Persoonia - Molecular Phylogeny and Evolution of Fungi

Online ISSN: 1878-9080
Novel species of microfungi described in the present study include the following from Australia: Diaporthe ceratozamiae on Ceratozamia robusta, Seiridium banksiae on Banksia marginata, Phyllosticta hymenocallidicola on Hymenocallis littoralis, Phlogicylindrium uniforme on Eucalyptus cypellocarpa, Exosporium livistonae on Livistona benthamii and Coleophoma eucalyptorum on Eucalyptus piperita. Several species are also described from South Africa, namely: Phoma proteae, Pyrenochaeta protearum and Leptosphaeria proteicola on Protea spp., Phaeomoniella niveniae on Nivenia stokoei, Toxicocladosporium leucadendri on Leucadendron sp. and Scorias leucadendri on Leucadendron muirii. Other species include Myrmecridium phragmitis on Phragmites australis (Netherlands) and Camarographium carpini on Carpinus betulus (Russia). Furthermore, Pseudoidriella syzygii on Syzygium sp. represents a novel genus of hyphomycetes collected in Australia. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Comparison of hosts, distribution and micromorphology of currently described Strelitziana species. 
Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliae-fistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided.
This supplement to the taxonomic monograph The Genera of Hyphomycetes summarises information on 23 accepted new genera and c. 160 species described in 2011. These include three dematiaceous genera (Funbolia, Noosia, Pyrigemmula, all related to Dothideomycetes), a bulbil-producing genus, Spiroplana (Pleosporales), and two endophytic genera, the sterile Periglandula (Clavicipitaceae), and the hyaline, sympodial Micronematobotrys (Pyronemataceae). Slow-growing, morphologically-reduced, darkly pigmented fungi continue to be the source of new taxa, including the new genus Atramixtia (Dothioraceae). Eight new genera of darkly pigmented chlamydospore-like anamorphs were described from marine or subtidal environments (Glomerulispora, Halozoön, Hiogispora, Matsusporium, Moheitospora, Moleospora, Moromyces), mostly associated with subclades of the Lulworthiales. Several genera that are morphologically similar to but phylogenetically distinct from genera of the Capnodiales (Pseudopassalora, Scleroramularia) were introduced, as well as segregates from the classical concepts of Alternaria (Sinomyces), Chalara and Phialophora (Brachyalara, Infundichalara, Lasiadelphia), and Paecilomyces (Purpureocillium for the former Paecilomyces lilacinus complex). In addition, in anticipation of the new nomenclatural rules, newly configured formerly-teleomorph genera were proposed as segregates from classical hyphomycete genera in the Hypocreales, namely Acremonium (Cosmospora), Fusarium (Cyanonectria, Dialonectria, Geejayessia, Macroconia, Stylonectria), and Volutella (Pseudonectria) and the Trichocomaceae, Eurotiales, Penicillium (Talaromyces for the former Penicillium subg. Biverticillium). Standardized generic mini-diagnoses are provided for the accepted new genera, along with details of distribution, substrates, numbers of new species and phylogenetic affinities within the Dikarya. GenBank accession numbers for ITS DNA-barcodes are provided where available. New information on generic concepts of previously recognised genera, phylogenetic relationships, and corrections of factual errors are also included. Only two newly described genera, Fecundostilbum and Utrechtiana, seem to be synonyms of previously described genera.
Novel species of microfungi described in the present study include the following from Australia: Bagadiella victoriae and Bagadiella koalae on Eucalyptus spp., Catenulostroma eucalyptorum on Eucalyptus laevopinea, Cercospora eremochloae on Eremochloa bimaculata, Devriesia queenslandica on Scaevola taccada, Diaporthe musigena on Musa sp., Diaporthe acaciigena on Acacia retinodes, Leptoxyphium kurandae on Eucalyptus sp., Neofusicoccum grevilleae on Grevillea aurea, Phytophthora fluvialis from water in native bushland, Pseudocercospora cyathicola on Cyathea australis, and Teratosphaeria mareebensis on Eucalyptus sp. Other species include Passalora leptophlebiae on Eucalyptus leptophlebia (Brazil), Exophiala tremulae on Populus tremuloides and Dictyosporium stellatum from submerged wood (Canada), Mycosphaerella valgourgensis on Yucca sp. (France), Sclerostagonospora cycadis on Cycas revoluta (Japan), Rachicladosporium pini on Pinus monophylla (Netherlands), Mycosphaerella wachendorfiae on Wachendorfia thyrsifolia and Diaporthe rhusicola on Rhus pendulina (South Africa). Novel genera of hyphomycetes include Noosia banksiae on Banksia aemula (Australia), Utrechtiana cibiessia on Phragmites australis (Netherlands), and Funbolia dimorpha on blackened stem bark of an unidentified tree (USA). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
A most likely tree obtained by RAxML for Ascomycota. Subphyla, class and rankless taxa are indicated. Classes containing fungi designated as earth tongues are indicated in black. The tree was rooted with outgroup Rhizopus oryzae (not shown). Bootstrap values are shown in orange and Bayesian posterior probabilities in blue. Orange, bold branches are supported by more than 80 % bootstrap and 95 % posterior probability, respectively. The full phylogeny, without collapsed clades, are shown in Fig. 2. The inset figures illustrate morphological ascomal diversity in the earth tongues. The species are as follows: A. Trichoglossum hirsutum; B. Geoglossum nigritum; C. Microglossum rufum; D. Spathularia velutipes; E. Geoglossum nigritum. Photo credits: A: Zhuliang Yang; B, D, E: Kentaro Hosaka; C: Dan Luoma. 
A most likely tree obtained by RAxML for Ascomycota (as in Fig. 1). Phyla, subphyla, class, order and rankless taxa are indicated. Taxa designated as earth tongues are indicated in orange. The tree is displayed as two subtrees-orange arrows indicate where the subtrees were joined. The tree was rooted with outgroup Rhizopus oryzae (not shown). Bootstrap values are shown in orange above nodes and Bayesian posterior probabilities in blue below. Numbers were removed for nodes with 100 % bootstrap and 100 % posterior probability. 
Featuring a high level of taxon sampling across Ascomycota, we evaluate a multi-gene phylogeny and propose a novel order and class in Ascomycota. We describe two new taxa, Geoglossomycetes and Geoglossales, to host three earth tongue genera: Geoglossum, Trichoglossum and Sarcoleotia as a lineage of 'Leotiomyceta'. Correspondingly, we confirm that these genera are not closely related to the genera Neolecta, Mitrula, Cudonia, Microglossum, Thuemenidum, Spathularia and Bryoglossum, all of which have been previously placed within the Geoglossaceae. We also propose a non-hierarchical system for naming well-resolved nodes, such as 'Saccharomyceta', 'Dothideomyceta', and 'Sordariomyceta' for supraordinal nodes, within the current phylogeny, acting as rankless taxa. As part of this revision, the continued use of 'Leotiomyceta', now as a rankless taxon, is proposed.
The first of 32 equally most parsimonious trees obtained from a heuristic search with 1 000 random taxon additions of the LSU alignment containing representative species that currently form well-supported clades within the Capnodiales. The scale bar indicates 10 changes and bootstrap support values from 1 000 replicates are indicated at the nodes. Thickened lines indicate conserved branches present in the strict consensus tree. 
Zymoseptoria brevis (CPC 18106) a. Pycnidium forming on barley leaves in vitro; b. colony sporulation on potato-dextrose agar; c. conidiogenous cells; d. colony on synthetic nutrient-poor agar, showing yeast-like growth; e. conidium undergoing microcyclic conidiation (arrows; Type III); f-h. pycnidiospores (Type I).-Scale bars = 10 μm. 
Zymoseptoria halophila (CPC 18105). a. Pycnidia forming on barley leaves in vitro, with oozing conidia cirrhus; b-e. conidiogenous cells formed in pycnidia; f. conidia (Type I); g. colony with yeast-like growth on synthetic nutrient-poor agar; h, j-l. conidia formed as phragmospores in aerial hyphae (Type II); i, m. conidia formed via microcyclic conidiation (Type III).-Scale bars = 10 μm. 
The Mycosphaerella complex is both poly- and paraphyletic, containing several different families and genera. The genus Mycosphaerella is restricted to species with Ramularia anamorphs, while Septoria is restricted to taxa that cluster with the type species of Septoria, S. cytisi, being closely related to Cercospora in the Mycosphaerellaceae. Species that occur on graminicolous hosts represent an as yet undescribed genus, for which the name Zymoseptoria is proposed. Based on the 28S nrDNA phylogeny derived in this study, Zymoseptoria is shown to cluster apart from Septoria. Morphologically species of Zymoseptoria can also be distinguished by their yeast-like growth in culture, and the formation of different conidial types that are absent in Septoria s.str. Other than the well-known pathogens such as Z. tritici, the causal agent of septoria tritici blotch on wheat, and Z. passerinii, the causal agent of septoria speckled leaf blotch of barley, both for which epitypes are designated, two leaf blotch pathogens are also described on graminicolous hosts from Iran. Zymoseptoria brevis sp. nov. is described from Phalaris minor, and Z. halophila comb. nov. from leaves of Hordeum glaucum. Further collections are now required to elucidate the relative importance, host range and distribution of these species.
Recent studies have found a wide range of ascomycetes to be associated with sooty blotch and flyspeck (SBFS) blemishes on the surfaces of pomaceous fruits, specifically apples. Based on collections of such fungi from apple orchards in Germany and Slovenia we introduce two novel genera according to analyses of morphological characters and nuclear ribosomal DNA sequences (large subunit and internal transcribed spacer regions). Microcyclosporella is represented by a single species, M. mali, and is presently known from Germany and Slovenia. Microcyclosporella is Pseudocercosporella-like in morphology, but genetically and morphologically distinct from Pseudocercosporella s.str., for which an epitype is designated based on a fresh collection of P. bakeri from Laos. Furthermore, Pseudocercosporella is shown to be paraphyletic within the Capnodiales. Microcyclospora gen. nov. is Pseudocercospora-like in morphology, but is genetically and morphologically distinct from Pseudocercospora s.str., which is based on P. vitis. Three species, Microcyclospora malicola, M. pomicola (both collected in Germany), and M. tardicrescens (collected in Slovenia) are described. Finally, a new species of Devriesia, D. pseudoamericana, is described from pome fruit surfaces collected in Germany. Devriesia is shown to be paraphyletic, and to represent several lineages of which only Devriesia s.str. is thermotolerant. Further collections are required, however, before the latter generic complex can be resolved.
