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Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

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  • Pierre Baduel

    (Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University)

  • Leandro Quadrana

    (Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University)

  • Ben Hunter

    (Harvard University)

  • Kirsten Bomblies

    (ETH Zürich)

  • Vincent Colot

    (Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University)

Abstract

Polyploidization is frequently associated with increased transposable element (TE) content. However, what drives TE dynamics following whole genome duplication (WGD) and the evolutionary implications remain unclear. Here, we leverage whole-genome resequencing data available for ~300 individuals of Arabidopsis arenosa, a well characterized natural diploid-autotetraploid plant species, to address these questions. Based on 43,176 TE insertions we detect in these genomes, we demonstrate that relaxed purifying selection rather than transposition bursts is the main driver of TE over-accumulation after WGD. Furthermore, the increased pool of TE insertions in tetraploids is especially enriched within or near environmentally responsive genes. Notably, we show that the major flowering-time repressor gene FLC is disrupted by a TE insertion specifically in the rapid-cycling tetraploid lineage that colonized mainland railways. Together, our findings indicate that tetrasomy leads to an enhanced accumulation of genic TE insertions, some of which likely contribute to local adaptation.

Suggested Citation

  • Pierre Baduel & Leandro Quadrana & Ben Hunter & Kirsten Bomblies & Vincent Colot, 2019. "Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13730-0
    DOI: 10.1038/s41467-019-13730-0
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    Cited by:

    1. Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Hanne De Kort & Sylvain Legrand & Olivier Honnay & James Buckley, 2022. "Transposable elements maintain genome-wide heterozygosity in inbred populations," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Yuyun Zhang & Zijuan Li & Jinyi Liu & Yu’e Zhang & Luhuan Ye & Yuan Peng & Haoyu Wang & Huishan Diao & Yu Ma & Meiyue Wang & Yilin Xie & Tengfei Tang & Yili Zhuang & Wan Teng & Yiping Tong & Wenli Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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