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Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Réunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.

The fungal pathogen Phoma clematidina is used as a biological agent to control the invasive plant species Clematis vitalba in New Zealand. Research conducted on P. clematidina as a potential biocontrol agent against C. vitalba, led to the discovery of two perithecial-forming strains. To assess the diversity of P clematidina and to clarify the teleomorph-anamorph relationship, phylogenetic analyses of 18 P. clematidina strains, reference strains representing the Phoma sections in the Didymellaceae and strains of related species associated with Clematis were conducted. Partial sequences of the ITS1, ITS2 and 5.8S rRNA gene, the beta-tubulin gene and 28S rRNA gene were used to clarify intra- and inter-species relationships. These analyses revealed that P clematidina resolves into three well-supported clades which appear to be linked to differences in host specificity. Based on these findings, Didymella clematidis is newly described and the descriptions of P. clematidina and D. vitalbina are amended.

The omnipresent dematiaceous hyphomycete genus Alternaria is associated with a wide variety of substrates including seeds, plants, agricultural products, humans, soil and even the atmosphere. It includes saprophytic, endophytic and pathogenic species, among which multiple plant pathogens, post-harvest pathogens, and human pathogens (causative agents of phaeohyphomycosis and hypersensitivity reactions). Molecular studies reveal that the Alternaria complex comprises nine genera. Within this complex several genera are non-monophyletic and Alternaria species cluster into multiple distinct species clades, which are not always correlated with species-groups based on morphological characteristics. The most commonly reported species in literature and type species of the genus Alternaria, A. alternata, also comprises one such species-group. The small-spored Alternaria species within this group are mainly described based on morphology and / or host-specificity, but are difficult to distinguish based on molecular techniques alone. As A. alternata is considered as one of the most prolific producers of fungal allergens and is reported as pathogen on over 100 host plants, correct species identification is of utmost importance. The research presented in this thesis discusses the taxonomic status of Alternaria and its related genera, with a further focus on the two biggest and most important species complexes; the large-spored A. porri and small-spored A. alternata species complexes. With the phylogenies and classifications presented in this thesis, more robust and understandable taxonomy and nomenclature in Alternaria and allied genera within the Alternaria complex are created. Chapter 1 gives a general introduction to the genus Alternaria and related genera. The history of the genus and its economic importance as plant pathogen, post-harvest pathogen, causative agent of phaeohyphomycosis and common allergen causing hypersensitivity reactions are summarized. The introduction of the morphological species complexes, based on characters of the conidia, the pattern of chain formation, and the nature of the apical extensions of conidia are treated. Molecular studies recognise seven Alternaria species-groups within the Alternaria complex. Besides Alternaria, eight other genera are assigned to the Alternaria complex based on molecular and morphological studies. Chapter 2 focusses on the relationship of Alternaria and its closely related genera within the broader Alternaria complex. The phylogenetic lineages within the Alternaria complex are delineated based on nucleotide sequence data of parts of the 18S nrDNA (SSU), 28S nrDNA (LSU), the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) gene regions. The phylogenetic data reveal a Stemphylium clade sister to Embellisia annulata and a big Alternaria clade. The Alternaria clade contains six monotypic lineages and 24 internal clades, which are treated as sections of Alternaria. In order to create a stable phylogenetic taxonomy, and supported by i) a well-supported phylogenetic node in multiple analyses, ii) a high-similarity of clades within Alternaria based on SSU, LSU and ITS data, and iii) variation in the clade order between the different gene phylogenies, 13 genera are placed into synonymy with Alternaria. Embellisia annulata is synonymized with Dendryphiella salina, and together with D. arenariae placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, with asexual forms linked to Alternaria, cluster within the Pleosporaceae, as does Alternaria, but outside Alternaria s. str. The genus Alternariaster, described to accommodate Alternaria helianthi, clusters within the Leptosphaeriaceae. Chapter 3 describes the reappraisal of the genus Alternariaster. Alternaria helianthi, the causal agent of leaf spot on Helianthus annuus (sunflower) was segregated from Alternaria based on conidial morphology, and placed in the new genus Alternariaster. A multi-gene phylogeny of parts of the ITS, LSU, RPB2 and GAPDH gene regions placed a fungal pathogen associated with leaf spot on Bidens sulphurea (yellow cosmos) in Brazil in close relation with Al. helianthi. Based on the close phylogenetic relation to Al. helianthi, but distinct morphological and pathogenicity characters, the fungal pathogen associated with leaf spot on B. sulphurea is newly described as Al. bidentis. Chapter 4 treats the Alternaria species which form the largest section of Alternaria, sect. Porri. This section contains almost all Alternaria species with medium to large conidia with long beaks, some of which are important plant pathogens. A multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alternaria major allergen (Alt a 1) gene regions, supplemented with morphological and cultural studies, forms the basis for species recognition in this section. The polyphasic data reveal 63 species in sect. Porri, of which 10 are newly described, and 27 names are synonymized. Chapter 5 treats the small-spored Alternaria species, which reside in sect. Alternaria. A lot of confusion around the naming of species within this section exists, since the naming is mostly based on morphology and host-specificity, although the molecular variation is minimal. Whole genome sequencing, combined with transcriptome profiling and multi-gene sequencing of nine gene regions, SSU, LSU, ITS, GAPDH, RPB2, TEF1, Alt a 1, endopolygalacturonase (endoPG) and an anonymous gene region (OPA10-2), is used to create a clear and stable species classification in this section. The nine sequenced Alternaria genomes range in size from 32.0 - 39.1 Mb. The number of repetitive sequences varies significantly, with a relative low percentage of repeats within sect. Alternaria. The genome identity within sect. Alternaria is high, compared to the genome identity for isolates from other sections to the A. alternata reference genome. Similarly, a relative low percentage of single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences between isolates from sect. Alternaria, compared to the percentage of SNP’s found in isolates from different sections compared to the A. alternata reference genome. A set of core proteins was extracted from the genome and transcriptome data, and primers were designed on two eukaryotic orthologous group (KOG) protein loci with a relatively low degree of conservation within section Alternaria. The phylogenies from these two gene regions, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria better than the phylogenies based on the nine commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies are synonymized under A. alternata. The subclades that are formed by these isolates are incongruent between the different gene regions sequenced; no two genes show the same groupings for any of the over 100 isolates. A sequence-based identification guide is provided for the species which are now recognized in sect. Alternaria. None of the genes sequenced in this study can distinguish all of the species recognized here on its own. Chapter 6 investigates the molecular diversity of indoor Alternaria isolates in the USA, with the help of a phylogeographic / population genetic approach. Isolates collected throughout the USA were identified using ITS, GAPDH and endoPG gene sequencing, followed by genotyping and population genetic inference of the sect. Alternaria isolates and 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that 98 % (153 isolates) of the indoor isolates consisted of species from Alternaria sect. Alternaria. The remaining 2 % (three isolates) represented one sect. Infectoriae and two sect. Pseudoulocladium isolates. From the 153 isolates that belonged to sect. Alternaria, one could be assigned to A. burnsii, 15 to the A. arborescens species complex and the remaining 137 isolates were identified as A. alternata. Based on the microsatellite data, no specific indoor population could be distinguished. Population assignment analyses of the A. alternata isolates suggested that subpopulations did not exist within the sample, which we thus divided into four artificial subpopulations to represent four quadrants of the USA. Genotypic diversity was extremely high for all quadrants and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. The SouthWest-USA population displayed the highest level of uniqueness, based on private alleles. Intriguingly, the highest amount of gene flow, between SouthWest-USA and SouthEast-USA, correlated with the west-to-east movement of the antitrade winds. This suggests that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent. Chapter 7 discusses the data presented in this thesis. The implications of the performed studies are placed in a broader context, with a focus on the relation between morphology and the new species classification based on molecular tools and the use of genome data in contrast to multi-gene data.

Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum.

Ascochyta and Phoma are fungal genera containing several important plant pathogenic species. These genera are morphologically similar, and recent molecular studies performed to unravel their phylogeny have resulted in the establishment of several new genera within the newly erected Didymellaceae family. An analysis of the structure of fungal mating-type genes can contribute to a better understanding of the taxonomic relationships of these plant pathogens, and may shed some light on their evolution and on differences in sexual strategy and pathogenicity. We analysed the mating-type loci of phylogenetically closely related Ascochyta and Phoma species (Phoma clematidina, Didymella vitalbina, Didymella clematidis, Peyronellaea pinodes and Peyronellaea pinodella) that co-occur on the same hosts, either on Clematis or Pisum. The results confirm that the mating-type genes provide the information to distinguish between the homothallic Pey. pinodes (formerly Ascochyta pinodes) and the heterothallic Pey. pinodella (formerly Phoma pinodella), and indicate the close phylogenetic relationship between these two species that are part of the disease complex responsible for Ascochyta blight on pea. Furthermore, our analysis of the mating-type genes of the fungal species responsible for causing wilt of Clematis sp. revealed that the heterothallic D. vitalbina (Phoma anamorph) is more closely related to the homothallic D. clematidis (Ascochyta anamorph) than to the heterothallic P. clematidina. Finally, our results indicate that homothallism in D. clematidis resulted from a single crossover between MAT1-1 and MAT1-2 sequences of heterothallic ancestors, whereas a single crossover event followed by an inversion of a fused MAT1/2 locus resulted in homothallism in Pey. pinodes.