Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire1,2,3,
- Bethan F. Manley1,2,3,
- Maya Wilkens4,
- Iliana Bista1,2,3,
- Clement Quan5,
- Edouard Evangelisti5,
- Charles R. Bradshaw1,
- Navin B. Ramakrishna1,2,
- Sebastian Schornack5,
- Falk Butter4,
- Uta Paszkowski6,7 and
- Eric A. Miska1,2,3,7
- 1Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom;
- 2Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom;
- 3Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom;
- 4Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany;
- 5Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom;
- 6Crop Science Centre, University of Cambridge, Cambridge CB3 0LE, United Kingdom
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↵7 These authors contributed equally to this work.
Abstract
Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements for generating such genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Whole-genome epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the genome, while DNA methylation and small RNA–mediated silencing keep their overproliferation in check. We propose that a well-controlled TE activity directly contributes to genome evolution in AM fungi.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275752.121.
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Freely available online through the Genome Research Open Access option.
- Received May 10, 2021.
- Accepted September 16, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
