Journal article
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversificiation
- Abstract:
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Background
The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 Ma fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event.
Results
Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor.
Conclusions
LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 2.3MB, Terms of use)
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- Publisher copy:
- 10.1186/s13059-017-1241-z
Authors
- Publisher:
- BioMed Central
- Journal:
- Genome Biology More from this journal
- Volume:
- 18
- Pages:
- 111
- Publication date:
- 2017-06-01
- Acceptance date:
- 2017-05-15
- DOI:
- EISSN:
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1465-6906
- ISSN:
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1474-760X
- Keywords:
- Pubs id:
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pubs:695414
- UUID:
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uuid:dcc8ccb0-6bd8-405c-99e7-1ad3220ff332
- Local pid:
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pubs:695414
- Source identifiers:
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695414
- Deposit date:
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2017-05-15
- ARK identifier:
Terms of use
- Copyright holder:
- Holland et al
- Copyright date:
- 2017
- Notes:
- © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Licence:
- CC Attribution (CC BY)
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