Revised taxonomy of Phoma and allied genera.
The molecular phylogeny of species of Phoma and allied genera was studied and the results obtained were used to revise the taxonomy. Chapter 1 provides the general introduction of Phoma. The results of the study conducted in The Netherlands during the last decades are described. Species of the genus Phoma were classified into the nine sections (Phoma, Heterospora, Macrospora, Paraphoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella) based on morphology. In chapter 2 several genes were studied to elucidate the molecular phylogeny of Phoma and allied genera. Sequence data of the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of the type species of the Phoma sections and morphologically similar coelomycetes and related teleomorphs were compared. The results justified the introduction of the new family Didymellaceae to accommodate the generic type species Didymella exigua and Phoma herbarum ([Phoma exigua var. exigua]). The type species of the Phoma sections Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea also grouped in Didymellaceae. The generic type species Ascochyta pisi and Microsphaeropsis olivacea also grouped in Didymellaceae and it shows that these genera are closely allied to Phoma. The type species of Phoma sections Heterospora, Paraphoma, Pilosa and Plenodomus grouped in different families outside Didymellaceae and were subject of following studies. Chapter 3 provides a molecular phylogenetic re-evaluation on Phoma-like species that appeared only distantly related to the generic type species Phoma herbarum and its related Didymella teleomorph (Didymellaceae). Phoma section Paraphoma, characterised by setose pycnidia, resembles species of Pyrenochaeta and Pleurophoma. Unnamed, often sterile Phoma-like strains in the collections were included. The molecular phylogeny of species that were classified in Phoma section Paraphoma appeared to be highly polyphyletic and a thorough reclassification of the species is provided. Paraphoma was reinstalled and grouped with the new genera Neosetophoma and Setophoma in Phaeosphaeriaceae. Pyrenochaeta and the new genus Pyrenochaetopsis, including mainly taxa formerly described in Phoma section Paraphoma, were closely allied in Cucurbitariaceae. In chapter 4 the molecular phylogeny of species of Phoma sections Plenodomus, Pleospora and Heterospora was determined using LSU, SSU and ITS. In a one species-one name approach, the species described in Phoma section Plenodomus and its teleomorph Leptosphaeria were reclassified in Leptosphaeria, Plenodomus and the new genera Paraleptosphaeria and Subplenodomus in Leptosphaeriaceae. Two species of Phoma section Heterospora, the type species Phoma heteromorphospora and its allied species Ph. dimorphospora, were transferred to the new genus Heterospora that also grouped in Leptosphaeriaceae. Leptosphaeria doliolum comprises a species complex that was revised based on multilocus sequence data of LSU, ITS, SSU, β-tubulin, and chitin synthase 1. The molecular phylogeny of species classified in Ascochyta and Phoma, section Pilosa in Pleosporaceae that produce morphologically similar pilose pycnidia, was determined based on analysis of actin sequence data. Several Phoma-like species grouped outside the suborder Pleosporineae in a LSU sequence analysis were transferred to the genera Aposphaeria (Melanommataceae), Paraconiothyrium (Montagnulaceae) and Westerdykella (Sporormiaceae). Coniothyrium palmarum and related species were described in Coniothyriaceae. The new genera Medicopsis (Trematosphaeriaceae) and Nigrograna, of which the family is still unknown, are introduced to accommodate two medically important species formerly classified in Pyrenochaeta. In chapter 5 specific real-time (TaqMan) PCR assays were developed for the detection of Stagonosporopsis andigena and S. crystalliniformis in potato and tomato leaves. The molecular phylogeny with related species of Stagonosporopsis, Boeremia and Phoma based on sequence polymorphisms in the actine gene, was determined.