+

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:

PAG Workshop: Wide Breadth of Research Benefiting from SMRT Sequencing

Wednesday, February 8, 2017

If you didn’t get to the Plant and Animal Genome meeting this year, you missed a great workshop featuring SMRT Sequencing users and the fascinating projects they’re working on across plant, animal, agricultural, and conservation sciences and human health. Here are quick summaries of each talk, with full video recordings available for more detail.

PAG2017-Workshop

Our event kicked off with PacBio CSO Jonas Korlach welcoming attendees and delivering an update on the genomics community’s impressive advances with SMRT Sequencing. There are now more than 2,000 publications citing the PacBio long-read technology — a rate of about 30 per week. He also spoke about improvements to the platform, including better assembly tools such as FALCON and FALCON-unzip as well as the recently released Sequel System chemistry that delivers 5-8 Gb of data per SMRT Cell and significantly reduces DNA input requirements. These improvements make it possible to run a broader range of projects on the Sequel System.

Representing the plant side of the conference, the University of Arizona’s Rod Wing spoke about using SMRT Sequencing to produce high-quality genome assemblies for several varieties of rice. He’s undertaken this project to help develop higher-yielding, hardier strains of rice to feed the rapidly growing global population. In the work he presented, his team sequenced two parents of a common hybrid strain, generating the highest-quality publicly available assemblies of Indica rice ever produced. His data illustrated how long-read PacBio sequencing allows for excellent contiguity in assemblies, with one strain represented in just 19 contigs and a strain featuring eight complete chromosomes, including centromeres. Wing also included data from a third genome being sequenced with the Sequel System.

Other speakers focused on animals or insects. Rebecca Johnson from the Australian Museum Research Institute reported on the de novo genome assembly of a koala, a genome about 3.6 Gb in size. The work was undertaken due to conservation concerns for these marsupials, which have many biologically interesting features such as a gestation period of just 35 days. With SMRT Sequencing, her team produced what Johnson called the best marsupial assembly to date; analysis showed that only 5% of BUSCO genes were not represented. The assembly allowed her team to study lactation-related genes that are important for koala development, as well as immune elements (for example, koalas have been found to harbor novel antimicrobials that show effectiveness against drug-resistant bacteria). Johnson’s genome work continues, and she told attendees that she fully expects to achieve a chromosome-level assembly for the animal.

Richard Kuo from the Roslin Institute spoke about using the Iso-Seq method to study brain and embryo tissues from chicken. He said this approach addresses the limitations of other gene expression methods that skip long non-coding RNA (lncRNAs), the full universe of isoforms, and more. By producing full-length transcripts from the transcription start site to the transcription end site without any assembly required, SMRT Sequencing is ideal for characterizing the transcriptome. With the chicken project, Kuo evaluated the importance of protocols such as normalization and using 5’ cap selection, both of which provided richer data sets. Kuo told attendees that using the Iso-Seq method allows scientists to immediately leapfrog to the best available annotations,  producing more information on the transcriptome than ever.

Rockefeller University’s Erich Jarvis presented an update on his work with bird genomes for the B10K project. He offered a comparison of assembly techniques for hummingbird, which has been analyzed with everything from short-read sequencers to genome mapping tools. The PacBio-powered assemblies consistently ranked as the highest quality, with the fewest contigs and best accuracy. He also included a look at four genes associated with vocal learning, which were complete in the PacBio assembly, showing the importance of incorporating long reads into the assembly.

Representing the insect front, Ben Matthews from Rockefeller University reported on a genome assembly project for Aedes aegypti, the common vector for Zika, dengue, and yellow fever. Noting that mosquitoes are believed to be the most deadly creature in the world, he said that a clear and complete understanding of their genomes will be essential to thwarting public health threats. The original assembly of the Aedes aegypti genome is nine years old and hasn’t been improved much, so Matthews and his colleagues turned to SMRT Sequencing for a new version of the same strain. The effort yielded a much better assembly, boosting the contig N50 from 83 kb to about 2 Mb. Further analysis showed that 7,500 transcripts map to the new assembly but not to the old, indicating a significant amount of new gene content. Matthews anticipates that this new assembly will replace the old one for the entire mosquito research community, and serve as an important resource for understanding resistance to repellants and designing guide RNAs for CRISPR genome modification to constrain population growth.

Many thanks to all of our workshop speakers for a great event!

Subscribe for blog updates:

Archives

Tags