Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
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...
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Biomed Central Ltd
2021
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Online Access: | https://eprints.utas.edu.au/38022/ https://eprints.utas.edu.au/38022/1/146514%20-%20Deploying%20new%20generation%20sequencing%20for%20the%20study%20of%20flesh.pdf |
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ftunivtasmania:oai:eprints.utas.edu.au:38022 2023-05-15T15:28:16+02:00 Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) Vo, TTM Nguyen, TV Amoroso, G Ventura, T Elizur, A 2021 application/pdf https://eprints.utas.edu.au/38022/ https://eprints.utas.edu.au/38022/1/146514%20-%20Deploying%20new%20generation%20sequencing%20for%20the%20study%20of%20flesh.pdf en eng Biomed Central Ltd https://eprints.utas.edu.au/38022/1/146514%20-%20Deploying%20new%20generation%20sequencing%20for%20the%20study%20of%20flesh.pdf 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 <http://dx.doi.org/10.1186/s12864-021-07884-9>. new generation sequencing Atlantic salmon pigmentation Article PeerReviewed 2021 ftunivtasmania https://doi.org/10.1186/s12864-021-07884-9 2021-11-01T23:17:49Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar University of Tasmania: UTas ePrints BMC Genomics 22 1 |
institution |
Open Polar |
collection |
University of Tasmania: UTas ePrints |
op_collection_id |
ftunivtasmania |
language |
English |
topic |
new generation sequencing Atlantic salmon pigmentation |
spellingShingle |
new generation sequencing Atlantic salmon pigmentation Vo, TTM Nguyen, TV Amoroso, G Ventura, T Elizur, A Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
topic_facet |
new generation sequencing Atlantic salmon pigmentation |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Vo, TTM Nguyen, TV Amoroso, G Ventura, T Elizur, A |
author_facet |
Vo, TTM Nguyen, TV Amoroso, G Ventura, T Elizur, A |
author_sort |
Vo, TTM |
title |
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
title_short |
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
title_full |
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
title_fullStr |
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
title_full_unstemmed |
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
title_sort |
deploying new generation sequencing for the study of flesh color depletion in atlantic salmon (salmo salar) |
publisher |
Biomed Central Ltd |
publishDate |
2021 |
url |
https://eprints.utas.edu.au/38022/ https://eprints.utas.edu.au/38022/1/146514%20-%20Deploying%20new%20generation%20sequencing%20for%20the%20study%20of%20flesh.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
https://eprints.utas.edu.au/38022/1/146514%20-%20Deploying%20new%20generation%20sequencing%20for%20the%20study%20of%20flesh.pdf 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 <http://dx.doi.org/10.1186/s12864-021-07884-9>. |
op_doi |
https://doi.org/10.1186/s12864-021-07884-9 |
container_title |
BMC Genomics |
container_volume |
22 |
container_issue |
1 |
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1766358642773196800 |