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...
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Umeå universitet, Institutionen för fysiologisk botanik
2018
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-155785 https://doi.org/10.1093/gbe/evy201 |
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ftumeauniv:oai:DiVA.org:umu-155785 2024-09-15T17:56:16+00:00 The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication Varadharajan, Srinidhi Sandve, Simen R. Gillard, Gareth B. Tørresen, Ole K. Mulugeta, Teshome D. Hvidsten, Torgeir R. Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander J. Jakobsen, Kjetill S. 2018 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-155785 https://doi.org/10.1093/gbe/evy201 eng eng UmeÃ¥ universitet, Institutionen för fysiologisk botanik UmeÃ¥ universitet, UmeÃ¥ Plant Science Centre (UPSC) Genome Biology and Evolution, 2018, 10:10, s. 2785-2800 orcid:0000-0002-2033-0758 orcid:0000-0001-6097-2539 orcid:0000-0001-5539-0999 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-155785 doi:10.1093/gbe/evy201 PMID 30239729 ISI:000455325000020 Scopus 2-s2.0-85055596805 info:eu-repo/semantics/openAccess Thymallus thymallus genome assembly salmonid WGD rediploidization lineage-specific ohnolog resolution Genetics Genetik Article in journal info:eu-repo/semantics/article text 2018 ftumeauniv https://doi.org/10.1093/gbe/evy201 2024-07-09T23:37:52Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Umeå University: Publications (DiVA) Genome Biology and Evolution 10 10 2785 2800 |
institution |
Open Polar |
collection |
Umeå University: Publications (DiVA) |
op_collection_id |
ftumeauniv |
language |
English |
topic |
Thymallus thymallus genome assembly salmonid WGD rediploidization lineage-specific ohnolog resolution Genetics Genetik |
spellingShingle |
Thymallus thymallus genome assembly salmonid WGD rediploidization lineage-specific ohnolog resolution Genetics Genetik Varadharajan, Srinidhi Sandve, Simen R. Gillard, Gareth B. Tørresen, Ole K. Mulugeta, Teshome D. Hvidsten, Torgeir R. Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander J. Jakobsen, Kjetill S. The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication |
topic_facet |
Thymallus thymallus genome assembly salmonid WGD rediploidization lineage-specific ohnolog resolution Genetics Genetik |
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. |
format |
Article in Journal/Newspaper |
author |
Varadharajan, Srinidhi Sandve, Simen R. Gillard, Gareth B. Tørresen, Ole K. Mulugeta, Teshome D. Hvidsten, Torgeir R. Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander J. Jakobsen, Kjetill S. |
author_facet |
Varadharajan, Srinidhi Sandve, Simen R. Gillard, Gareth B. Tørresen, Ole K. Mulugeta, Teshome D. Hvidsten, Torgeir R. Lien, Sigbjørn Vøllestad, Leif Asbjørn Jentoft, Sissel Nederbragt, Alexander J. Jakobsen, Kjetill S. |
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 |
publisher |
Umeå universitet, Institutionen för fysiologisk botanik |
publishDate |
2018 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-155785 https://doi.org/10.1093/gbe/evy201 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Genome Biology and Evolution, 2018, 10:10, s. 2785-2800 orcid:0000-0002-2033-0758 orcid:0000-0001-6097-2539 orcid:0000-0001-5539-0999 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-155785 doi:10.1093/gbe/evy201 PMID 30239729 ISI:000455325000020 Scopus 2-s2.0-85055596805 |
op_rights |
info:eu-repo/semantics/openAccess |
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 |
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1810432482026192896 |