During a survey of Penicillium spp. in soils from the diverse fynbos region in the Western Cape, South Africa, a number of previously undescribed species were isolated. Three of these belong to subg. Biverticillium sensu Pitt, recently incorporated into its previously associated teleomorph genus, Talaromyces s.str. These species displayed symmetrical biverticillate penicilli, acerose phialides and poor growth at reduced water activity, typical of this group. Morphological characters of the new species were compared to known Talaromyces species. The ITS and β-tubulin gene regions were used for phylogenetic comparisons, which confirmed the distinct nature of the three fynbos soil species described here as Talaromyces chloroloma sp. nov., T. ptychoconidium sp. nov. and T. solicola sp. nov., respectively. Talaromyces chloroloma is typically recognised by its strongly funiculose colony texture and after prolonged incubation, synnemata can be observed on CYA. Talaromyces ptychoconidium is characterised by closely appressed conidiophores that produce spirally rough-walled conidia, while T. solicola typically struggle to grow on CYA and is distinguished from similar species by its prominently rough-walled, spheroid conidia.
Discosia (teleomorph unknown) and Seimatosporium (teleomorph Discostroma) are saprobic or plant pathogenic, coelomycetous genera of so-called 'pestalotioid fungi' within the Amphisphaeriaceae (Xylariales). They share several morphological features and their generic circumscriptions appear unclear. We investigated the phylogenies of both genera on the basis of SSU, LSU and ITS nrDNA and β-tubulin gene sequences. Discosia was not monophyletic and was separated into two distinct lineages. Discosia eucalypti deviated from Discosia clade and was transferred to a new genus, Immersidiscosia, characterised by deeply immersed, pycnidioid conidiomata that are intraepidermal to subepidermal in origin, with a conidiomatal beak having periphyses. Subdividing Discosia into 'sections' was not considered phylogenetically significant at least for the three sections investigated (sect. Discosia, Laurina, and Strobilina). We recognised Seimatosporium s.l. as a monophyletic genus. An undescribed species belonging to Discosia with its associated teleomorph was collected on living leaves of Symplocos prunifolia from Yakushima Island, Japan. We have therefore established a new teleomorphic genus, Adisciso, for this new species, A. yakushimense. Discostroma tricellulare (anamorph: Seimatosporium azaleae), previously described from Rhododendron species, was transferred to Adisciso based on morphological and phylogenetic grounds. Adisciso is characterised by relatively small-sized ascomata without stromatic tissue, obclavate to broadly cylindrical asci with biseriate ascospores that have 2 transverse septa, and its Discosia anamorph. Based on these features, it can easily be distinguished from Discostroma, a similar genus within the Amphisphaeriaceae.
During the course of research on mammal mycophagy and movement in the Northern Tablelands of New South Wales, Australia, extensive collections of sequestrate fungi were made, including numerous cortinarioid taxa. Historically any novel taxa would have been described in the cortinarioid sequestrate genera Descomyces, Hymenogaster, Protoglossum, Quadrispora, Thaxterogaster or Timgrovea based on broad morphological similarities of the sporocarps and spore ornamentation. However, consistent with other recent analyses of nuclear DNA regions, taxa from sequestrate genera were found to have affinities with Cortinarius and Descolea or Hebeloma, and to be scattered across many sections within Cortinarius. None of the historical sequestrate cortinarioid genera are monophyletic in our analyses. In particular, the gastroid genus Hymenogaster is paraphyletic, with one clade including two species of Protoglossum in Cortinarius, and a second clade sister to Hebeloma. Eight new species of sequestrate Cortinarius are described and illustrated, and discussion of their affinities with various sections provided: C. argyronius, C. caesibulga and C. cinereoroseolus in section Purpurascentes, C. maculobulga in section Rozites, C. sinapivelus in section Splendidi, C. kaputarensis in a mixed section Phlegmacium/Myxacium within a broader section Dermocybe, C. basorapulus in section Percomes and C. nebulobrunneus in section Pseudotriumphantes. Keys to genera of the Bolbitiaceae and Cortinariaceae containing sequestrate taxa and to currently known Australian species of sequestrate Cortinarius and Protoglossum are provided. As with the related agaricoid taxa, macroscopic characters such as colour and texture of basidioma, degree of loculisation of the hymenophore, and stipe-columella development and form remain useful for distinguishing species, but are generally not so useful at the sectional level within Cortinarius. Microscopic characters such as spore shape, size, and ornamentation, and pileipellis structure (simplex vs duplex and size of hyphal elements) are essential for determining species, and also appear to follow sectional boundaries.
Baobab tree (A. digitata) in the northern Kruger National Park damaged by elephants.
a–d. Graphium adansoniae. a. A 14 d old culture on MEA; b. synnema; c. conidia; d. annellidic conidiogenesis, SEM. — e – h. Graphium madagascariense . e. A 14 d old culture on MEA; f. synnema; g. conidia; h. annellidic conidiogenesis, SEM. — i – l Graphium fabiforme. i. A 14 d old culture on MEA; j. synnema; k. conidia; l. annellidic conidiogenesis, SEM (a – d: CMW 30618, Group A; e – h: CMW 30628, Group B; i – l, CMW 30626; Group C). — Scale bars: b, f, j = 50 μm; in c, d, g, h, k, l = 10 μm.  
Baobabs (Adansonia spp.) are iconic trees, known for their immense size, strange forms, sources of food and as the subjects of myths and mysteries. It is thus surprising that little is known regarding the fungi that infect these trees. During a survey to determine which wound infecting fungi occur on baobabs, synnematous structures were observed and Graphium-like isolates were obtained. Culture characteristics and micro-morphology, together with DNA sequence comparisons for the SSU rRNA, rRNA-ITS and TEF-1α gene regions were used to characterise these fungi. These data revealed three novel Graphium spp. and these are described as G. adansoniae, G. madagascariense and G. fabiforme.
One of four trees resulting from parsimony analysis of Thecaphora and closely related species, based on sequence data from the large subunit rDNA region. Thickened black lines indicate groups with strong support in all analysis (parsimony bootstrap > 80; Bayesian posterior probability > 0.95; Maximum likelihood bootstrap > 80). Thickened grey lines indicate groups with strong support using model based methods and moderate support for parsimony analysis (parsimony bootstrap between 70 and 80).  
Light and electron micrographs of Thecaphora capensis and T. oxalidis on Oxalis sp. a. Healthy O. lanata var. rosea flower; b. Oxalis lanata flower showing mass of T. capensis teliospores replacing pollen in anthers; c. close-up of healthy anthers (petals removed); d. close-up of infected anthers (petals removed); e. light micrograph of T. capensis teliospores mounted in lactophenol; f, g. scanning electron micrographs of T. capensis teliospores; h. light micrograph of T. oxalidis teliospores mounted in lactophenol; i, j. scanning electron micrographs of T. oxalidis teliospores. — Scale bars = 10 µm.  
The smut genus Thecaphora contains plant parasitic microfungi that typically infect very specific plant organs. In this study, we describe a new species of Thecaphora from Oxalis lanata var. rosea (Oxalidaceae) in the Cape Floristic Region of South Africa. Molecular phylogenetic reconstructions based on large subunit ribosomal DNA sequence data confirmed the generic placement of the fungus and confirmed that it represents an undescribed species for which the name T. capensis sp. nov. is provided. The closest known sister species of the new taxon is T. oxalidis that infects the fruits of Oxalis spp. in Europe, Asia and the Americas. In contrast, T. capensis produces teliospores within the anthers of its host. This is the first documented case of an anther-smut from an African species of Oxalis and the first Thecaphora species described from Africa.
Three Leohumicola species growing from macerated inocula on PDA (left column), as three point inocula on PDA (middle column) and OA (right column), after 2 wk at room temperature. a – c. L. levissima HNLHM2; d – f. L. incrustata DAOM 239498; g – i. L. atra DAOM 239515. Reflections on the shiny agar surface from the middle column pictures were removed digitally. — Petri dish diam = 9 cm.  
Leohumicola incrustata. a, e. Aleurioconidial development; b – d, f – l. terminal cells of aleurioconidia are often incrusted with a brown slime or warts around the apex. Panels a – c, e, j = DAOM 239501; d, f–i, k, l = DAOM239502. The background of panel j was altered digitally for aesthetic reasons. — Scale bar = 5 µm.  
Leohumicola levissima. a. Aleurioconidial development, with younger aleurioconidia (left) and older aleurioconidia (right); b. laterial aleurioconidia; c. terminal aleurioconidium; d. laterial (left) and terminal (right) aleurioconidia; e. basal cell of aleurioconidium rupturing during secession; f. terminal chlamydospore ; g–i. intercalary chlamydospores; j. single-celled aleurioconidium; k. functionally single-celled aleurioconidum bearing the remnant of the basal cell. Panels a, d, e, k = DAOM239511; b, c, j = DAOM 239509; f – i = DAOM 239513. The background of panels a and c were altered digitally for aesthetic reasons. — Scale bar = 5 µm.  
Leohumicola atra. a. Sporulating part of colony on PDA; b. aleurioconidial development; c. single-celled aleurioconidium (left) and terminal aleurioconidium (right); d –f. mature aleurioconidia; g, h. lighter coloured aleurioconidia. All panels = DAOM 239515. — Scale bars: a = 50 µm, b – h = 5 µm. c  
Three new species of Leohumicola (anamorphic Leotiomycetes) are described using morphological characters and phylogenetic analyses of DNA barcodes. Leohumicola levissima and L. atra were isolated from soils collected after forest fires in Crater Lake National Park, United States. Leohumicola incrustata was isolated from burned fynbos from the Cape of Good Hope Nature Reserve, South Africa. The three species exhibit characteristic Leohumicola morphology but are morphologically distinct based on conidial characters. Two DNA barcode regions, the Internal Transcribed Spacer (ITS) nuclear rDNA region and the cytochrome oxidase subunit I (Cox1) mitochondrial gene, were sequenced. Single-gene parsimony, dual-gene parsimony and dual-gene Bayesian inference phylogenetic analyses support L. levissima, L. atra, L. incrustata as distinct phylogenetic species. Both ITS and Cox1 barcodes are effective for the molecular identification of Leohumicola species.
