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The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.

Helvella is a widespread, speciose genus of large apothecial ascomycetes (Pezizomycete: Pezizales) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci - heat shock protein 90 (hsp), translation elongation factor alpha (tef), RNA polymerase II (rpb2) and the nuclear large subunit ribosomal DNA (LSU) - to assess species boundaries in an expanded sample of Helvella specimens from Europe. We combine the morphological and phylogenetic information from 55 Helvella species from Europe with a small sample of Helvella species from other regions of the world. Little intraspecific variation was detected within the species using these molecular markers; hsp and rpb2 markers provided useful barcodes for species delimitation in this genus, while LSU provided more variable resolution among the pertinent species. We discuss typification issues and identify molecular characteristics for 55 European Helvella species, designate neo- and epitypes for 30 species, and describe seven Helvella species new to science, i.e., H. alpicola, H. alpina, H. carnosa, H. danica, H. nannfeldtii, H. pubescens and H. scyphoides.

During various surveys of Phytophthora diversity in Europe, Chile and Vietnam slow growing oomycete isolates were obtained from rhizosphere soil samples and small streams in natural and planted forest stands. Phylogenetic analyses of sequences from the nuclear ITS, LSU, β-tubulin and HSP90 loci and the mitochondrial cox1 and NADH1 genes revealed they belong to six new species of a new genus, officially described here as Nothophytophthora gen. nov., which clustered as sister group to Phytophthora. Nothophytophthora species share numerous morphological characters with Phytophthora: persistent (all Nothophytophthora spp.) and caducous (N. caduca, N. chlamydospora, N. valdiviana, N. vietnamensis) sporangia with variable shapes, internal differentiation of zoospores and internal, nested and extended (N. caduca, N. chlamydospora) and external (all Nothophytophthora spp.) sporangial proliferation; smooth-walled oogonia with amphigynous (N. amphigynosa) and paragynous (N. amphigynosa, N. intricata, N. vietnamensis) attachment of the antheridia; chlamydospores (N. chlamydospora) and hyphal swellings. Main differing features of the new genus are the presence of a conspicuous, opaque plug inside the sporangiophore close to the base of most mature sporangia in all known Nothophytophthora species and intraspecific co-occurrence of caducity and non-papillate sporangia with internal nested and extended proliferation in several Nothophytophthora species. Comparisons of morphological structures of both genera allow hypotheses about the morphology and ecology of their common ancestor which are discussed. Production of caducous sporangia by N. caduca, N. chlamydospora and N. valdiviana from Valdivian rainforests and N. vietnamensis from a mountain forest in Vietnam suggests a partially aerial lifestyle as adaptation to these humid habitats. Presence of tree dieback in all forests from which Nothophytophthora spp. were recovered and partial sporangial caducity of several Nothophytophthora species indicate a pathogenic rather than a saprophytic lifestyle. Isolation tests from symptomatic plant tissues in these forests and pathogenicity tests are urgently required to clarify the lifestyle of the six Nothophytophthora species.

Species of Colletotrichum are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on citrus, either as agents of pre- or post-harvest infections, such as anthracnose, postbloom fruit drop, tear stain and stem-end rot on fruit, or as wither-tip of twigs. In this study we explored the occurrence, diversity and pathogenicity of Colletotrichum spp. associated with Citrus and allied genera in European orchards, nurseries and gardens. Surveys were carried out during 2015 and 2016 in Greece, Italy, Malta, Portugal and Spain. A total of 174 Colletotrichum strains were isolated from symptomatic leaves, fruits, petals and twigs. A multi-locus phylogeny was established based on seven genomic loci (ITS, GAPDH, ACT, CAL, CHS-1, HIS3 and TUB2), and the morphological characters of the isolates determined. Preliminary pathogenicity tests were performed on orange fruits with representative isolates. Colletotrichum strains were identified as members of three major species complexes. Colletotrichum gloeosporioides s.str. and two novel species (C. helleniense and C. hystricis) were identified in the C. gloeosporioides species complex. Colletotrichum karstii, C. novae-zelandiae and two novel species (C. catinaense and C. limonicola) in the C. boninense species complex, and C. acutatum s.str. was also isolated as member of C. acutatum species complex. Colletotrichum gloeosporioides and C. karstii were the predominant species of Colletotrichum isolated. This study represents the first report of C. acutatum on citrus in Europe, and the first detection of C. novae-zelandiae from outside New Zealand. Pathogenicity tests revealed C. gloeosporioides s.str. to be the most virulent species on fruits. The present study improves our understanding of species associated with several disease symptoms on citrus fruits and plants, and provides useful information for effective disease management.

