Phylogenetic and Phylogenomic Definition of Rhizopus Species

© 2018 Gryganskyi et al. Phylogenomicapproaches have the potential to improve confidence about the inter-relationships of species in the order Mucoraleswithin the fungal treeof life. Rhizopusspecies 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 Rhizopusstrains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopusconsists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar. A comparative analysis of the mating typelocus across Rhizopusreveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopusand other mucoralean fungi. The topology of singlegene phylogenies built for two genes involved in mating is similar to the phylogenomictree. Comparison of the total length of the genome assemblies showed that genome sizevaries by as much as threefold within a species and is driven by changes in transposable elementcopy numbers and genome duplications.