Species from Entoloma subg. Entoloma are commonly recorded from both the Northern and Southern Hemispheres and, according to literature, most of them have at least Nearctic-Palearctic distributions. However, these records are based on morphological analysis, and studies relating morphology, molecular data and geographical distribution have not been reported. In this study, we used phylogenetic species recognition criteria through gene genealogical concordance (based on nuclear ITS, LSU, rpb2 and mitochondrial SSU) to answer specific questions considering species limits in Entoloma subg. Entoloma and their geographic distribution in Europe, North America and Australasia. The studied morphotaxa belong to sect. Entoloma, namely species like the notorious poisonous E. sinuatum (E. lividum auct.), E. prunuloides (type-species of sect. Entoloma), E. nitidum and the red-listed E. bloxamii. With a few exceptions, our results reveal strong phylogeographical partitions that were previously not known. For example, no collection from Australasia proved to be conspecific with the Northern Hemisphere specimens. Almost all North American collections represent distinct and sister taxa to the European ones. And even within Europe, new lineages were uncovered for the red-listed E. bloxamii, which were previously unknown due to a broad morphological species concept. Our results clearly demonstrate the power of the phylogenetic species concept to reveal evolutionary units, to redefine the morphological limits of the species addressed and to provide insights into the evolutionary history of key morphological characters for Entoloma systematics. New taxa are described, and new combinations are made, including E. fumosobrunneum, E. pseudoprunuloides, E. ochreoprunuloides and E. caesiolamellatum. Epitypes are selected for E. prunuloides and E. bloxamii. In addition, complete descriptions are given of some other taxa used in this study for which modern descriptions are lacking, viz. E. subsinuatum, E. whiteae, E. flavifolium, E. luridum, E. bloxamii, E. madidum, E. corneri, E. callidermum and E. coeruleoviride.
Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports their identity, mating type, and pathogenicity to young Agathosma plants. Using morphological and sequence data seven Phytophthora taxa were identified: the A1 mating type of P. cinnamomi var. cinnamomi, P. cinnamomi var. parvispora and P. cryptogea, the A2 mating type of P. drechsleri and P. nicotianae, and two homothallic taxa from the P. citricola complex. The identity of isolates in the P. citricola complex was resolved using reference isolates of P. citricola CIT groups 1 to 5 sensu Oudemans et al. (1994) along with multi-locus phylogenies (three nuclear and two mitochondrial regions), isozyme analyses, morphological characteristics and temperature-growth studies. These analyses revealed the isolates from Agathosma to include P. multivora and a putative novel species, P. taxon emzansi. Furthermore, among the P. citricola reference isolates the presence of a new species was revealed, described here as P. capensis. Findings of our study, along with some recent other studies, have contributed to resolving some of the species complexity within the P. citricola complex, resulting in the identification of a number of phylogenetically distinct taxa. The pathogenicity of representative isolates of the taxa from Agathosma was tested on A. betulina seedlings. The putative novel species, P. taxon emzansi, and P. cinnamomi var. parvispora were non-pathogenic, whereas the other species were pathogenic to this host.
Phylogeny of Mucor irregularis obtained from a Neighbour-Joining analysis of Internal Transcribed Spacer (ITS) using Mega 5 software. Bootstrap support values were estimated based on 500 replicates, and are shown by the numbers near the branches (Neighbour-Joining bootstrap values / Bayesian posterior probabilities, boldface branch for values ≥ 80). Strains forming well-supported subgroups are marked in colour. Three Mucor species were taken as outgroup. Species names are given only for ex-type strains. Geographic origins of isolates are given with strain numbers. T = ex-type strain; NT = ex-neotype strain; = strains from clinical samples; = isolates from soil; = isolates from plants; = isolates from animals or animal excretion.
Neighbour-Joining phylograms of 21 isolates of Mucor irregularis based on four different markers: a. LSU; b. RPB1; c. RPB2; d. multilocus, combining sequences of LSU, ITS, RPB1 and RPB2 by Mega 5 software. Branches with bootstrap values, estimated based on 500 replicates in the Neighbour-Joining analysis, are printed in bold when 70 or higher. Branch support values are indicated by the numbers near the branches (Neighbour-Joining bootstrap values / Bayesian posterior probabilities). Group colours used in four phylograms per strain are the same as in the ITS phylogram. CBS 243.35 and CBS 201.65 were taken as outgroup. T = ex-type strain; NT = ex-neotype strain. 
Dendrogram of amplified fragment length polymorphism (AFLP) profiles of 21 Mucor irregularis isolates. Mucor hiemalis (CBS 201.65) and Mucor luteus (CBS 243.35) are taken as outgroup. The scale bar on the top indicates the percentage similarity. Strain colours: blue = ITS subgroup 1; green = ITS subgroup 2; yellow = ITS subgroup 3; red = ITS subgroup 4; ochre = ITS subgroup 5. 
Mucormycosis usually presents as a progressive infection with significant angio-invasion. Mucormycosis due to Mucor irregularis (formerly Rhizomucor variabilis var. variabilis), however, is exceptional in causing chronic cutaneous infection in immunocompetent humans, ultimately leading to severe morbidity if left untreated. More than 90 % of the cases known to date were reported from Asia, mainly from China. The nearest neighbour of M. irregularis is the saprobic species M. hiemalis. The aim of this study was to evaluate the taxonomic position, epidemiology, and intra- and inter-species diversity of M. irregularis based on 21 strains (clinical n = 17) by multilocus analysis using ITS, LSU, RPB1 and RPB2 genes, compared to results of cluster analysis with amplified fragment length polymorphism (AFLP) data. By combining MLST and AFLP analyses, M. irregularis was found to be monophyletic with high bootstrap support, and consisted of five subgroups, which were not concordant in all partitions. It was thus confirmed that M. irregularis is a single species at 96.1-100 % ITS similarity and low recombination rates between populations. Some geographic structuring was noted with some localised populations, which may be explained by limited air-dispersal. The natural habitat of the species is likely to be in soil and decomposing plant material.
Bayesian inference tree using rDNA ITS sequences showing phylogenetic relationships between (A) clade 2 species and representative species from other clades and (B) isolates from the P. citricola complex. Numbers above branches represent posterior probability based on Bayesian analysis of the dataset. Both trees result from a single analysis as given in TreeBASE (SN4153). For tree A, clades were collapsed to show the relationship between isolates from P. citricola complex and other species in clade 2. Tree B shows the finer details within the P. citricola complex (node enclosed in circle on tree A) and the relationship between P. multivora and other P. citricola and P. 'inflata' isolates including the ex-type of P. citricola (IMI 021173).  
Bayesian inference tree using sequences of mitochondrial gene cox1 showing phylogenetic relationships between P. multivora and P. citricola, including the ex-type of P. citricola (IMI 021173).  
Semipapillate sporangia of Phytophthora multivora on V8 agar. — a–i after 12 –24 h flooding with soil extract. a. Ovoid, the left sporangium with swollen papilla shortly before release of the already differentiated zoospores; b. ovoid; c. limoniform; d. obpyriform; e. bipapillate; f. bipapillate, bilobed; g. limoniform, laterally inserted to the sporangiophore (arrow); h. ovoid, shortly before release of zoospores; i. limoniform, intercalary inserted, with conspicuous basal plug (arrow) protruding into empty sporangium after release of zoospores. — j – l direct germination after 48 h flooding. j. Bipapillate, bilobed with several germ tubes growing from each papilla; k, l. bipapillate, bell-shaped with one germ tube growing from each papilla. — Scale bar = 50 µm, applies to a – l.  
a–d. Oogonia of Phytophthora multivora with paragynous antheridia and plerotic oospores on V8 agar. a. Juvenile oogonium with thin-walled oospore and undifferentiated cytoplasm; b–d. mature oogonia with thick-walled oospores and ooplast; b. oogonium on the left side is aborted; e. direct germination of oospores with several germtubes through the oogonial bases (arrow) after 5 wk incubation at 20 °C; f. tubular, irregular lateral hyphae. — Scale bars = 25 µm.  
Colony morphology of isolates WAC13201 (ex-type) and WAC13205 of Phytophthora multivora, and the ex-type isolate of P. citricola (from top to bottom ) after 6 d growth at 20 °C on V8 agar, malt extract agar, cornmeal agar and potato-dextrose agar (from left to right).  
A new Phytophthora species, isolated from rhizosphere soil of declining or dead trees of Eucalyptus gomphocephala, E. marginata, Agonis flexuosa, and another 13 plant species, and from fine roots of E. marginata and collar lesions of Banksia attenuata in Western Australia, is described as Phytophthora multivora sp. nov. It is homothallic and produces semipapillate sporangia, smooth-walled oogonia containing thick-walled oospores, and paragynous antheridia. Although morphologically similar to P. citricola, phylogenetic analyses of the ITS and cox1 gene regions demonstrate that P. multivora is unique. Phytophthora multivora is pathogenic to bark and cambium of E. gomphocephala and E. marginata and is believed to be involved in the decline syndrome of both eucalypt species within the tuart woodland in south-west Western Australia.
Phylogenetic tree inferred from Minimum Evolution analysis based on concatenated ITS and cox2 sequences. Numbers above branches indicate the respective support in ME, MP and ML analyses. A. = Albugo, I. = Ipomoea, W. = Wilsoniana. Numbers preceding taxon names correspond to the numbers given in Table 1. 
Morphological characteristics of Albugo species on Arabidopsis thaliana. a-f. New species discovered on Arabidopsis thaliana; g, h. Albugo candida on Arabidopsis thaliana.-a. Sporogenous hyphae; b. primary sporangia; c. secondary sporangia; d. haustorium; e, g. surface ornamentation of oospores; f, h. protuberances (arrows) as seen in lateral view.-Scale bars: a-c = 20 µm, d = 10 µm, e-h = 50 µm. Sources: a-f (DAR 73071), g, h (BP 75214). 
