+

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:

Hummingbird Study Uses Iso-Seq Method to Hunt for Metabolic Function

Tuesday, April 4, 2017

Photo of ruby-throated hummingbird by Michelle Lynn Reynolds

Photo of ruby-throated hummingbird by Michelle Lynn Reynolds

A new preprint offers an enticing look at transcriptome results from analysis of a hummingbird using SMRT Sequencing. In this study, scientists found new clues to explain unique attributes of the bird’s metabolism. The work was made possible through full-length isoform sequencing, which allowed deep, assembly-free analysis even though no reference genome was available.

Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris” is now available on BioRxiv. From Rachael Workman, Alexander Myrka, Elizabeth Tseng, William Wong, Kenneth Welch, and Winston Timp, the paper describes a project designed to better understand how hummingbirds switch metabolic gears to focus on sugars or lipids as needed. “This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes,” they write, “and in that de novo lipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight.”

The team used the Iso-Seq method with long-read PacBio data to generate full-length isoform sequences, focusing on the liver of Archilochus colubris. According to the paper, this represents “the first high-coverage transcriptome of any single avian tissue.” They also aligned transcripts to Calypte anna, a recently completed hummingbird assembly that also made use of SMRT Sequencing.

Workman et al. report that the use of long-read PacBio data allowed for more accurate views of isoforms and alternative splicing, even without a reference genome. “Using full-length transcript data, we found alignment unnecessary to generate clear pictures of the gene isoforms,” they note. “The long reads negate the need for transcript assembly, a precarious analysis in the absence of a genome.” Nearly half of the reads in the final analysis covered full-length genes, including the 5’ and 3’ ends as well as the polyA tail.

The team used the COGENT pipeline to assign transcripts to gene families and focus on unique isoforms. “COGENT is specifically designed for transcriptome assembly in the absence of a reference genome, allowing for isoforms of the same gene to be distinctly identified from different gene families,” the scientists write. Their analysis generated a highly diverse set of isoforms, which the authors believe “represents a nearly complete transcriptome of the hummingbird liver.”

With that dataset, the scientists found genes unique to hummingbird. “These genes showed a specific enrichment for pathways involved in lipid metabolism — suggesting that the hummingbird has evolved variants of these genes to achieve its high levels of metabolic efficiency,” they report.

The scientists note that follow-up functional assays will be an important next step in understanding and verifying the function of many genes of interest.

Subscribe for blog updates:

Archives