Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A.M. Martin, Peter W. H. Holland, Simen R. Sandve, Daniel J. Macqueen
doi: https://doi.org/10.1101/098582
Fiona M. Robertson
1Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Manu Kumar Gundappa
1Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fabian Grammes
2Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Torgeir R. Hvidsten
3Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway.
4Umeå Plant Science Centre, Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187 Umeå, Sweden.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anthony K. Redmond
1Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
5Centre for Genome-Enabled Biology & Medicine (CGEBM), University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sigbjørn Lien
2Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Samuel A.M. Martin
1Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter W. H. Holland
6Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simen R. Sandve
2Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel J. Macqueen
1Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

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 highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. ‘Ss4R’), 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 called ‘Lineage-specific Ohnologue Resolution’ (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. 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 4,500 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 promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than ‘older’ ohnologues that began diverging in the salmonid ancestor. 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.

Footnotes

  • Email addresses: Fiona M. Robertson: r01fl13{at}abdn.ac.uk, Manu Kumar Gundappa: r01mkg15{at}abdn.ac.uk, Fabian Grammes: fabian.grammes{at}nmbu.no, Torgeir R. Hvidsten: torgeir.r.hvidsten{at}nmbu.no, Anthony K. Redmond: a.redmond{at}abdn.ac.uk, Sigbjørn Lien: sigbjorn.lien{at}nmbu.no, Samuel A.M. Martin: sam.martin{at}abdn.ac.uk, Peter W. H. Holland: peter.holland{at}zoo.ox.ac.uk, Simen R. Sandve: simen.sandve{at}nmbu.no, Daniel J. Macqueen: daniel.macqueen{at}abdn.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted January 05, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A.M. Martin, Peter W. H. Holland, Simen R. Sandve, Daniel J. Macqueen
bioRxiv 098582; doi: https://doi.org/10.1101/098582
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A.M. Martin, Peter W. H. Holland, Simen R. Sandve, Daniel J. Macqueen
bioRxiv 098582; doi: https://doi.org/10.1101/098582

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4222)
  • Biochemistry (9096)
  • Bioengineering (6744)
  • Bioinformatics (23927)
  • Biophysics (12077)
  • Cancer Biology (9485)
  • Cell Biology (13722)
  • Clinical Trials (138)
  • Developmental Biology (7614)
  • Ecology (11652)
  • Epidemiology (2066)
  • Evolutionary Biology (15469)
  • Genetics (10613)
  • Genomics (14289)
  • Immunology (9453)
  • Microbiology (22767)
  • Molecular Biology (9057)
  • Neuroscience (48818)
  • Paleontology (354)
  • Pathology (1479)
  • Pharmacology and Toxicology (2560)
  • Physiology (3820)
  • Plant Biology (8307)
  • Scientific Communication and Education (1467)
  • Synthetic Biology (2285)
  • Systems Biology (6168)
  • Zoology (1297)