The obligate biotrophic lineages of the white blister rusts (Albuginales, Oomycota) are of ancient origin compared to the rather recently evolved downy mildews, and sophisticated mechanisms of biotrophy and a high degree of adaptation diversity are to be expected in these organisms. Speciation in the biotrophic Oomycetes is usually thought to be the consequence of host adaptation or geographic isolation. Here we report the presence of two distinct species of Albugo on the model plant Arabidopsis thaliana, Albugo candida and Albugo laibachii, the latter being formally described in this manuscript. Both species may occupy the same host within the same environment, but are nevertheless phylogenetically distinct, as inferred from analyses of both mitochondrial and nuclear DNA sequences. Different ways of adapting to their host physiology might constitute an important factor of their different niches. Evidence for this can be gained from the completely different host range of the two pathogens. While Albugo candida is a generalist species, consisting of several physiological varieties, which is able to parasitize a great variety of Brassicaceae, Albugo laibachii has not been found on any host other than Arabidopsis thaliana. Therefore, Albugo laibachii belongs to a group of highly specialised species, like the other known specialist species in Albugo s.s., Albugo koreana, Albugo lepidii and Albugo voglmayrii. The comparative investigation of the effector genes and host targets in the generalist and the specialist species may constitute a model system for elucidating the fundamental processes involved in plant pathogen co-adaptation and speciation.
Strains of Sodiomyces alkalinus (former Heleococcum alkalinum) used in the study. Locations, characteristics of soil samples and isolation date are indicated.
Position of Sodiomyces alkalinus strains within Plectosphaerellaceae family. Bayesian 50 % majority-rule consensus tree based on two-locus phylogenetic analysis (ITS+LSU). Thickened branches indicate ML > 90 and BI posterior probability (PP) > 0.95.
Growth rate on different carbon sources of Sodiomyces alkalinus (CBS 110278).
Sodiomyces alkalinus (CBS 110278). a. Ten-day-old colony on alkaline agar (9 cm Petri dish); b. young conidial head on monophialide (cryoSEM); c. matured conidial head on (branched) monophialide (cryoSEM); d. colony overview (LM); e. acremonium-like conidial heads (SEM); f. conidia (SEM); g. cleistothecia; h. hyphal cords (SEM); i. colony overview on alkaline agar (SEM); j. open cleistothecium, surrounded by conidia, at the arrowhead a two- celled ascospore; k. multilayered exoperidium of ascoma (SEM); l. two-celled ascospore (LM). — Scale bars: b = 4 μm; c = 5 μm; d, i = 100 μm; e = 10 μm; f, l = 3 μm; g = 50 μm; h, k = 30 μm; j = 15 μm 
In this study we reassess the taxonomic reference of the previously described holomorphic alkaliphilic fungus Heleococcum alkalinum isolated from soda soils in Russia, Mongolia and Tanzania. We show that it is not an actual member of the genus Heleococcum (order Hypocreales) as stated before and should, therefore, be excluded from it and renamed. Multi-locus gene phylogeny analyses (based on nuclear ITS, 5.8S rDNA, 28S rDNA, 18S rDNA, RPB2 and TEF1-alpha) have displayed this fungus as a new taxon at the genus level within the family Plectosphaerellaceae, Hypocreomycetidae, Ascomycota. The reference species of actual Heleococcum members showed clear divergence from the strongly supported Heleococcum alkalinum position within the Plectosphaerellaceae, sister to the family Glomerellaceae. Eighteen strains isolated from soda lakes around the world show remarkable genetic similarity promoting speculations on their possible evolution in harsh alkaline environments. We established the pH growth optimum of this alkaliphilic fungus at c. pH 10 and tested growth on 30 carbon sources at pH 7 and 10. The new genus and species, Sodiomyces alkalinus gen. nov. comb. nov., is the second holomorphic fungus known within the family, the first one being Plectosphaerella - some members of this genus are known to be alkalitolerant. We propose the Plectosphaerellaceae family to be the source of alkaliphilic filamentous fungi as also the species known as Acremonium alcalophilum belongs to this group.
Amniculicola immersa (from holotype). a. Ascomata on host surface; b. habit section of ascomata. Note the purple colour in the ascomata and substrate; c. asci in pseudoparaphyses; d, e. ascospores with sheath; f. ascus; g. dehiscent ascus. c, e–g in water; d in Indian ink. — Scale bars: a = 0.5 mm; b = 200 μm; c–g = 20 μm.
a–c. Amniculicola immersa (from holotype). a. Section of ascoma. Note the thick apical wall; b. section of ascoma. Note the purple colour in the ascomata and substrate; c. section of ascoma. Note the peridium structure. — d, e. Amniculicola parva (from holotype). d. Section of ascoma; e. section of the peridium near base. Note the tubercule. — Scale bars: a, b = 0.1 mm; c–e = 50 μm.
Amniculicola parva (from holotype). a, b. Ascomata on host surface. Note the purple substrate; c. habit section of ascoma; d. ascospores with sheath; e. asci in thin anastomosing pseudoparaphyses; f. ascus. d in Indian ink; e in cotton blue; f in water. — Scale bars: a = 0.5 mm; b, c = 0.1 mm; d–f = 10 μm.
Maximum parsimony tree generated from partial 28S rDNA and with gaps as missing data. Designated outgroup is Diaporthe phaseolorum (AY346279). Bootstrap support values above 50 % (based on 1 000 replicates) are shown on nodes, and those lower than 50 % are marked as *. Newly generated sequences are marked as * on the right top corner of the GenBank accession numbers.
a. Massariosphaeria typhicola (from IFRD 2018). a. Asci in pseudoparaphyses. — b, c, d. Pleospora rubicunda (from IFRD 2017). b. Ascus; c. ascomata on the host surface; d. ascospore with wide sheath. a, b in water; d in Indian ink. — Scale bars: a, b, d = 20 μm; c = 0.5 mm.
Two new species of Amniculicola, A. immersa sp. nov. and A. parva sp. nov. from submerged wood in a freshwater environment in Denmark and France are respectively described and illustrated. In addition, partial 28S rDNA sequence data is analysed to investigate their phylogenetic relationships with other pleosporalean taxa. All presently known Amniculicola species, A. immersa, A. lignicola and A. parva, form a robust clade together with the anamorphic species Anguillospora longissima, Spirosphaera cupreorufescens and Repetophragma ontariense. These six species, which are all from freshwater and mostly from Europe, constitute a well-supported group containing Pleospora rubicunda and Massariosphaeria typhicola. This putative monophyletic assemblage may represent an aquatic group in the Pleosporales. It is also pertinent that all five ascomycete taxa in this group stain their host substrates purple.
Disease symptoms on almond trees on the island of Mallorca associated with fungal trunk pathogens. a, b. Dieback and wilting of branches; c – h. internal symptoms visible when transversal and longitudinal cuts were made in branches used for fungal isolation: black spots and dark brown to black streaking of the xylem tissue (d, h), circular (c, g) or sectorial necrosis (f), and wood discoloration (e).  
One of two most parsimonious trees obtained from heuristic searches of ITS, GAPDH and EF-1α gene sequences of Collophora species. Bootstrap support (1 000 replicates) above 70 % are shown at the nodes. Cadophora luteo-olivacea CBS 141.41 was used as outgroup. Ex-type strains for each species are indicated with a 'T' after the strain number.  
Names, accession numbers, and collection details of isolates studied. 
Collophora hispanica. a. Colony on MEA that is stained red by the pigment exuded by the fungus; b. conidioma on pine needle; c – h. conidiogenous cells and conidia on hyphal cells; i, j. conidiophores formed in conidiomata on pine needles; k, l. microcyclic conidiation (indicated by arrows) in conidia from conidiomata (k) and from hyphal cells (l); m. conidia formed in conidiomata after 4 wk; n, o. endoconidia; p, q. conidia formed on hyphal cells after 4 wk; r. conidia formed on hyphal cells after 2 wk. a, b: DIC, c – r: DM. — Scale bars: a = 1 mm; b = 100 µm; c = 5 µm; scale bar for c applies to c – r.  
Phaeoacremonium amygdalinum. a – c. Sixteen-day-old colonies incubated at 25 °C on MEA (a), PDA (b) and OA (c); d – j. aerial structures on MEA; d – f. conidiophores with polyphialides (indicated by arrows); g, h. type III phialides; i. type III and type II phialides (indicated by arrow); j. type I phialides; k – t. aerial structures by using slide culture technique; k – m. branched conidiophores and type I phialides (indicated by arrows); n – p. type II phialides; q. type I phialides; r–s. Microcyclic conidiation; t. conidia; u – w. structures on the surface of and in MEA; u – v. adelophialides with conidia; w. conidia. — Scale bars: d = 10 µm; scale bar for d applies to d – w.  
Severe decline of almond trees has recently been observed in several orchards on the island of Mallorca (Balearic Islands, western Mediterranean Sea). However, the identity of the causal agents has not yet been investigated. Between August 2008 and June 2010, wood samples from branches of almond trees showing internal necroses and brown to black vascular streaking were collected in the Llevant region on the island of Mallorca. Several fungal species were subsequently isolated from the margin between healthy and symptomatic tissue. Five species of Botryosphaeriaceae (namely Botryosphaeria dothidea, Diplodia olivarum, D. seriata, Neofusicoccum australe and N. parvum), Eutypa lata, Phaeoacremonium iranianum and Phomopsis amygdali were identified based on morphology, culture characteristics and DNA sequence comparisons. Neofusicoccum parvum was the dominant species, followed by E. lata, D. olivarum and N. australe. First reports from almond include D. olivarum and Pm. iranianum. Two species are newly described, namely Collophora hispanica sp. nov. and Phaeoacremonium amygdalinum sp. nov.
Bayesian 50 % majority rule consensus tree based on the ITS and LSU sequences of 61 strains. The Bayesian posterior probabilities (PP) of 0.95 and above are given at the nodes. Thickened lines indicate a PP of 1.0. The tree was rooted using Phoma herbarum (CBS 615.75). 
