From field sampled spores to whole genome analysis, of the arbuscular mycorrhizal fungi Funneliformis geosporum. undefined

Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and most of them complete their lifecycle underground. Whole genome analysis of AM fungi have long been restricted to species and strains for which larger biological sampled can be collected because they can be maintained under controlled conditions for several years. There is some evidence suggesting this AM fungi can adapt to their cultivation system resulting in phenotypic and possibly also genotypic changes in the fungi. Being able to generate and analyze whole genome assemblies of AM fungi directly from the field may bring us closer to fully understand these important plant symbionts. In this study, we isolated spores of AM fungi from a field, and identified the spores as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two spores using DNA sequences of 24 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum when compared to the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble the genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic analysis and to study genomic variation in natural populations of these important plant symbionts.