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The grayling genome reveals selection on gene expression regulation after whole genome duplication

View ORCID ProfileSrinidhi Varadharajan, View ORCID ProfileSimen R. Sandve, Ole K. Tørresen, Sigbjørn Lien, Leif Asbjørn Vøllestad, Sissel Jentoft, View ORCID ProfileAlexander J. Nederbragt, Kjetill S. Jakobsen
doi: https://doi.org/10.1101/153270
Srinidhi Varadharajan
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
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  • ORCID record for Srinidhi Varadharajan
Simen R. Sandve
2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway
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  • For correspondence: simen.sandve@nmbu.no k.s.jakobsen@ibv.uio.no
Ole K. Tørresen
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
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Sigbjørn Lien
2Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway
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Leif Asbjørn Vøllestad
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
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Sissel Jentoft
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
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Alexander J. Nederbragt
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
3Biomedical Informatics Research Group, Department of Informatics, University of Oslo, Oslo NO-0316, Norway
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Kjetill S. Jakobsen
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway
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  • For correspondence: simen.sandve@nmbu.no k.s.jakobsen@ibv.uio.no
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Abstract

Whole genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates, yet little is known about how selection operates on the resulting gene duplicates. Here, we present a draft genome assembly of a salmonid species, European grayling (Thymallus thymallus) and use comparative genomics and transcriptomics to understand evolutionary consequences of WGD in the genome of salmonid ancestor ~80 million years ago (Ss4R). We find evidence for lineage-specific rates in rediploidization and that ~60% of the Ss4R ohnologs have experienced different types of non-neutral evolution of tissue-specific gene expression regulation. Distinct selective pressures were associated with tissue type, biological function and selection pressure on protein coding sequence. Finally, our results indicate the role of adaptive divergence of Ss4R duplicates in the evolution of salmonid metabolism and identifies loss of purifying selection on one Ss4R ohnolog encoding a key chloride pump linked to the evolution of anadromy.

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Posted June 22, 2017.
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The grayling genome reveals selection on gene expression regulation after whole genome duplication
Srinidhi Varadharajan, Simen R. Sandve, Ole K. Tørresen, Sigbjørn Lien, Leif Asbjørn Vøllestad, Sissel Jentoft, Alexander J. Nederbragt, Kjetill S. Jakobsen
bioRxiv 153270; doi: https://doi.org/10.1101/153270
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The grayling genome reveals selection on gene expression regulation after whole genome duplication
Srinidhi Varadharajan, Simen R. Sandve, Ole K. Tørresen, Sigbjørn Lien, Leif Asbjørn Vøllestad, Sissel Jentoft, Alexander J. Nederbragt, Kjetill S. Jakobsen
bioRxiv 153270; doi: https://doi.org/10.1101/153270

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