+

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:

A New Look at an Old Favorite: Cabernet Sauvignon Study Generates a Transcriptome of Ripening Berries

Monday, March 12, 2018

Photo by H. Zell

A new preprint from scientists at the University of California, Davis, demonstrates the usefulness of SMRT Sequencing and the Iso-Seq method to enable comprehensive transcriptome analysis even in the absence of a reference genome assembly. The team conducted this study on the grape used to make Cabernet Sauvignon.

Lead author Andrea Minio, senior author Dario Cantu, and collaborators used SMRT Sequencing to generate full-length transcripts of Vitis vinifera cv. Cabernet Sauvignon, analyzing RNA collected from four replicates at each of four important stages of ripening. Previously, this team used PacBio sequencing to generate a highly contiguous genome assembly for the wine grape. In this new effort, they focused on characterizing the networks associated with metabolism and berry development.

Cantu and his team are used to studying plants that lack reference-grade genome assemblies. They adopted the Iso-Seq method for this new project as a means of evaluating it for use on other targets without references in the future. “Iso-Seq is an ideal technology for reconstructing a transcriptome without a reference sequence and for resolving isoforms,” they report in the preprint, noting that full-length transcripts capture splice variants and noncoding RNAs. Their wine grape analysis yielded more than 170,000 transcripts associated with 13,402 genes. “Full-length transcripts refined approximately one third of the gene models predicted using several ab initio and evidence-based methods,” the scientists write. “The Iso-Seq information also helped identify 563 additional genes, 4,803 new alternative transcripts, and the 5’ and 3’ UTRs in the majority of predicted genes.”

The results indicated significant changes in gene expression depending on developmental stage. Just a quarter of loci were represented at all four stages tested; a third of loci were detected only at specific stages, “confirming the importance of collecting different stages of development to capture the complexity of the berry transcriptome,” the authors note.

“This study demonstrates that Iso-Seq data can be used to compile a comprehensive reference transcriptome that represents most genes expressed in a tissue undergoing extensive transcriptional reprogramming,” the scientists conclude. “The pipeline described here can be of even greater value for projects aiming to reconstruct the gene space in plant species with complex and large genomes that have not been resolved yet.”

Subscribe for blog updates:

Archives