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Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)


Vo, TTM and Nguyen, TV and Amoroso, G and Ventura, T and Elizur, A, Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar), BMC Genomics, 22 Article 545. ISSN 1471-2164 (2021) [Refereed Article]


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Copyright 2021 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0)

DOI: doi:10.1186/s12864-021-07884-9


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.

Item Details

Item Type:Refereed Article
Keywords:new generation sequencing, Atlantic salmon, pigmentation
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Fisheries sciences
Research Field:Aquaculture
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - aquaculture
Objective Field:Aquaculture fin fish (excl. tuna)
UTAS Author:Amoroso, G (Dr Gianluca Amoroso)
ID Code:146514
Year Published:2021
Web of Science® Times Cited:5
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2021-09-10
Last Modified:2021-10-26
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