RT Journal
A1 Dallaire, Alexandra
A1 Manley, Bethan F.
A1 Wilkens, Maya
A1 Bista, Iliana
A1 Quan, Clement
A1 Evangelisti, Edouard
A1 Bradshaw, Charles R.
A1 Ramakrishna, Navin B.
A1 Schornack, Sebastian
A1 Butter, Falk
A1 Paszkowski, Uta
A1 Miska, Eric A.
T1 Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
JF Genome Research 
JO Genome Research 
YR 2021 
FD December 01 
VO 31 
IS 12 
SP 2290 
OP 2302 
DO 10.1101/gr.275752.121 
UL http://genome.cshlp.org/content/31/12/2290.abstract 
AB 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.