The lifestyle of Mucoromycotina 'Fine Root Endophytes' through the genomic lens

Fine Root Endophytes belonging to the Mucoromycotina clade (MFRE) play a key role in terrestrial nutrient cycling through their

dual saprotrophic and mycorrhizal traits. Over the past decade, microscopic and physiological studies have yielded valuable insights

into the mycorrhizal relationship between MFRE and plants, demonstrating intracellular colonisation and nutrient-for-carbon

exchange. However, our understanding of the molecular mechanisms underpinning the saprotrophic and mycorrhizal lifestyles of

MFRE remains limited. In this study, we apply genomic and molecular genetic approaches to two MFRE isolates to investigate

symbiotic and saprotrophic strategies in this mycorrhizal lineage. We generated the first genome assemblies corresponding to

MFRE by combining complementary short-read (Illumina) and long-read (Nanopore) sequencing technologies. Leveraging

comparative genomic and transcriptomic analyses, we have identified distinct signatures for transporters and secreted proteins

(hydrolases, effector candidates) during in vitro and in planta conditions. Collectively, our findings underscore a unique molecular

blueprint characterising the saprotrophic and mycorrhizal lifestyles of MFRE, setting them apart from other mycorrhizal fungi.