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3 Publications visible to you, out of a total of 3
SALARECON connects the Atlantic salmon genome to growth and feed efficiency

Abstract (Expand)

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients … must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon. We present SALARECON, a model focusing on energy, amino acid, and nucleotide metabolism that links the Atlantic salmon genome to metabolic fluxes and growth. It performs well in standardized tests and captures expected metabolic (in)capabilities. We show that it can explain observed hypoxic growth in terms of metabolic fluxes and apply it to aquaculture by simulating growth with commercial feed ingredients. Predicted limiting amino acids and feed efficiencies agree with data, and the model suggests that marine feed efficiency can be achieved by supplementing a few amino acids to plant- and insect-based feeds. SALARECON is a high-quality model that makes it possible to simulate Atlantic salmon metabolism and growth. It can be used to explain Atlantic salmon physiology and address key challenges in aquaculture such as development of sustainable feeds.

Authors: Maksim Zakhartsev, Filip Rotnes, Marie Gulla, Ove Oyas, Jesse van Dam, Maria Suarez Diez, Fabian Grammes, Robert Hafthorsson, Wout van Helvoirt, Jasper Koehorst, Peter Schaap, Yang Jin, Liv Torunn Mydland, Arne Gjuvsland, Sandve Simen, Vitor Martins dos Santos, Jon Olav Vik

Date Published: 1st Jun 2022

Publication Type: Journal

The Atlantic salmon genome provides insights into rediploidization

Abstract (Expand)

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about … the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

Authors: S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent, T. Nome, T. R. Hvidsten, J. S. Leong, D. R. Minkley, A. Zimin, F. Grammes, H. Grove, A. Gjuvsland, B. Walenz, R. A. Hermansen, K. von Schalburg, E. B. Rondeau, A. Di Genova, J. K. Samy, J. Olav Vik, M. D. Vigeland, L. Caler, U. Grimholt, S. Jentoft, D. Inge Vage, P. de Jong, T. Moen, M. Baranski, Y. Palti, D. R. Smith, J. A. Yorke, A. J. Nederbragt, A. Tooming-Klunderud, K. S. Jakobsen, X. Jiang, D. Fan, Y. Hu, D. A. Liberles, R. Vidal, P. Iturra, S. J. Jones, I. Jonassen, A. Maass, S. W. Omholt, W. S. Davidson

Date Published: 18th Apr 2016

Publication Type: Not specified

Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon.

Abstract (Expand)

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the … environment, including water salinity, exposure to pathogens, and shift in dietary lipid availability. Many changes in physiology and metabolism occur across this life-stage transition, but little is known about the molecular nature of these changes. Here we use a long term feeding experiment to study transcriptional regulation of lipid metabolism in Atlantic salmon gut and liver in both fresh- and saltwater. We find that lipid metabolism becomes significantly less plastic to differences in dietary lipid composition when salmon transitions to saltwater and experiences increased dietary lipid availability. Expression of genes in liver relating to lipogenesis and lipid transport decrease overall and become less responsive to diet, while genes for lipid uptake in gut become more highly expressed. Finally, analyses of evolutionary consequences of the salmonid specific whole-genome duplication on lipid metabolism reveals several pathways with significantly different (p<0.05) duplicate retention or duplicate regulatory conservation. We also find a limited number of cases where the whole genome duplication has resulted in an increased gene dosage. In conclusion, we find variable and pathway-specific effects of the salmonid genome duplication on lipid metabolism genes. A clear life-stage associated shift in lipid metabolism regulation is evident, and we hypothesize this to be, at least partly, driven by non-dietary factors such as the preparatory remodeling of gene regulation and physiology prior to sea migration. This article is protected by copyright. All rights reserved.

Authors: G. Gillard, T. N. Harvey, A. Gjuvsland, Y. Jin, M. Thomassen, S. Lien, M. Leaver, J. S. Torgersen, T. R. Hvidsten, J. O. Vik, S. R. Sandve

Date Published: No date defined

Publication Type: Not specified

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