X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

Scientists Publish High-Quality, Near-Complete Genome of Resurrection Grass Oropetium

Wednesday, November 11, 2015

nature-logoWe’re excited about a new Nature paper from the winners of our 2014 “Most Interesting Genome in the World” SMRT Grant program. “Single-molecule sequencing of the desiccation tolerant grass Oropetium thomaeum” comes from lead authors Robert VanBuren and Doug Bryant along with senior author Todd Mockler at the Donald Danforth Plant Science Center, as well as a number of collaborators at other institutions. In it, the authors report a virtually complete genome of Oropetium thomaeum, a grass with an estimated genome size of 245 Mb and the handy ability to regrow even after extreme drought once water becomes available.

The scientists believe that a better understanding of the plant’s genome could shed light on the mechanisms underpinning these so-called resurrection plants, and ultimately enable the engineering of crop plants to withstand severe drought and stress.

For this study, the team worked with about 72x coverage of the Oropetium genome generated by the PacBio system. That’s “equivalent to <1 week of sequencing time and <$10k in reagents,” according to the paper. Based on HGAP and Quiver, the resulting assembly covered 99% of the genome in 625 contigs, with an accuracy of 99.99995% and a contig N50 length of 2.4 Mb.

VanBuren et al. note that the contiguity of the assembly sets it apart from draft genomes produced from short-read sequencers. “Most NGS-based genomes have on the order of tens of thousands of short contigs distributed in thousands of scaffolds,” the scientists write. Because the assemblies are so fragmented, “they are missing biologically meaningful sequences including entire genes, regulatory regions, transposable elements (TEs), centromeres, telomeres and haplotype-specific structural variations.”

Instead, SMRT Sequencing is pushing new limits to characterize those elements in the Oropetium genome, with its predicted 28,446 protein-coding genes and a significant proportion of repeat regions. The authors noted that “the largest tandem array contains five identical and one partial 9 kb repeats collectively spanning 51 kb; this is approaching the theoretical limit given the current read-length distributions of PacBio.” The assembly includes telomere and centromere sequence, long terminal-repeat retrotransposons, tandem duplicated genes, and other difficult-to-access genomic elements. In addition, the scientists produced the full chloroplast genome in a single contig that includes “~25 kb of inverted repeat regions which typically collapse into a single copy during assembly,” they report.

“The Oropetium genome showcases the utility of SMRT sequencing for assembling high-quality plant and other eukaryotic genomes,” the scientists note, “and serves as a valuable resource for the plant comparative genomics community.”

Subscribe for blog updates:

Archives