Genome-wide methylation in the panmictic European eel (Anguilla anguilla)
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel...
Published in: | Molecular Ecology |
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Language: | English |
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2022
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Online Access: | https://pure.au.dk/portal/da/publications/genomewide-methylation-in-the-panmictic-european-eel-anguilla-anguilla(5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee).html https://doi.org/10.1111/mec.16586 https://pure.au.dk/ws/files/272949069/Eel_methylation_paper.pdf |
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ftuniaarhuspubl:oai:pure.atira.dk:publications/5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee 2023-12-24T10:08:17+01:00 Genome-wide methylation in the panmictic European eel (Anguilla anguilla) Liu, Shenglin Tengstedt, Aja Noersgaard Buur Jacobsen, Magnus W. Pujolar, Jose Martin Jónsson, Bjarni Lobón-Cervià, Javier Bernatchez, Louis Hansen, Michael Møller 2022-08 application/pdf https://pure.au.dk/portal/da/publications/genomewide-methylation-in-the-panmictic-european-eel-anguilla-anguilla(5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee).html https://doi.org/10.1111/mec.16586 https://pure.au.dk/ws/files/272949069/Eel_methylation_paper.pdf eng eng https://pure.au.dk/portal/da/publications/genomewide-methylation-in-the-panmictic-european-eel-anguilla-anguilla(5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee).html info:eu-repo/semantics/restrictedAccess Liu , S , Tengstedt , A N B , Jacobsen , M W , Pujolar , J M , Jónsson , B , Lobón-Cervià , J , Bernatchez , L & Hansen , M M 2022 , ' Genome-wide methylation in the panmictic European eel (Anguilla anguilla) ' , Molecular Ecology , vol. 31 , no. 16 , pp. 4286-4306 . https://doi.org/10.1111/mec.16586 Anguilla anguilla Hox clusters adaptive processes epigenetics hybridization methylation article 2022 ftuniaarhuspubl https://doi.org/10.1111/mec.16586 2023-11-30T00:01:17Z The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with Hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, probably reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggest interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight Hox clusters, and the results suggest important roles of methylation at Hox genes for adaptive processes. Article in Journal/Newspaper Anguilla anguilla Subarctic Aarhus University: Research Molecular Ecology 31 16 4286 4306 |
institution |
Open Polar |
collection |
Aarhus University: Research |
op_collection_id |
ftuniaarhuspubl |
language |
English |
topic |
Anguilla anguilla Hox clusters adaptive processes epigenetics hybridization methylation |
spellingShingle |
Anguilla anguilla Hox clusters adaptive processes epigenetics hybridization methylation Liu, Shenglin Tengstedt, Aja Noersgaard Buur Jacobsen, Magnus W. Pujolar, Jose Martin Jónsson, Bjarni Lobón-Cervià, Javier Bernatchez, Louis Hansen, Michael Møller Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
topic_facet |
Anguilla anguilla Hox clusters adaptive processes epigenetics hybridization methylation |
description |
The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with Hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, probably reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggest interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight Hox clusters, and the results suggest important roles of methylation at Hox genes for adaptive processes. |
format |
Article in Journal/Newspaper |
author |
Liu, Shenglin Tengstedt, Aja Noersgaard Buur Jacobsen, Magnus W. Pujolar, Jose Martin Jónsson, Bjarni Lobón-Cervià, Javier Bernatchez, Louis Hansen, Michael Møller |
author_facet |
Liu, Shenglin Tengstedt, Aja Noersgaard Buur Jacobsen, Magnus W. Pujolar, Jose Martin Jónsson, Bjarni Lobón-Cervià, Javier Bernatchez, Louis Hansen, Michael Møller |
author_sort |
Liu, Shenglin |
title |
Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
title_short |
Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
title_full |
Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
title_fullStr |
Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
title_full_unstemmed |
Genome-wide methylation in the panmictic European eel (Anguilla anguilla) |
title_sort |
genome-wide methylation in the panmictic european eel (anguilla anguilla) |
publishDate |
2022 |
url |
https://pure.au.dk/portal/da/publications/genomewide-methylation-in-the-panmictic-european-eel-anguilla-anguilla(5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee).html https://doi.org/10.1111/mec.16586 https://pure.au.dk/ws/files/272949069/Eel_methylation_paper.pdf |
genre |
Anguilla anguilla Subarctic |
genre_facet |
Anguilla anguilla Subarctic |
op_source |
Liu , S , Tengstedt , A N B , Jacobsen , M W , Pujolar , J M , Jónsson , B , Lobón-Cervià , J , Bernatchez , L & Hansen , M M 2022 , ' Genome-wide methylation in the panmictic European eel (Anguilla anguilla) ' , Molecular Ecology , vol. 31 , no. 16 , pp. 4286-4306 . https://doi.org/10.1111/mec.16586 |
op_relation |
https://pure.au.dk/portal/da/publications/genomewide-methylation-in-the-panmictic-european-eel-anguilla-anguilla(5bb760bb-6036-4fc2-99dc-2aba1a0cc4ee).html |
op_rights |
info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1111/mec.16586 |
container_title |
Molecular Ecology |
container_volume |
31 |
container_issue |
16 |
container_start_page |
4286 |
op_container_end_page |
4306 |
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1786187298536161280 |