Karst caves are distinctly characterised by darkness, low to moderate temperatures, high humidity, and scarcity of organic matter. During the years of 2014-2015, we explored the mycobiota in two unnamed Karst caves in Guizhou province, China, and obtained 563 fungal strains via the dilution plate method. Preliminary ITS analyses of these strains suggested that they belonged to 246 species in 116 genera, while 23.5 % were not identified to species level. Among these species, 85.8 % (211 species) belonged to Ascomycota; 7.3 % (18 species) belonged to Basidiomycota; 6.9 % (17 species) belonged to Mucoromycotina. The majority of these species have been previously known from other environments, mostly from plants or animals as pathogens, endophytes or via a mycorrhizal association. We also found that 59 % of these species were discovered for the first time from Karst caves, including 20 new species that are described in this paper. The phylogenetic tree based on LSU sequences revealed 20 new species were distributed in six different orders. In addition, ITS or multi-locus sequences were employed to infer the phylogenetic relationships of new taxa with closely related allies. We conclude that Karst caves encompass a high fungal diversity, including a number of previously unknown species. Novel species described include: Amphichorda guana, Auxarthronopsis guizhouensis, Biscogniauxia petrensis, Cladorrhinum globisporum, Collariella quadrum, Gymnoascus exasperatus, Humicola limonisporum, Metapochonia variabilis, Microascus anfractus, Microascus globulosus, Microdochium chrysanthemoides, Paracremonium variiforme, Pectinotrichum chinense, Phaeosphaeria fusispora, Ramophialophora globispora, Ramophialophora petraea, Scopulariopsis crassa, Simplicillium calcicola, Volutella aeria, and Wardomycopsis longicatenata.

Though most of the lichenicolous fungi belong to the Ascomycetes, their phylogenetic placement based on molecular data is lacking for numerous species. In this study the phylogenetic placement of 19 species of lichenicolous fungi was determined using four loci (LSU rDNA, SSU rDNA, ITS rDNA and mtSSU). The phylogenetic analyses revealed that the studied lichenicolous fungi are widespread across the phylogeny of Lecanoromycetes. One species is placed in Acarosporales, Sarcogyne sphaerospora; five species in Dactylosporaceae, Dactylospora ahtii, D. deminuta, D. glaucoides, D. parasitica and Dactylospora sp.; four species belong to Lecanorales, Lichenosticta alcicorniaria, Epicladonia simplex, E. stenospora and Scutula epiblastematica. The genus Epicladonia is polyphyletic and the type E. sandstedei belongs to Leotiomycetes. Phaeopyxis punctum and Bachmanniomyces uncialicola form a well supported clade in the Ostropomycetidae. Epigloea soleiformis is related to Arthrorhaphis and Anzina. Four species are placed in Ostropales, Corticifraga peltigerae, Cryptodiscus epicladonia, C. galaninae and C. cladoniicola comb. nov. (= Lettauia cladoniicola). Three new species are described, Dactylospora ahtii, Cryptodiscus epicladonia and C. galaninae.