Alternariaster bidentis. a. Flowering healthy plants of Bidens sulphurea; b. leaves with leaf spot and necrosis; c. extensive blight; d-h. conidia attached to conidiogenous cells; i. spermogonium on SNA.-Scale bars = 10 µm, except i = 100 µm. 
Alternariaster helianthi. a. Helianthus annuus with leaf spot and necrosis; b-e. conidia; f-h. conidia attached to conidiogenous cells.-Scale bars = 10 µm. 
a, b. Alternariaster bidentis sp. nov. (CBS 134021) on Bidens sulphurea: a. Pathogenicity test evaluated at 14 d after inoculation (control left, inoculated right); b. detail of necrosis.-c. Alternariaster helianthi (CBS 134018) on Bidens sulphurea, no observed injury (control left, inoculated right).-d, e. Alternariaster helianthi (CBS 134018) on H. annuus: d. Pathogenicity test evaluated at 4 d after inoculation (control left, inoculated right); e. detail of necrosis.f. Alternariaster bidentis sp. nov. (CBS 134021) on H. annuus, no observed injury (control left, inoculated right). 
Alternariaster was erected in 2007 to accommodate Alternaria helianthi, a fungal species known to cause leaf spots on Helianthus annuus (sunflower). It was segregated from Alternaria based on conidial morphology. Recently an unknown alternaria-like dematiaceous fungus was found associated with leaf spots on Bidens sulphurea (yellow cosmos) in Brazil. Based on a multi-gene phylogeny of parts of the ITS and LSU genes, this fungus was placed within the Leptosphaeriaceae with Alternariaster helianthi as its closest neighbour. Additional genes sequenced, RPB2 and GAPDH, confirmed this close relationship. The fungus on B. sulphurea has smaller conidia, 50-97.5 × 12.5-20 μm, compared to Al. helianthi, 80-160 × 18-30 μm, and lacks oblique or transverse septa which can be present in Al. helianthi. Pathogenicity studies on 18 plant species belonging to the Compositae showed that the B. sulphurea fungus only infected B. sulphurea, whereas Al. helianthi infected H. annuus and Galinsoga quadriradiata, a yet unreported host of Al. helianthi. The fungus causing disease on B. sulphurea is hence closely related but phylogenetically, morphologically and pathologically distinct from Al. helianthi, and therefore newly described as Alternariaster bidentis. The collection of a second species in the genus Alternariaster and the multigene phylogenetic analysis of these two species, confirmed Alternariaster to be a well-delimited genus in the Leptosphaeriaceae rather than the Pleosporaceae, to which Alternaria belongs.
Two new species of Cladosporium found on necrotic needles of Pinus ponderosa trees in Patagonia, Argentina, are described as C. chubutense and C. pini-ponderosae. An additional isolate from dead leaves of Cortaderia collected in Colombia, which is a sister taxon to the species occurring on Pinus, is described as Cladosporium colombiae. These species are phylogenetically closely related, but differ from each other and other known species by multilocus sequence data, phenetic characters and culture characteristics.
Best tree from the Maximum Likelihood Analysis based on concatenated ITS and nrLSU sequences with bootstrap support values in Maximum Likelihood and Minimum Evolution analyses and Bayesian posterior probabilities in the respective order on the branches. Type species are underlined. 
Collection and strain details for the oomycete isolates investigated in this study. 
Photographs of colonies of: a-c. Halophytophthora s.str. and d-f. Salisapilia spp. isolates. a. LT6430; b. LT6465; c. H. vesicula CBS 152.96; d. S. tartarea CBS 208.95; e. S. sapeloensis LT6440; f. S. nakagirii LT6456. 
Summary of some morphological features for species of Salisapilia and Halophytophthora s.str. -NA = not available. 
Micrographs of Salisapilia. a-d. Micrographs of Salisapilia sapeloensis LT6440. a. Branching hyphae with septae; b. ripe sporangium, note plug of material at tip of discharge tube; c. maturing oospore with simple paragynous antheridum; d. two fertilised oospores (on the left, a lobed paragynous antheridium is seen, and on the right, a branching paragynous antheridium is present).-e-h. Micrographs of Salisapilia nakagirii LT6456. e. Branching hyphae with septations; f. oogonium with antheridial cell attached; g. maturing oospore with diclinous antheridum; h. two fertilised oospores.-i. Micrographs of hyphae of Salisapilia sp. LT6471.-Scale bars: a, e, i = 10 µm; b-d, f-h = 40 µm. 
Several filamentous oomycete species of the genus Halophytophthora have recently been described from marine environments, mostly from subtropical and tropical ecosystems. During a survey of oomycetes from leaf litter of Spartina alterniflora in salt marshes of southeastern Georgia, isolates of four taxa were recovered that bore similarity to some members of Halophytophthora but were highly divergent from isolates of Halophytophthora s.str. based on a combined sequence analysis of two nuclear loci. In phylogenetic analyses, these isolates were placed basal to a monophyletic group comprised of Pythium of the Pythiaceae and the Peronosporaceae. Sequence and morphology of these taxa diverged from the type species Halophytophthora vesicula, which was placed within the Peronosporaceae with maximum support. As a consequence a new family, the Salisapiliaceae, and a new genus, Salisapilia, are described to accommodate the newly discovered species, along with one species previously classified within Halophytophthora. Morphological features that separate these taxa from Halophytophthora are a smaller hyphal diameter, oospore production, lack of vesicle formation during sporulation, and a plug of hyaline material at the sporangial apex that is displaced during zoospore release. Our findings offer a first glance at the presumably much higher diversity of oomycetes in estuarine environments, of which ecological significance requires further exploration.
a. Upper crown of a mature declining beech (Fagus sylvatica) with high transparency, brush-and claw-like structures and severe dieback of branches due to extensive fine root losses; b. crown of a mature declining oak (Quercus robur) with high transparency, formation of leaf clusters and dieback of branches due to extensive fine root losses; c. small woody root (diam 2-3 mm) of a declining mature beech with severe losses of lateral roots and fine roots caused by P. plurivora; d. small woody roots (diam 2-3 mm) of a declining mature oak with severe losses of lateral roots and fine roots caused by P. plurivora; e. collar rot of mature beech caused by P. plurivora with tarry spots on the outer bark; f. stem of declining mature beech in a mountain forest in Bavaria with a series of isolated aerial cankers caused by P. plurivora; g. leaf necrosis and shoot dieback of Rhododendron sp. caused by P. plurivora. 
One of 16 most parsimonious trees of 200 steps based on analysis of mitochondrial gene cox1 sequence, showing phylogenetic relationships within the P. citricola complex. Numbers above branches in bold represent posterior probability based on Bayesian analysis of the dataset, numbers in italics represent bootstrap support for the nodes. Different colour boxes are used to differentiate the species recognised in the P. citricola complex. 
Semipapillate sporangia of Phytophthora plurivora on V8 agar flooded with soil extract: a-i after 24-36 h flooding. a. Ovoid, the cytoplasm differentiating into zoospores; b. laterally inserted mature sporangium with markedly curved apex, and dense sympodium of empty ovoid sporangia with conspicuous basal plugs; c. mature sporangium with markedly curved apex, and empty limoniform sporangium; d. limoniform with tapering base and conspicuous basal plug; e. limoniform, in the background small hyphal swelling on a sporangiophore; f. obpyriform; g. ovoid, intercalary inserted; h. bipapillate; i. bilobed; limoniform; j. young growing sporangium and bipapillate mature sporangium shortly before release of the zoospores; k. ovoid sporangium with conspicuous basal plug releasing zoospores and proliferating externally; l. bipapillate sporangium germinating directly through both papillae after 48 h flooding with soil extract.-Scale bar = 50 µm, applies to a-l. 
Morphological structures of Phytophthora plurivora formed on solid V8 agar. a-g. Mature oogonia with oospores containing ooplasts: a. oogonium with slightly aplerotic oospore and paragynous antheridium; b. oogonium with plerotic golden-brown oospore and paragynous antheridium; c. oogonium with slightly aplerotic golden-brown oospore and paragynous antheridium with finger-like hyphal projections; d. oogonium with plerotic golden-brown oospore and multiple paragynous antheridia; e. elongated oogonia with long tapering bases and plerotic oospores; f. oogonium with markedly aplerotic oospore and paragynous antheridium with finger-like hyphal projections; g. oogonium with markedly aplerotic oospore and amphigynous antheridium; h. hyphal swellings on the underside of a six weeks old culture; i. brush-like dense clusters of lateral hyphae on the underside of a 6 wk old culture.-Scale bar = 25 µm, applies to all. 
Colony morphology of isolates CBS 124093 (ex-type) and CBS 124091 of Phytophthora plurivora, CIT-US10 of P. citricola I, the ex-type (CBS 221.88) and the authentic type isolate (CBS 295.29) of P. citricola s.str. and the ex-type isolate of P. multivora (CBS 124094) after 7 d growth at 20 °C on V8 agar, malt extract agar and potato-dextrose agar (from top to bottom). 
During large-scale surveys for soilborne Phytophthora species in forests and semi-natural stands and nurseries in Europe during the last decade, homothallic Phytophthora isolates with paragynous antheridia, semipapillate persistent sporangia and a growth optimum around 25 degrees C which did not form catenulate hyphal swellings, were recovered from 39 host species in 16 families. Based on their morphological and physiological characters and the similarity of their ITS DNA sequences with P. citricola as designated on GenBank, these isolates were routinely identified as P. citricola. In this study DNA sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and 5.8S gene of the rRNA operon, the mitochondrial cox1 and beta-tubulin genes were used in combination with morphological and physiological characteristics to characterise these isolates and compare them to the ex-type and the authentic type isolates of P. citricola, and two other taxa of the P. citricola complex, P. citricola I and the recently described P. multivora. Due to their unique combination of morphological, physiological and molecular characters these semipapillate homothallic isolates are described here as a new species, P. plurivora sp. nov.
