Summary

Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the estab- lishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear.

Toaddressthisissue,weimprovedthegenomeassemblyandgeneannotationofthemodel strain Rhizophagus irregularis DAOM197198, and compared its gene content with five iso- lates of R. irregularis sampled in the same field.
All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variabil- ity affects all gene ontology terms and PFAM protein domains, as well as putative mycor- rhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements.

Overall, these findings indicate a substantial divergence in the functioning capacity of iso- lates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant–AMF interactions that link AMF genome variation with plant phenotype and fitness.