Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon
Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favoured by gene duplication events, which generate redundant genomic material that may evolve divergen...
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ftzenodo:oai:zenodo.org:4962316 2023-06-06T11:52:01+02:00 Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon Warren, Ian A. Ciborowski, Kate L. Casadei, Elisa Hazlerigg, David G. Martin, Sam A. M. Sumner, Seirian Jordan, William C. 2014-06-27 https://zenodo.org/record/4962316 https://doi.org/10.5061/dryad.h02b3 unknown doi:10.1093/gbe/evu131 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435393 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435329 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435483 https://zenodo.org/communities/dryad https://zenodo.org/record/4962316 https://doi.org/10.5061/dryad.h02b3 oai:zenodo.org:4962316 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode gene duplication Salmo salar whole genome duplication genome evolution info:eu-repo/semantics/other dataset 2014 ftzenodo https://doi.org/10.5061/dryad.h02b310.1093/gbe/evu131 2023-04-13T21:28:35Z Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favoured by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole genome duplications are sparse, although one example is the salmonids, which have undergone a whole genome duplication event within the last 100 million years. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high throughput sequencing to characterise the transcriptomes of three key organs involved in regulating migration in S. salar: brain, pituitary and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences, and designed an analytic workflow to distinguish between paralogs originating from local duplication events or from whole genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole genome duplication event. Many of the identified paralog pairs have either diverged in function or become non-coding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle. Assembly of 454 reads from the brainAssembly of the 454 reads from the brains of Salmo salar parrDRYAD_Brain.zipAssembly of 454 reads from olfactory epitheliumAssembly of 454 reads from olfactory epithelium from Salmo salar at the parr stageDRYAD_OLF.zipAssembly of 454 reads from pituitary glandAssembly of 454 reads from pituitary gland of Salmo salar at the parr ... Dataset Atlantic salmon Salmo salar Zenodo |
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Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
gene duplication Salmo salar whole genome duplication genome evolution |
spellingShingle |
gene duplication Salmo salar whole genome duplication genome evolution Warren, Ian A. Ciborowski, Kate L. Casadei, Elisa Hazlerigg, David G. Martin, Sam A. M. Sumner, Seirian Jordan, William C. Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
topic_facet |
gene duplication Salmo salar whole genome duplication genome evolution |
description |
Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favoured by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole genome duplications are sparse, although one example is the salmonids, which have undergone a whole genome duplication event within the last 100 million years. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high throughput sequencing to characterise the transcriptomes of three key organs involved in regulating migration in S. salar: brain, pituitary and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences, and designed an analytic workflow to distinguish between paralogs originating from local duplication events or from whole genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole genome duplication event. Many of the identified paralog pairs have either diverged in function or become non-coding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle. Assembly of 454 reads from the brainAssembly of the 454 reads from the brains of Salmo salar parrDRYAD_Brain.zipAssembly of 454 reads from olfactory epitheliumAssembly of 454 reads from olfactory epithelium from Salmo salar at the parr stageDRYAD_OLF.zipAssembly of 454 reads from pituitary glandAssembly of 454 reads from pituitary gland of Salmo salar at the parr ... |
format |
Dataset |
author |
Warren, Ian A. Ciborowski, Kate L. Casadei, Elisa Hazlerigg, David G. Martin, Sam A. M. Sumner, Seirian Jordan, William C. |
author_facet |
Warren, Ian A. Ciborowski, Kate L. Casadei, Elisa Hazlerigg, David G. Martin, Sam A. M. Sumner, Seirian Jordan, William C. |
author_sort |
Warren, Ian A. |
title |
Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
title_short |
Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
title_full |
Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
title_fullStr |
Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
title_full_unstemmed |
Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon |
title_sort |
data from: extensive local gene duplication and functional divergence among paralogs in atlantic salmon |
publishDate |
2014 |
url |
https://zenodo.org/record/4962316 https://doi.org/10.5061/dryad.h02b3 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.1093/gbe/evu131 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435393 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435329 https://www.ncbi.nlm.nih.gov/sra/?term=SRR1435483 https://zenodo.org/communities/dryad https://zenodo.org/record/4962316 https://doi.org/10.5061/dryad.h02b3 oai:zenodo.org:4962316 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.h02b310.1093/gbe/evu131 |
_version_ |
1767957837233782784 |