The genus Vermisporium presently accommodates 13 species, 11 of which are associated with leaf spots of eucalypts in the Southern Hemisphere. Vermisporium is chiefly distinguished from Seimatosporium (Amphisphaeriaceae) on the basis of a short exogenous basal appendage, and the absence of a recognisable apical appendage. Due to the increasing importance of these species in native forests, and confusion pertaining to their taxonomy, a revision of the genus was undertaken based on fresh collections and dried herbarium specimens. Results from DNA sequence data analyses of the nrDNA-ITS and 28S nrRNA genes for species of Vermisporium indicated the genus to be a synonym of Seimatosporium. New combinations are introduced in Seimatosporium for several species: S. acutum, S. biseptatum, S. brevicentrum, S. obtusum, S. orbiculare, S. verrucisporum and S. walkeri. An updated key to all species occurring on eucalypts is also provided.
Phylogenetic tree generated from parsimony analysis based on 28S rDNA sequences. Data were analysed with random addition sequence, and treating gaps as missing data. Bootstrap values ≥ 50 % are shown above or below branches. Thickened branches indicate Bayesian posterior probabilities ≥ 95 %. The tree is rooted with Aniptodera chesapeakensis.
Phylogenetic tree generated from parsimony analysis based on ITS rDNA sequences. Data were analysed with random addition sequence and treating gaps as missing data. Bootstrap values ≥ 50 % are shown above or below branches. Thickened branches indicate Bayesian posterior probabilities ≥ 95 %. The tree is rooted with Botryosphaeria corticis.
Cheirosporium triseriale. a. Sporodochial conidiomata on the host surface; b. squash mount of the conidiophores and conidia; c, d. conidiophores bearing conidia (note numerous sterile apices of the conidiophores); e, f. individual conidiophores. Note the sterile branches; g–j. conidia. — Scale bars: a = 200 μm, b = 40 μm, c–j = 20 μm.
Cheirosporium gen. nov. is characterised by the production of sporodochial conidiomata, semi-macronematous to macronematous conidiophores that possess several distinct sterile branches, and cheiroid, smooth-walled conidia with rhexolytic secession. The 28S rDNA and ITS rDNA operon of this taxon were amplified and sequenced. A BLAST search revealed low homology between Cheirosporium triseriale and existing sequences in public databases, supporting the hypothesis that the species is new to science. Phylogenetic analysis showed that C. triseriale groups with Dictyosporium and allied species, and nests within the Pleosporales (Dothideomycetes, Ascomycota). Cheirosporium is morphologically distinct from the cheirosporous genera Cheiromyces, Cheiromycina, Dictyosporium, Digitomyces, Digitodesmium and Pseudodictyosporium and these differences are discussed.
Species of Mycosphaerella and their related anamorphs represent potentially serious foliar pathogens of Eucalyptus. The fungi treated in the present study were isolated from symptomatic Eucalyptus leaves collected in Thailand during June-October 2007. Species were initially identified based on morphological and cultural characteristics. Identifications were confirmed using comparisons of DNA sequence data of the internal transcribed spacers (ITS1, 5.8S nrDNA, ITS2) and the 28S nrDNA (LSU) regions. To help distinguish species of Pseudocercospora, the dataset was expanded by generating partial sequences of the translation elongation factor 1-alpha and actin genes. By integrating the morphological and molecular datasets, five new taxa were distinguished, namely Mycosphaerella irregulari, M. pseudomarksii, M. quasiparkii, Penidiella eucalypti and Pseudocercospora chiangmaiensis, while M. vietnamensis represents a new record for Thailand.
The core species of the family Planistromellaceae are included in the teleomorphic genera Planistroma and Planistromella and the connected anamorphic, coelomycetous genera Alpakesa, Kellermania, and Piptarthron. These genera have been defined primarily on the basis of ascospore septation or number of conidial appendages. Due to a lack of DNA sequence data, phylogenetic placement of these genera within the Dothideomycetes, evaluation of monophyly, and questions about generic boundaries could not be adequately addressed in the past. Isolates of nearly all of the known species in these genera were studied genetically and morphologically. DNA sequence data were generated for the nSSU, ITS, nLSU, and RPB1 markers and analysed phylogenetically. These results placed the Planistromellaceae, herein recognised as a distinct family, in an unresolved position relative to other genera within the order Botryosphaeriales. Species representing the core genera of the Planistromellaceae formed a clade and evaluation of its topology revealed that previous morphology-based definitions of genera resulted in an artificial classification system. Alpakesa, Kellermania, Piptarthron, Planistroma, and Planistromella are herein recognised as belonging to the single genus Kellermania. The following new combinations are proposed: Kellermania crassispora, K. dasylirionis, K. macrospora, K. plurilocularis, and K. unilocularis. Five new species are described, namely K. con- fusa, K. dasylirionicola, K. micranthae, K. ramaleyae, and K. rostratae. Descriptions of species in vitro and a key to species known from culture are provided.
Byssochlamys and related Paecilomyces strains are often heat resistant and may produce mycotoxins in contaminated pasteurised foodstuffs. A comparative study of all Byssochlamys species was carried out using a polyphasic approach to find characters that differentiate species and to establish accurate data on potential mycotoxin production by each species. Phylogenetic analysis of the ITS region, parts of the beta-tubulin and calmodulin genes, macro- and micromorphological examinations and analysis of extrolite profiles were applied. Phylogenetic analyses revealed that the genus Byssochlamys includes nine species, five of which form a teleomorph, i.e. B. fulva, B. lagunculariae, B. nivea, B. spectabilis and B. zollerniae, while four are asexual, namely P. brunneolus, P. divaricatus, P. formosus and P. saturatus. Among these, B. nivea produces the mycotoxins patulin and byssochlamic acid and the immunosuppressant mycophenolic acid. Byssochlamys lagunculariae produces byssochlamic acid and mycophenolic acid and thus chemically resembles B. nivea. Some strains of P. saturatus produce patulin and brefeldin A, while B. spectabilis (anamorph P. variotii s.s.) produces viriditoxin. Some micro- and macromorphological characters are valuable for identification purposes, including the shape and size of conidia and ascospores, presence and ornamentation of chlamydospores, growth rates on MEA and CYA and acid production on CREA. A dichotomous key is provided for species identification based on phenotypical characters.
Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.
The majority of mesophilic waterborne species of the black yeast genus Exophiala (Chaetothyriales) belong to a single clade judging from SSU rDNA data. Most taxa are also found to cause cutaneous or disseminated infections in cold-blooded, water animals, occasionally reaching epidemic proportions. Hosts are mainly fish, frogs, toads, turtles or crabs, all sharing smooth, moist or mucous skins and waterborne or amphibian lifestyles; occasionally superficial infections in humans are noted. Cold-blooded animals with strictly terrestrial life styles, such as reptiles and birds are missing. It is concluded that animals with moist skins, i.e. those being waterborne and those possessing sweat glands, are more susceptible to black yeast infection. Melanin and the ability to assimilate alkylbenzenes are purported general virulence factors. Thermotolerance influences the choice of host. Exophiala species in ocean water mostly have maximum growth temperatures below 30 °C, whereas those able to grow until 33(-36) °C are found in shallow waters and occasionally on humans. Tissue responses vary with the phylogenetic position of the host, the lower animals showing poor granulome formation. Species circumscriptions have been determined by multilocus analyses involving partial ITS, TEF1, BT2 and ACT1.
Phylogenetic tree resulting from the alignment of 350 characters of the TEF-1α region. The phylogenetic tree was inferred using the Maximum Likelihood method based on the Hasegawa-Kishino-Yano model. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1 000 replicates) are shown next to the branches. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1.7408)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Species described in this work are highlighted. Ex-type cultures are in bold.  
Diaporthe gulyae (ex-type BRIP 54025). a. Cultures on PDA (left), OA (right) after 7 d (top) and 28 d (bottom); b. pycnidial beaks on sterilised wheat straw; c. alpha conidia; d. conidia and conidiophores. — Scale bars: b = 100 µm; c, d = 10 µm.  
Diaporthe kongii (ex-type BRIP 54031) and D. kochmanii (ex-type BRIP 54033). a. Diaporthe kongii cultures on PDA (left), OA (right) after 7 d (top) and 28 d (bottom); b. Diaporthe kochmanii cultures on PDA (left), OA (right) after 7 d (top) and 28 d (bottom); c. pycnidial beaks of D. kongii on sterilised wheat straw; d. perithecial necks of D. kochmanii on sterilised wheat straw; e. alpha and beta conidia of D. kongii; f. alpha and beta conidia of D. kochmanii; g. beta conidia of D. kochmanii; h. asci and ascospores of D. kochmanii. — Scale bars: c, d = 1 mm; e– h = 10 µm.  
The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are believed to represent novel species. Diaporthe gulyae sp. nov. is described for isolates that caused a severe stem canker, specifically pale brown to dark brown, irregularly shaped lesions centred at the stem nodes with pith deterioration and mid-stem lodging. This pathogenicity of D. gulyae was confirmed by satisfying Koch's Postulates. These symptoms are almost identical to those of sunflower stem canker caused by D. helianthi that can cause yield reductions of up to 40 % in Europe and the USA, although it has not been found in Australia. We show that there has been broad misapplication of the name D. helianthi to many isolates of Diaporthe (Phomopsis) found causing, or associated with, stem cankers on sunflower. In GenBank, a number of isolates had been identified as D. helianthi, which were accommodated in several clades by molecular phylogenetic analysis. Two less damaging species, D. kochmanii sp. nov. and D. kongii sp. nov., are also described from cankers on sunflower in Australia.
