Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiontRhizophagus irregularis

Abstract

AbstractTransposable elements (TE) are repetitive DNA that can create variability in genome structure and regulation. The genome ofRhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises approximately 50% repetitive sequences that include transposable elements (TE). Despite their abundance, two-thirds of TE remain unclassified, and their regulation among AMF life-stages remains unknown. Here, we aimed to improve our understanding of TE diversity and regulation in this model species by curating repeat datasets obtained from chromosome-level assemblies and by investigating their expression across multiple conditions. Our analyses uncovered new TE superfamilies and families in this model symbiont and revealed significant differences in how these sequences evolve both within and betweenR. irregularisgenomes. With this curated TE annotation, we detected that the number of upregulated TE families in colonized roots is four times higher than extraradical mycelium, and their overall expression differs depending on their host. This work provides a fine-scale view of TE diversity and evolution in model plant symbionts and highlights their transcriptional dynamism and specificity during host-microbe interactions. We also provide Hidden Markov Model profiles of TE domains are now available for future manual curation of uncharacterized sequences (https://github.com/jordana-olive/TE-manual-curation/tree/main).