The genus Erysiphe (including powdery mildew fungi only known as anamorph, Pseudoidium) is the largest genus in the Erysiphaceae and contains more than 50% of all species in this family. Little is known about the phylogenetic structure of this genus. We conducted a comprehensive phylogenetic analysis of the Microsphaera-lineage, a monophyletic group including species of sects. Microsphaera and Erysiphe, using 401 sequences of nuc ITS1-5.8S-ITS2 and the 28S rDNA regions. This analysis gave many small clades delimited by the host plant genus or family. We identified two deep branches, albeit with moderate bootstrap supports, that divided the 401 sequences into three large groups. In addition, we identified four large clades consisting of homogeneous sequences of powdery mildews from a wide range of host plants beyond family level, namely, the E. aquilegiae clade, the E. alphitoides clade, the E. quercicola clade, and the E. trifoliorum s. lat. clade. Isolates from herbaceous plants were mostly situated in the E. aquilegiae clade and in Group III that was located at the most derived position of the Microsphaera-lineage. On the other hand, the basal part of the Microsphaera-lineage was occupied by isolates from woody plants except for E. glycines that was used as an outgroup taxon. This supports our previous hypothesis that tree-parasitic powdery mildews are phylogenetically primitive in the Erysiphaceae in general, and host-shift from trees to herbs occurred many times independently during the evolution of powdery mildews. Molecular clock analyses suggested that the divergence of the Microsphaera-lineage began ca. 20 million years ago in the Miocene Epoch of the Neogene Period.

Phylogenetic relationships of the Uncinula lineage, which is the basal group in the genus Erysiphe, were investigated with 167 sequences of nuc ITS1-5. 8S-ITS2 and the 28S rDNA regions. Backbone tree analyses with six datasets and two tree-constructing methods revealed that the Uncinula lineage is divided into seven distinct clades. Clades 1-5 each contained a representative powdery mildew species, namely E. australiana in Clade 1, E. liquidambaris in Clade 2, E. adunca in Clade 3, E. fraxinicola in Clade 4 and E. actinidiae in Clade 5. Clade 6 comprises 71 sequences including the Microsphaera lineage and 17 species of the Uncinula lineage, such as E. carpinicola, E. carpinilaxiflorae, E. miyabei, E. glycines and E. necator. Topology tests supported the Microsphaera lineage forming a monophyletic clade in Clade 6, suggesting that Microsphaera-type appendages appeared only once in this clade to diverge into the Microsphaera lineage. Clade 7 consists of 72 sequences containing 30 species, including species of sects. Californiomyces and Typhulochaeta, four species from Nothofagus, species of sect. Erysiphe parasitising herbaceous plants belonging to the Asteraceae, Rosaceae and Saxifragaceae. Molecular clock analysis suggests that the major seven clades appeared 50-30 million years ago (Ma) in the Paleogene Period. The Microsphaera lineage may have split from the Uncinula lineage at the boundary of the Paleogene and Neogene, when appendages with dichotomously branched tips appeared. The clade of the species on Nothofagus split from the northern hemisphere species about 20-10 million years ago (Ma) in the Miocene Epoch, and host-shift from trees to herbs also might have occurred in this period.