The genus The genus Dinemasporium is used as a case study to evaluate the importance of conidial appendages for generic level classification of coelomycetous fungi. Based on morphology and sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers and 5.8S rRNA gene of the nrDNA operon, the genus Dinemasporium is circumscribed, and an epitype designated for D. strigosum, the type of the genus. A further five species are introduced in Dinemasporium, namely D. pseudostrigosum (isolated from Triticum aestivum, Germany and Stigmaphyllon sagraeanum, Cuba), D. americana (soil, USA), D. polygonum (Polygonum sachalinense, Netherlands), D. pseudoindicum (soil, USA), and D. morbidum (human sputum, Netherlands and hare dung, New Zealand). Brunneodinemasporium, based on B. brasiliense, is introduced to accommodate Dinemasporium-like species with tightly aggregated brown conidiogenous cells, and pale brown conidia. Dendrophoma (= Amphitiarospora) is reinstated as distinct from Dinemasporium, and an epitype designated for D. cytisporoides, characterised by its superficial, stipitate to cupulate conidiomata, and small conidia with two polar, tubular, exogenous appendages. The genus Stauronema is reduced to synonymy under Dinemasporium. Pseudolachnea (1-septate conidia) is supported as distinct from Dinemasporium (aseptate conidia), and P. fraxini introduced as a novel species. Taxa in this generic complex differ by combination of morphological characters of conidiomata, setae, conidia and appendages. Appendage morphology alone is rejected as informative at the generic level.
Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia.
Harknessiaceae is introduced as a new family in the ascomycete order Diaporthales to accommodate species of Harknessia with their Wuestneia-like teleomorphs. The family is distinguished by having pycnidial conidiomata with brown, furfuraceous margins, brown conidia with hyaline, tube-like basal appendages, longitudinal striations, and rhexolytic secession. Six species occurring on Eucalyptus are newly introduced, namely H. australiensis, H. ellipsoidea, H. pseudohawaiiensis, and H. ravenstreetina from Australia, H. kleinzeeina from South Africa, and H. viterboensis from Italy. Epitypes are designated for H. spermatoidea and H. weresubiae, both also occurring on Eucalyptus. Members of Harknessia are commonly associated with leaf spots, but also occur as saprobes and endophytes in leaves and twigs of various angiosperm hosts.
During a survey of Prunus wood from South Africa, isolations were made of three presumably Calosphaerialean fungi that formed hyphomycetous, phialidic anamorphs in culture. In order to reveal the phylogenetic relationship of these fungi, they were characterised on a morphological and molecular (LSU and ITS rDNA) basis. Two isolates that formed a teleomorph in culture are newly described as Calosphaeria africana sp. nov. Although asci of Calosphaeria are characterised by having non-amyloid apical rings, two functional wall layers were observed in asci of C. africana, which has hitherto not been observed in any member of the Calosphaeriaceae. However, Calosphaeriaceae (Calosphaeriales, Sordariomycetes) are not closely related to other bitunicate fungi like Dothideomycetes, Chaetothyriales and bitunicate lichens. Possession of two separating wall layers is considered to be a result of both inherited abilities and convergent evolution under a strong selection pressure of the environmental conditions that favour an extension of the ascus. The other two species represented a separate lineage within Calosphaeriaceae, and formed phialophora-like anamorphs. By obtaining the teleomorph in culture, one of them could be identified as a species of Jattaea, described here as Jattaea prunicola sp. nov., while the second, which only produced the anamorph, is named as Jattaea mookgoponga sp. nov. These findings suggest that some species of Jattaea are true members of the Calosphaeriaceae, though the phylogenetic relation of the type, J. algeriensis, remains unknown. Furthermore, it also represents the first report of Jattaea on Prunus wood, and from South Africa.
The ML tree showing two distinct clusters among β-tubulin sequences of taxa belonging to A. aculeatus clade that were deposited in GenBank. The introns were removed from the alignment. Only bootstrap values > 60 % are shown. The accession numbers of sequences deposited in this study and the names of the type specimens are in bold print.
Codon usage bias parameters characterising sequences of benA and tubC used in the construction of the phylogram shown in Fig. 2. The examined alignment included 207 positions corresponding to 69 amino acid residues. The benA gene shows a notably higher level of codon bias. Black dots indicate values of A. nidulans (CBI: benA-0.638, tubC-0.339; F OP : benA-0.764, tubC-0.571). CBI = codon bias index; F OP = frequency of optimal codons.
The electrophoretogram showing amplification products of the β -tubulin gene. The PCR reaction was performed at an annealing temperature of 55 °C. The reaction with primers Bt2a and Bt2b is shown on the upper part of the image. The lower part shows a reaction with primers Ben2f and Bt2b . The taxa used for primer testing are listed in Table 1 and designated A-L. The specificity of the Bt2a and Bt2b primer pair is apparently low in contrast to primer pair Ben2f and Bt2b that is highly benA specific. 
The electrophoretogram showing the behaviour of primer pair Bt2a and Bt2b in a temperature gradient (annealing 50–60 °C). The specificity for the tubC paralogue increases with increasing annealing temperature. Aspergillus aculeatus CBS 172.66 T , A. violaceofuscus CBS 114.51 (the ex-type of A. japonicus ) and A. violaceofuscus CBS 123.27 NT were used for testing. 
β-tubulin (benA, tub-2) and calmodulin (caM) are crucial genes in the taxonomy of Aspergillus section Nigri. Widely used β-tubulin primers are not specific for the benA gene for some taxa and preferentially amplify the tubC paralogue. Sequences of the tubC paralogue are widely combined with benA sequences in recent taxonomical works as well as other works, resulting in incongruent trees. In this study we newly provide benA sequences for several ex-type strains, which were characterised using the tubC gene only. We designed a highly specific forward primer to benA designated Ben2f for use in Aspergillus section Nigri, and tested specificity of numerous primer combinations to β-tubulin paralogs. The primer pairs with the highest specificity to the benA gene and functional across species in section Nigri includes Ben2f/Bt2b, Ben2f/T22 and T10/T22. We also provide tools based on codon usage bias analysis that reliably distinguish both paralogues. Exon/intron arrangement is the next distinctive characteristic, although this tool is not valid outside section Nigri. The species identity of taxa from the A. aculeatus clade used in previous molecular studies was revised using combined molecular data (ITS, benA, caM). These data together with two different PCR-fingerprinting methods indicated that A. japonicus should be treated as a synonym of A. violaceofuscus. Similarly, A. fijiensis is reduced to synonymy with A. brunneoviolaceus.
A 50 % majority rule Bayesian Inference phylogram resulting from analysis of the ITS, the nLSU, and associated indels. The scale bar is proportional to the amount of character evolution on the tree. The ITS and nLSU Genbank accession numbers are provided on terminals, in that order, after each taxon name. Only a single accession is labelled on terminals where the Genbank record contains concatenated ITS and nLSU sequences. Taxon names in bold indicate ex-types.
Cultures and microscopic features of Asperisporium caricae. a–d. Ex-epitype (CBS 130298) at approximately 1 mo at 24 °C with a 12 h light/dark regimen: a. PDA; b. reverse on PDA; c. SDA; d. reverse on SDA. — e. Lectotype packet, No. 2739 (LPS). — f–m. Ex-epitype (CBS 130298) on SDA; f–h. conidiophores and conidia; i–l. conidia; m. spermatia. — Scale bars = 10 μm for all.
Cultures and microscopic features of Pantospora guazumae. a–d. Ex-epitype (CBS 130299) at approximately 1 mo at 24 °C with a 12 h light/dark regimen: a. PDA; b. reverse on PDA; c. SDA; d. reverse on SDA. — e. Leaf spot on abaxial surface of Guazuma ulmifoliae (BPI 880778, designated epitype); f. synnema on Guazumae ulmifoliae (BPI 880778, designated epitype); g–i. conidia from ex-epitype (CBS 130299) on PDA. — Scale bars = 1 mm for e, 10 μm for f–i.
The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem requires phylogenetic placement of type species of key genera. We present an examination of the type species of the anamorphic Asperisporium and Pantospora. Cultures isolated from recent port interceptions were studied and described, and morphological studies were made of historical and new herbarium specimens. DNA sequence data from the ITS region and nLSU were generated from these type species, analysed phylogenetically, placed into an evolutionary context within Mycosphaerellaceae, and compared to existing phylogenies. Epitype specimens associated with living cultures and DNA sequence data are designated herein. Asperisporium caricae, the type of Asperisporium and cause of a leaf and fruit spot disease of papaya, is closely related to several species of Passalora including P. brachycarpa. The status of Asperisporium as a potential generic synonym of Passalora remains unclear. The monotypic genus Pantospora, typified by the synnematous Pantospora guazumae, is not included in Pseudocercospora sensu stricto or sensu lato. Rather, it represents a distinct lineage in the Mycosphaerellaceae in an unresolved position near Mycosphaerella microsora.
Phylogenetic analysis of the divergent domains D1 and D2 sequences of the 28S rDNA for 54 sequences from Neoerysiphe with Arthrocladiella used as outgroup taxon. The tree is a phylogram of the tree with the highest likelihood score among the 14 MP trees with 87 steps, which was obtained and constructed as described for Fig. 1. Bold lines denote branches present in the strict consensus tree. Nodes with asterisks (*) denote that the nodes collapsed in the strict consensus tree.  
Morphology within phylogenetic subclade B4. a, b, g, i – n: Neoerysiphe hiratae (isotype, KW 34787F) on Ligularia stenocephala; c – f, h: N. hiratae (KW 34783F) on L. delphiniifolia. a. The infected host; b. chasmothecia in reflected light covered by the secondary mycelium; c, d. hyphae of the primary mycelium with appressoria; e. conidiophores; f. conidia; g, i, j. chasmothecia viewed by scanning electron microscope: g, j – covered by hyphae of the secondary mycelium, i – side view; h. basal part of conidiophore; k. chasmothecial appendages; l. chasmothecium viewed by light microscope; m. peridial cells; n. asci. — Scale bars: a = 1 cm; b = 100 µm; c, e, f, h, k– n = 20 µm; d = 5 µm; g, i, j = 50 µm.  
Morphology within phylogenetic subclades C1, B2 and C3. a – g: Neoerysiphe joerstadii (holotype, KW 35717F, subclade C1) on Phagnalon rupestre; h – l: N. cumminsiana (isotype, HAL 1462F, subclade B2) on Senecio seemannii; m – o: N. geranii (KW 34782F, subclade C3) on Geranium sp. a. Chasmothecia in reflected light; b, c. chasmothecia viewed by scanning electron microscope: c – side view; d. chasmothecium in transmitted light; e. peridial cells; f. chasmothecial appendages; g. asci; h. chasmothecium with evagination on the lower side, side view; i – k. chasmothecia viewed by scanning electron microscope: i – side view, j – bottom view; l. chasmothecium in transmitted light; m. conidium with longitudinal ridges; n. chasmothecia; o. asci. — Scale bars: a = 200 µm; b – d, h–l, n = 50 µm; e–g, o = 20 µm; m = 5 µm.  
