The effect of hybridization on transposable element accumulation in an undomesticated fungal species

Abstract

Transposable elements (TEs) are mobile genetic elements that can profoundly impact the evolution of genomes and species. A long-standing hypothesis suggests that hybridization could deregulate TEs and trigger their accumulation, although it received mixed support from studies in plants and animals. Here, we tested this hypothesis in fungi using incipient species of the undomesticated yeast Saccharomyces paradoxus. Population genomic data revealed no signature of higher transposition in natural hybrids. As we could not rule out the elimination of past transposition increase signatures by natural selection, we performed a laboratory evolution experiment on a panel of artificial hybrids to measure TE accumulation in the near absence of selection. Changes in TE copy numbers were not predicted by the level of evolutionary divergence between the parents of a hybrid genotype. Rather, they were highly dependent on the individual hybrid genotypes, showing that strong genotype-specific deterministic factors govern TE accumulation in yeast hybrids.

Data availability

Illumina short read sequencing data of the MA lines is available at NCBI under accession PRJNA515073. Genome assemblies and Nanopore long read sequencing data of wild isloates are available at NCBI under accession PRJNA514804. Illumina short read sequencing data of wild isolates is available at NCBI under accessions PRJNA277692, PRJNA324830 and PRJNA479851.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Mathieu Hénault

    Département de biochimie, microbiologie et bio-informatique, Département de biologie, PROTEO, BDRC_UL, Université Laval, Québec, Canada
    For correspondence
    mathieu.henault.1@ulaval.ca
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0760-7545
  2. Souhir Marsit

    Département de biochimie, microbiologie et bio-informatique, PROTEO, BDRC_UL, Université Laval, Québec, Canada
    Competing interests
    No competing interests declared.
  3. Guillaume Charron

    Département de biologie, PROTEO, BDRC_UL, Université Laval, Québec, Canada
    Competing interests
    No competing interests declared.
  4. Christian R Landry

    Département de biologie, Université Laval, Québec, Canada
    Competing interests
    Christian R Landry, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3028-6866

Funding

Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-03755)

  • Christian R Landry

Natural Sciences and Engineering Research Council of Canada (NSERC Alexander Graham-Bell doctoral scholarship)

  • Mathieu Hénault
  • Guillaume Charron

Fonds de recherche du Québec – Nature et technologies (FRQNT doctoral scholarship)

  • Mathieu Hénault
  • Guillaume Charron

Fonds de Recherche du Québec - Santé (FRQS postdoctoral scholarship)

  • Souhir Marsit

Canada Research Chairs (Canada Research Chair in Evolutionary Cell and Systems Biology)

  • Christian R Landry

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kevin J Verstrepen, VIB-KU Leuven Center for Microbiology, Belgium

Version history

  1. Received: June 27, 2020
  2. Accepted: September 21, 2020
  3. Accepted Manuscript published: September 21, 2020 (version 1)
  4. Version of Record published: October 23, 2020 (version 2)

Copyright

© 2020, Hénault et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Mathieu Hénault
  2. Souhir Marsit
  3. Guillaume Charron
  4. Christian R Landry
(2020)
The effect of hybridization on transposable element accumulation in an undomesticated fungal species
eLife 9:e60474.
https://doi.org/10.7554/eLife.60474

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https://doi.org/10.7554/eLife.60474

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