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Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)2.42 MB
Published VersionCC BY V4.0, Open Access
CorrectionCC BY V4.0, Open Access
Journal article
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
BMC Genomics, Vol.22, pp.1-22
2021
Abstract
Background: The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3' mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3' mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes.
Details
- Title
- Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
- Authors
- Thu Vo (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - LegacyTuan Nguyen (Author) - Agriculture VictoriaGianluca Amoroso (Author) - Petuna AquacultureTomer Ventura (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - LegacyAbigail Elizur (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
- Publication details
- BMC Genomics, Vol.22, pp.1-22
- Publisher
- BioMed Central Ltd.
- Date published
- 2021
- DOI
- 10.1186/s12864-021-07884-9
- ISSN
- 1471-2164
- Copyright note
- © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- Organisation Unit
- University of the Sunshine Coast, Queensland; GeneCology Research Centre - Legacy; USC International - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99552408902621
- Output Type
- Journal article
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