Arbuscular mycorrhizal (AM) fungi are essential to terrestrial ecosystems, yet their genomic study is fraught with challenges. Traditional sequencing methods are often limited by difficulties in obtaining pure, high-quality DNA and the complexity of AM fungal genomes. This paper describes a refined protocol for single nuclei sequencing of AM fungi, addressing key obstacles and providing practical solutions to enhance genomic research in this ecologically important group. The protocol involves outsourcing certain steps, such as sequencing library preparation and Illumina sequencing, to other facilities, while other steps, like generating single nuclei and combined assemblies, follow a published method and are not described in detail here. This method allows for the direct acquisition of sequence data from single nuclei, circumventing the time-consuming and laborious process of cultivating axenic cultures.
