Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
Abstract Background 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 deple...
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ftdatacite:10.6084/m9.figshare.c.5516781 2023-05-15T15:30:34+02:00 Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) Vo, Thu Thi Minh Nguyen, Tuan Viet Amoroso, Gianluca Ventura, Tomer Elizur, Abigail 2021 https://dx.doi.org/10.6084/m9.figshare.c.5516781 https://springernature.figshare.com/collections/Deploying_new_generation_sequencing_for_the_study_of_flesh_color_depletion_in_Atlantic_Salmon_Salmo_salar_/5516781 unknown figshare https://dx.doi.org/10.1186/s12864-021-07884-9 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Genetics FOS Biological sciences Collection article 2021 ftdatacite https://doi.org/10.6084/m9.figshare.c.5516781 https://doi.org/10.1186/s12864-021-07884-9 2021-11-05T12:55:41Z Abstract Background 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. Results In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR. Conclusions Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1. Article in Journal/Newspaper Atlantic salmon Salmo salar DataCite Metadata Store (German National Library of Science and Technology) |
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DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
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language |
unknown |
topic |
Genetics FOS Biological sciences |
spellingShingle |
Genetics FOS Biological sciences Vo, Thu Thi Minh Nguyen, Tuan Viet Amoroso, Gianluca Ventura, Tomer Elizur, Abigail Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar) |
topic_facet |
Genetics FOS Biological sciences |
description |
Abstract Background 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. Results In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR. Conclusions Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1. |
format |
Article in Journal/Newspaper |
author |
Vo, Thu Thi Minh Nguyen, Tuan Viet Amoroso, Gianluca Ventura, Tomer Elizur, Abigail |
author_facet |
Vo, Thu Thi Minh Nguyen, Tuan Viet Amoroso, Gianluca Ventura, Tomer Elizur, Abigail |
author_sort |
Vo, Thu Thi Minh |
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 |
figshare |
publishDate |
2021 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.5516781 https://springernature.figshare.com/collections/Deploying_new_generation_sequencing_for_the_study_of_flesh_color_depletion_in_Atlantic_Salmon_Salmo_salar_/5516781 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
https://dx.doi.org/10.1186/s12864-021-07884-9 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.5516781 https://doi.org/10.1186/s12864-021-07884-9 |
_version_ |
1766361031552008192 |