Methods for Arbuscular Mycorrhizal Fungal Genome Characterization

Arbuscular mycorrhizal fungi (AMF) are difficult to study due to their obligate biotrophy and large, complex genomes. Limited fungal biomass and high genomic polymorphism have long hindered accurate sequencing and assemblies. Recent advances, in particular long-read sequencing combined with Hi-C analysis, now allow chromosome-level assemblies of AMF genomes. This chapter outlines the methods used to characterize AMF genomes through Long-Read and Hi-C sequencing, from fungal material production to DNA preparation, using spores of Gigaspora margarita (BEG34 strain) as a case study.