146514 - Deploying new generation sequencing for the study of flesh.pdf (2.63 MB)
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
journal contribution
posted on 2023-05-21, 02:22 authored by Vo, TTM, Nguyen, TV, Gianluca AmorosoGianluca Amoroso, Ventura, T, Elizur, AThe 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.
History
Publication title
BMC GenomicsVolume
22Article number
545Number
545Pagination
1-21ISSN
1471-2164Department/School
Institute for Marine and Antarctic StudiesPublisher
Biomed Central LtdPlace of publication
Middlesex House, 34-42 Cleveland St, London, England, W1T 4LbRights statement
Copyright 2021 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/Repository Status
- Open