Phylogenetic analyses show the Select Agent Coniothyrium glycines represents a single species that has significant morphological and genetic variation.

Soybean red leaf blotch (RLB), caused by the fungus Coniothyrium glycines, represents a foliar disease of soybean that is thus far restricted to Africa. The fungus is listed as a Select Agent by the Federal Select Agent Program because it could pose a severe threat to plant health were it to establish in the United States. Previous work uncovered tremendous molecular diversity at the internal transcribed spacer region, suggesting that there may be multiple species causing RLB. To determine whether multiple species cause RLB, we reconstructed the phylogeny of C. glycines and taxonomic allies using sequence data from four genes. We included 33 C. glycines isolates collected from six African countries and determined that all isolates form a well-supported, monophyletic lineage. Within this lineage there are at least six well-supported clades that largely correspond to geography, with one clade exclusively composed of isolates from Ethiopia, another exclusively composed of isolates from Uganda, and four composed of isolates from southern Africa. However, we did not detect any concordance for these clades between the four genes, indicating that all isolates included in this analysis are representative of a single species. Isolates in the Ethiopia clade are morphologically distinct from isolates in the other clades, as they produce larger sclerotia and smaller pycnida and more sclerotia in planta. Additionally, ancestral range estimations suggest that the C. glycines lineage emerged in southern Africa. These results show that there is significantly more genetic and morphological diversity than was initially suspected with this high-consequence fungal plant pathogen.