2015
- Source:
- Donald Danforth Plant Science Center
- Summary:
- A new paper reports the virtually complete draft genome of Oropetium thomaeum, a grass species that can regrow after exposed to extreme drought when water becomes available. 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.
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A new paper released in Nature has 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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Materials provided by Donald Danforth Plant Science Center. Note: Content may be edited for style and length.
Journal References:
- Antonio Bernardo Carvalho, Beatriz Vicoso, Claudia A. M. Russo, Bonnielin Swenor, Andrew G. Clark. Birth of a new gene on the Y chromosome ofDrosophila melanogaster. Proceedings of the National Academy of Sciences, 2015; 112 (40): 12450 DOI: 10.1073/pnas.1516543112
- André E. Minoche, Juliane C. Dohm, Jessica Schneider, Daniela Holtgräwe, Prisca Viehöver, Magda Montfort, Thomas Rosleff Sörensen, Bernd Weisshaar, Heinz Himmelbauer. Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. Genome Biology, 2015; 16 (1) DOI: 10.1186/s13059-015-0729-7
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