Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory d...
Main Authors: | , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
2021
|
Subjects: | |
Online Access: | https://zenodo.org/record/4658861 https://doi.org/10.5061/dryad.t4b8gtj1b |
id |
ftzenodo:oai:zenodo.org:4658861 |
---|---|
record_format |
openpolar |
spelling |
ftzenodo:oai:zenodo.org:4658861 2023-05-15T15:31:54+02:00 Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon Verta, Jukka-Pekka Barton, Henry Pritchard, Victoria Primmer, Craig 2021-03-30 https://zenodo.org/record/4658861 https://doi.org/10.5061/dryad.t4b8gtj1b unknown doi:10.1093/gbe/evab059 https://zenodo.org/communities/dryad https://zenodo.org/record/4658861 https://doi.org/10.5061/dryad.t4b8gtj1b oai:zenodo.org:4658861 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode info:eu-repo/semantics/other dataset 2021 ftzenodo https://doi.org/10.5061/dryad.t4b8gtj1b10.1093/gbe/evab059 2023-03-11T01:50:28Z Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift. The results presented in the main article can be reproduced by running the R Markdown scripts in this Dryad repository. Funding provided by: H2020 European Research CouncilCrossref Funder ... Dataset Atlantic salmon Salmo salar Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
description |
Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift. The results presented in the main article can be reproduced by running the R Markdown scripts in this Dryad repository. Funding provided by: H2020 European Research CouncilCrossref Funder ... |
format |
Dataset |
author |
Verta, Jukka-Pekka Barton, Henry Pritchard, Victoria Primmer, Craig |
spellingShingle |
Verta, Jukka-Pekka Barton, Henry Pritchard, Victoria Primmer, Craig Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
author_facet |
Verta, Jukka-Pekka Barton, Henry Pritchard, Victoria Primmer, Craig |
author_sort |
Verta, Jukka-Pekka |
title |
Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
title_short |
Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
title_full |
Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
title_fullStr |
Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
title_full_unstemmed |
Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon |
title_sort |
data from: genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in atlantic salmon |
publishDate |
2021 |
url |
https://zenodo.org/record/4658861 https://doi.org/10.5061/dryad.t4b8gtj1b |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.1093/gbe/evab059 https://zenodo.org/communities/dryad https://zenodo.org/record/4658861 https://doi.org/10.5061/dryad.t4b8gtj1b oai:zenodo.org:4658861 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.t4b8gtj1b10.1093/gbe/evab059 |
_version_ |
1766362407443103744 |