Phylogenetic and Phylogenomic Definition of <i>Rhizopus</i> Species

Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. <i>Rhizopus</i> species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 <i>Rhizopus</i> strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus <i>Rhizopus</i> consists of three major clades, with <i>R. microsporus</i> as the basal species and the sister lineage to <i>R. stolonifer</i> and two closely related species <i>R. arrhizus</i> and <i>R. delemar</i> A comparative analysis of the mating type locus across <i>Rhizopus</i> reveals that its structure is flexible even between different species in the same genus, but shows similarities between <i>Rhizopus</i> and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.