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

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Vo, TTM, Nguyen, TV, Amoroso, G ORCID: 0000-0003-2985-4205, Ventura, T and Elizur, A 2021 , 'Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)' , BMC Genomics, vol. 22 , pp. 1-21 , doi: 10.1186/s12864-021-07884-9.

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Abstract

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 Type: Article
Authors/Creators:Vo, TTM and Nguyen, TV and Amoroso, G and Ventura, T and Elizur, A
Keywords: new generation sequencing, Atlantic salmon, pigmentation
Journal or Publication Title: BMC Genomics
Publisher: Biomed Central Ltd
ISSN: 1471-2164
DOI / ID Number: 10.1186/s12864-021-07884-9
Copyright Information:

Copyright 2021 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

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