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:

New Isoform-Level Transcriptome Reference Helps Shrimp Industry Ward Off Disease

Tuesday, March 26, 2019

Pacific white shrimpOne of the fastest growing global foods is also one of its most vulnerable. Without an adaptive immune system, the Pacific white shrimp, Litopenaeus vannamei, rely on cellular and humoral defenses, such as the release of antimicrobial peptides, in their battle against invading microbes and pathogen infections. A battle they’re losing, leading to massive mortality and devastating economic losses.

A full-length transcriptome analysis using the PacBio Iso-Seq method has resulted in an isoform-level reference transcriptome that is shedding new light into the shrimp’s innate immune system, providing hope for the shrimp aquaculture industry.

One of the most economically important shrimp species in the global aquaculture industry, Pacific white shrimp global production grew from 2,688,901 tons in 2010 to 4,168,417 tons in 2016, according to The Food and Agriculture Organization of the United Nations. However, farmed shrimp supplies are under significant threat from three major shrimp pathogens: acute hepatopancreatic necrosis disease (AHPND), white spot syndrome virus (WSSV) and bacteria in the genus Vibrio.

By interrogating the transcriptome of the vulnerable species, a team of scientists from the Guangdong Institute of Applied Biological Resources in China were able to identify more than 5,000 full-length transcripts involved in its innate immune system, including nine immune-related processes, 19 immune-related pathways and 10 other immune-related systems. They also found wide transcript variants, including toll-like receptors (TLRs) and interferon regulatory factors (IRFs), which increased the number and function complexity of immune molecules.

Reporting in Fish and Shellfish Immunology, Chen Jinping and first author Zhang Xiujuan described how they combined PacBio isoform sequence (Iso-Seq) analysis and Illumina paired-end short read methods to discover 72,648 nonredundant full-length transcripts (unigenes) with an average length of 2,545 bp from five main tissues: the hepatopancreas, cardiac stomach, heart, muscle, and pyloric stomach.

The team turned to targeted isoform sequencing due to the difficulty they would have faced trying to sequence the entire L. vannamei genome, which currently has no reference. The genome is large and contains highly repetitive sequences; previous attempts to characterize its transcriptome using short reads restricted the yield of full-length cDNA molecules, the authors wrote.

“Using short read RNA-Seq strategies, extensive alternative prediction is impractical and a high variability of isoforms expression quantification is impossible in shrimp without a true genome reference,” the authors wrote. “The PacBio Iso-Seq strategy provides the convenience of finding more numbers of AS events of genes in many species, including reference-free species.”

The scientists used homology-based cDNA cloning to amplify full-length sequences of the shrimp’s immune genes to generate a high-confidence isoform dataset that was sequenced at Nextomics Biosciences in Wuhan, China. After annotating these full-length transcripts with well-curated databases, long noncoding RNAs (lncRNAs) and alternative splicing events were characterized.

Using the full-length isoform transcripts yielded from the SMRT Iso-Seq analysis as reference sequences, the unigene expression levels among the various tissues of L. vannamei were further analyzed based on short read datasets generated by the Illumina sequencing platform.

“Understanding the innate immune system of shrimp and revealing their immune responses against invading pathogens might contribute to developing strategies for the prevention and treatment of these diseases, which is essential for the shrimp aquaculture industry,” the authors wrote.

This survey of transcript variants and expression profiles of the immune-related molecules of L. vannamei have contributed to a comprehensive insight into the immune system, and will provide a valuable resource for geneticists and the commercial sector alike, they concluded.

 

Subscribe for blog updates:

Archives