A call for reform: implementing genome-based approaches for species classification in Glomeromycotina

In arbuscular mycorrhizal (AM) fungi, only c. 370 species have been formally described despite these fungal organisms having coevolved with plants for hundreds of millions of years. In contrast to this, dozens of thousands of species are known for many fungal lineages with shorter evolutionary timescales. This Viewpoint highlights some plausible reasons for these striking discrepancies in species description. These include paralogs of ribosomal genes leading to the misidentification of AM fungal species in phylogenetic analyses and polymorphism in homologous morphological traits. We propose to address issues surrounding AM fungal taxonomy using genome-based approaches that will allow the determination of whether individual AM fungal isolates really belong to the same species.