The family Lophiotremataceae (Pleosporales, Dothideomycetes) is taxonomically revised on the basis of morphological observations and phylogenetic analyses of sequences of nuclear rDNA SSU, ITS, and LSU regions and tef1 and rpb2 genes. A total of 208 sequences were generated from species of Lophiotremataceae and its relatives. According to phylogenetic analyses, Lophiotremataceae encompasses the genus Lophiotrema and five new genera: Atrocalyx, Crassimassarina, Cryptoclypeus, Galeaticarpa, and Pseudocryptoclypeus. These genera are characterised by ascomata with or without a slit-like ostiole and pycnidial conidiomata. Three new families, Aquasubmersaceae, Cryptocoryneaceae, and Hermatomycetaceae, are proposed. Two genera previously recognised as members of Lophiotremataceae, namely, Aquasubmersa having ascomata with a papillate ostiolar neck and pycnidial conidiomata and Hermatomyces possessing sporodochial conidiomata and dimorphic (lenticular and cylindrical) conidia, are included in Aquasubmersaceae and Hermatomycetaceae, respectively. Cryptocoryneum, characterised by the presence of stromatic sporodochia, cheiroid conidia, and conidial arms developed downward from the cap cells, is placed in Cryptocoryneaceae. Two new genera, Antealophiotrema and Pseudolophiotrema, are established, but their familial placements remain unresolved. Antealophiotrema bears ascomata morphologically similar to those of Lophiotrema, but is differentiated from the latter by having ascomata with a well-developed peridium and a monodictys-like asexual morph. Pseudolophiotrema is also similar to Lophiotrema, but can be distinguished by ascomata with a thin peridium. A total of three new families, seven new genera, eight new species, and two new combinations are described and illustrated.

Cortinarius is the largest genus of ectomycorrhizal fungi worldwide. Recent molecular studies have shown high levels of morphological homoplasy within the genus. Importantly, DNA phylogenies can reveal characteristics that have been either over- or underemphasized in taxonomic studies. Here we sequenced and phylogenetically analysed a large set of pan-European and North American collections taxonomically studied and placed in Cortinarius sect. Bicolores and sect. Saturnini, according to traditional morpho-anatomical criteria. Our goal was to circumscribe the evolutionary boundaries of the two sections, to stabilize both the limits and nomenclature of relevant species, and to identify described taxa which, according to our current understanding, belong to other lineages. Our analysis resolves two clades: /Bicolores, including 12 species, one of which is new to science, and /Saturnini, including 6 species. Fifteen binomials, traditionally treated in these two sections based on morphology, do not belong to the above two phylogenetic clades. Instead, six of these latter are clearly placed in other clades that represent sect. Bovini, sect. Sciophylli, sect. Duracini and sect. Brunneotincti. The presence or absence of blue pigments and the detection of specific odours emerge as clearly misleading taxonomic features, but more surprisingly, spore size and ecology can be misleading as well. A total of 63 type specimens were sequenced, 4 neotypes and 2 epitypes are proposed here, and 1 new combination is made.

Species of Nigrospora commonly occur as plant pathogens, endophytes or saprobes, and have been shown to be extremely interesting for the discovery of novel metabolites. The familial placement, as well as phylogenetic relationships among Nigrospora species remain ambiguous. In this study, Nigrospora (= Khusia) is confirmed as a monophyletic genus belonging to Apiosporaceae (Xylariales), based on a phylogeny inferred from LSU sequence data. A multi-locus phylogeny based on ITS, TEF1-α and TUB2, in conjunction with morphological characters, host associations, and ecological data was employed for species delimitation in Nigrospora, as well as identification of 165 recently collected isolates from China, and three from Europe. In total 13 novelties are proposed including 12 new species and 1 new combination. Five species are re-described based on an examination of type specimens and/or fresh collections. New species described in this paper include: N. aurantiaca, N. bambusae, N. camelliae-sinensis, N. chinensis, N. guilinensis, N. hainanensis, N. lacticolonia, N. osmanthi, N. pyriformis, N. rubi, N. vesicularis and N. zimmermanii. Furthermore, N. vietnamensis is transferred to Arthrinium. Our results indicate a high level of species diversity within Nigrospora, with a general lack in host specificity. Taxa that cluster basal in Nigrospora have wide host ranges, whereas those that diverged later tend to have narrow host ranges. The currently available data suggest, therefore, that the general evolutionary direction in the genus Nigrospora is from a wide to a narrow host range.