Abstract Arbuscular mycorrhizal (AM) fungi form obligate symbiosis with the roots of the majority of land plants and are found in all terrestrial ecosystems. The source and structure of genetic variation in AM fungi has remained an enigma due to difficulties in the axenic cultivation and generation of high-quality genome assemblies from most species. Furthermore, how AM fungi survives long-term without a single nuclear stage per cell life history is puzzling, prompting hypotheses on selection at the nuclear level which functions to purge deleterious mutations. In this study, we aimed to characterize both intra- and inter-organismal genetic variation in AM fungi by analyzing genomic information from individual nuclei of three strains from two species of the genus Claroideoglomus . We observed overall low levels of genetic variation within the strains, most of which represent rare variants likely kept at low frequency by purifying selection. We also observed variants that have been maintained as polymorphic across both strains and species. The results in this study affirm our conceptual understanding that nuclei in AM fungal strains function as populations of asexually reproducing units. Further, we propose that selection acts on different levels within the organism, with strong signals of purifying selection on nuclei within strain.

Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal (AM) Fungi