The grayling genome reveals selection on gene expression regulation after whole-genome duplication
Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to...
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Online Access: | https://hdl.handle.net/11250/2690310 https://doi.org/10.1093/gbe/evy201 |
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ftunivmob:oai:nmbu.brage.unit.no:11250/2690310 2023-05-15T15:31:41+02:00 The grayling genome reveals selection on gene expression regulation after whole-genome duplication Varadharajan, Srinidhi Sandve, Simen Rød Gillard, Gareth Benjamin Tørresen, Ole K. Mulugeta, Teshome Dagne Hvidsten, Torgeir Rhoden Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander Johan Jakobsen, Kjetill Sigurd 2018-12-04T14:23:40Z application/vnd.openxmlformats-officedocument.wordprocessingml.document https://hdl.handle.net/11250/2690310 https://doi.org/10.1093/gbe/evy201 eng eng Genome Biology and Evolution. 2018, 10 (10), 2785-2800. urn:issn:1759-6653 https://hdl.handle.net/11250/2690310 https://doi.org/10.1093/gbe/evy201 cristin:1639030 Attribution-NonCommercial-NoDerivatives 4.0 Internasjonal http://creativecommons.org/licenses/by-nc-nd/4.0/deed.no CC-BY-NC-ND 2785-2800 10 Genome Biology and Evolution Peer reviewed Journal article 2018 ftunivmob https://doi.org/10.1093/gbe/evy201 2021-09-23T20:15:50Z Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein–protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution. acceptedVersion Article in Journal/Newspaper Atlantic salmon Salmo salar Open archive Norwegian University of Life Sciences: Brage NMBU Genome Biology and Evolution 10 10 2785 2800 |
institution |
Open Polar |
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Open archive Norwegian University of Life Sciences: Brage NMBU |
op_collection_id |
ftunivmob |
language |
English |
description |
Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein–protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution. acceptedVersion |
format |
Article in Journal/Newspaper |
author |
Varadharajan, Srinidhi Sandve, Simen Rød Gillard, Gareth Benjamin Tørresen, Ole K. Mulugeta, Teshome Dagne Hvidsten, Torgeir Rhoden Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander Johan Jakobsen, Kjetill Sigurd |
spellingShingle |
Varadharajan, Srinidhi Sandve, Simen Rød Gillard, Gareth Benjamin Tørresen, Ole K. Mulugeta, Teshome Dagne Hvidsten, Torgeir Rhoden Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander Johan Jakobsen, Kjetill Sigurd The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
author_facet |
Varadharajan, Srinidhi Sandve, Simen Rød Gillard, Gareth Benjamin Tørresen, Ole K. Mulugeta, Teshome Dagne Hvidsten, Torgeir Rhoden Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander Johan Jakobsen, Kjetill Sigurd |
author_sort |
Varadharajan, Srinidhi |
title |
The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
title_short |
The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
title_full |
The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
title_fullStr |
The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
title_full_unstemmed |
The grayling genome reveals selection on gene expression regulation after whole-genome duplication |
title_sort |
grayling genome reveals selection on gene expression regulation after whole-genome duplication |
publishDate |
2018 |
url |
https://hdl.handle.net/11250/2690310 https://doi.org/10.1093/gbe/evy201 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
2785-2800 10 Genome Biology and Evolution |
op_relation |
Genome Biology and Evolution. 2018, 10 (10), 2785-2800. urn:issn:1759-6653 https://hdl.handle.net/11250/2690310 https://doi.org/10.1093/gbe/evy201 cristin:1639030 |
op_rights |
Attribution-NonCommercial-NoDerivatives 4.0 Internasjonal http://creativecommons.org/licenses/by-nc-nd/4.0/deed.no |
op_rightsnorm |
CC-BY-NC-ND |
op_doi |
https://doi.org/10.1093/gbe/evy201 |
container_title |
Genome Biology and Evolution |
container_volume |
10 |
container_issue |
10 |
container_start_page |
2785 |
op_container_end_page |
2800 |
_version_ |
1766362212678500352 |