Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis.

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.This work was supported in whole or in part by Cancer Research UK (C13474/A18583, C6946/A14492) and the Wellcome Trust (219475/Z/19/Z, 092096/Z/10/Z) to E.A.M. Research in U.P lab was supported by the Engineering the Nitrogen Symbiosis for Africa (ENSA) project, which is funded by a grant to the University of Cambridge by the Bill & Melinda Gates Foundation. Research in the S.S. lab was supported by the Gatsby Charitable Foundation (GAT3395/GLD) and the Royal Society (UF110073 and UF160413). A.D. was supported by a Natural Sciences and Engineering Research Council of Canada postdoctoral fellowship (PDF-532905-19). IB, was supported by Wellcome grant WT207492 and 104640/Z/14/Z, 092096/Z/10/Z