eCite Digital Repository
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
Citation
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]
 | PDF 3Mb |
Copyright Statement
Copyright 2021 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/
DOI: doi:10.1186/s12864-021-07884-9
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 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 |
| Downloads: | 14 View Download Statistics |
Repository Staff Only: item control page