Arbuscular mycorrhizal fungi are common plant symbionts, that support the development of the plants they grow on by providing them with nutrients. They can interact with the majority of land plants, including important crop species like rice, maize, wheat and potato. Their whole mycelium consists of a single cell, containing millions of nuclei. Isolates of the fungus Rhizophagus irregularis vary in how genetically different these nuclei are from each other, but the roles of these different nucleotypes in the symbiosis is still unclear. In this thesis I use whole genome and single nuclei sequencing of isolate C3 to show that the nuclear composition of this fungus varies between lineages, and that the two main nucleotypes can genetically recombine. Furthermore, I show that fungal isolates differ in the benefit they provide to certain plant hosts, and which genes they express to do so.