Morphology within phylogenetic subclade C4. a, b, d-g, q: Neoerysiphe nevoi (KW 35726F) on Thrincia tuberosa; c, h-j, l-p: N. nevoi (holotype, KW 34802F) on Tolpis virgata; k: N. nevoi var. scolymi (holotype, KW 34800F) on Scolymus hispanicus. a-c. Hyphae of the primary mycelium with appressoria; d. secondary hypha arisen from the primary hypha; e. conidiophore; f-h. conidia; g. germinated conidium with a hypha extending from a lobed appressorium of the Striatoidium type; i-k. chasmothecia viewed by scanning electron microscope; l. chasmothecium viewed by light microscope; m. peridial cells; n-q. asci.-Scale bars: a, f, g, o, p = 10 µm; b, c, h = 5 µm; d, e, l-n, q = 20 µm; i-k = 50 µm.
Because Eurasian samples of Neoerysiphe collected on the Asteraceae were not identical in morphology, the molecular and morphological differences among these specimens were compared with those of the American N. cumminsiana. Neoerysiphe on Asteraceae was found to consist of at least four different species. Three of them are described as new species, viz. N. hiratae, N. joerstadii, and N. nevoi. Neoerysiphe hiratae is a Japanese species parasitizing hosts belonging to the genera Cacalia and Ligularia (tribe Senecioneae). Neoerysiphe joerstadii was found in Israel on Phagnalon rupestre (tribe Gnaphalieae). Neoerysiphe nevoi was recorded in Israel and Ukraine on a number of hosts in different genera but all belonging to tribe Cichorieae. Thus, Eurasian Neoerysiphe species infecting the Asteraceae are strongly specialised to particular tribes of this family. Phylogenetic analyses indicated that the three new species were not closely allied. Neoerysiphe hiratae is related to the American N. cumminsiana and species belonging to Oidium subg. Striatoidium. Neoerysiphe nevoi is sister to N. geranii, and N. joerstadii is allied to N. galii. In addition, Ukrainian Neoerysiphe samples on Geranium were phylogenetically and morphologically identical to Japanese samples of N. geranii, and this fungus seems to be an invasive species in Ukraine.
Morphological structures of Phytophthora gibbosa. a-l. Structures formed on V8 agar flooded with soil extract: a, b. ovoid semipapillate sporangia; c. ovoid semipapillate sporangium with external proliferation; d. obpyriform sporangium with nonpapillate pointed apex; e. nonpapillate ellipsoid sporangium; f. ovoid slightly excentric sporangium; g. ovoid sporangium with swollen apex shortly before release of the already differentiated zoospores; h. same sporangium as in g releasing zoospores; i, j. empty elongated ovoid and limoniform sporangium, respectively, showing both internal extended proliferation and formation of an additional basal undeveloped sporangiophore (arrows); k, l. intercalary hyphal swellings originating from undeveloped sporangia that did not form a basal septum and continued to grow at their apex; m. immature ornamented oogonium with aplerotic oospore and amphigynous intercalary antheridium; n-s. mature often bronze-brown oogonia with amphigynous antheridia and thick-walled aplerotic oospores each containing a large ooplast: n. smooth-walled; o, q-s. ornamented gibbose oogonia; p. excentric smooth-walled oogonium with two oospores; t. gibbose oogonium with thickwalled aborted oospore; u. gibbose golden-brown oogonium aborted before oospore formation.-Scale bar = 25 µm.
Colony morphology of Phytophthora gibbosa isolates CBS127951 (ex-type) and VHS22007, P. gregata isolates CBS127952 (ex-type), MJS235 and VHS9854, and P. taxon paludosa isolate MUCC765 (from top to bottom) after 7 d growth at 20 °C on V8 agar, malt extract agar, corn meal agar and potato- dextrose agar (from left to right). 
Colony morphology of Phytophthora litoralis isolates CBS127953 (ex-type) and MUCC762, P. thermophila isolates CBS127954 (ex-type) and MUCC764, P. gonapodyides isolate MUCC761 and P. megasperma isolate DDS3432 (from top to bottom) after 7 d growth at 20 °C on V8 agar, malt extract agar, corn meal agar and potato-dextrose agar (from left to right). 
Mean radial growth rates of Phytophthora gibbosa (four isolates), P. gregata (eight isolates), P. litoralis and P. thermophila (each four isolates), P. taxon paludosa, P. gonapodyides and P. megasperma (each one isolate) on V8 agar at different temperatures. 
Radial phylogenetic tree generated after Bayesian analysis of ITS rDNA sequences, showing relationships between species and designated taxa in Clade 6 of Phytophthora. The branches corresponding to the subclades are coloured accordingly.
During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox 1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scat tered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread.
Three new species of Pythium, namely, P. oopapillum, P. emineosum and P. camurandrum are presented in this paper based on morphological descriptions and molecular phylogenetic characterisation. These new species were isolated from various ecological regions in Canada. They have unique morphological features in the genus Pythium, and form distinct clades in maximum parsimony analyses, which are also supported by maximum likelihood phylogeny using general time reversible model (GTR), and Bayesian inference (BI) phylogeny using Markov Chain Monte Carlo (MCMC) analysis methods. A comparative study of the new species with closely related taxa, their clade positions, and morphological features are described in this paper.
Primers used in this study for generic amplification and sequencing. 
Lecanosticta guatemalensis (IMI 281598). a. Colony sporulating on PDA; b. colony sporulating on SNA; c-e. conidiogenous cells giving rise to conidia; f, g. conidia.-Scale bars = 10 µm. 
Lecanosticta longispora (CPC 17940). a-d. Conidiogenous cells giving rise to conidia; e. conidia.-Scale bars = 10 µm c b d a e 
The trees resulting from the Bayesian analyses of the seven individual loci showed that most loci have difficulty discriminating between closely related Septoria and Pseudocercospora species. Deciding the sequence difference 
The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included β-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1α) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1α or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.
The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.
ML tree obtained from β-tubulin sequence data of Leptographium isolates from China (bold type). Dark branches indicate posterior probabilities > 0.95. Bootstrap values at nodes are for 1 000 replicates (Maximum Likelihood/Maximum Parsimony). * are bootstrap values < 75%.  
a–f: Leptographium manifestum sp. nov. a, d. Conidiophore; b, e. conidiogenous cells; c, f. conidia. — g. Hyalorhinocladiella-like synanamorph. — h–m: L. gracile sp. nov. h, k. conidiophore; i, l. conidiogenous cells; j, m. conidia. — Scale bars: a, d, h, k = 10 µm; b, c, i, j = 5 µm; e – g, l, m = 1 µm.  
a–f: Leptographium curviconidium sp. nov. a, d. Conidiophore; b, e. conidiogenous cells; c, f. conidia. — g. Hyalorhinocladiella-like synanamorph. — h – m: L. altius sp. nov. h, k. conidiophore; i, l. conidiogenous cells; j, m. conidia. — Scale bars: a, d, h, k = 20 µm; b, c, e, f, g, i, j, l, m = 5 µm.  
a–f: Leptographium conjunctum sp. nov. a, d. Conidiophore; b, e. conidiogenous cells; c, f. conidia. — g – l: L. celere sp. nov. g, j. conidiophore; h, k. conidiogenous cells; i, l. conidia. — Scale bars: a, d, g, j = 20 µm; b, c, h, i = 5 µm; e, f, k, l = 1 µm.  
a–f: Leptographium latens sp. nov. a, d. Conidiophore; b, e. conidiogenous cells; c, f. conidia. — g – l: L. pistaciae sp. nov. g, j. conidiophore; h, k. conidiogenous cells; i, l. conidia. — Scale bars: a, d, j = 20 µm; b, c, h, i = 5 µm; g = 50 µm; e, f, k, l = 1 µm.  
Leptographium spp. are anamorphs of Grosmannia residing in the order Ophiostomatales. These fungi are typically associated with bark-beetles and are common causal agents of sapstain in lumber and some are important tree pathogens. In this study, Leptographium spp. associated with bark beetles collected during a survey in Jilin and Yunnan provinces of China, were identified. Identifications were achieved using comparisons of morphological characters and DNA sequence data for the ITS2-partial LSU rDNA region, as well as the β-tubulin and EF-1α gene regions. Eight unknown species of Leptographium are recognised and described from conifer and hardwood hosts, associated with beetles including Ips subelongatus, Tomicus yunnanensis, Hylurgops minor, Polygraphus verrucifrons and a Pissodes sp. Six of the new species are morphologically and phylogenetically related to species known to occur in Asia such as G. yunnanense, L. bhutanense, L. bistatum and L. sinoprocerum. The remaining two taxa are related to those in a group containing G. americana and L. abietinum, found in North America. This study also provides the first report of L. pineti on Pinus kesiya in China.
Phylograms obtained from Neighbour-joining analyses of DNA sequences of (a) the nuclear ITS region and (b-d) the β-tubulin (BT) gene. Bootstrap support values (1 000 replicates) above 75 % are indicated at the nodes (normal type for Neighbour-joining, bold type for maximum parsimony). Posterior probabilities (above 90 %) obtained from Bayesian analyses are indicated by bold lines at the relevant branching points. * = bootstrap values lower than 75 %. Isolate numbers of sequences obtained in this study are printed in bold type.-Scale bar = total nucleotide difference between taxa. 
Morphological characters of Ophiostoma denticiliatum (holotype) teleomorph structures. a. Ascoma; b. scanning electron micrograph (SEM) of ostiolar hyphae with denticulate apex, starting to form Sporothrix-like anamorph; c. ostiolar hyphae; d. ascospores.-Scale bars: a = 100 μm; b = 3 μm; c, d = 10 μm. c 
Morphological characters of Ophiostoma denticiliatum (holotype) anamorph structures. a. Pesotum anamorph; b. scanning electron micrograph (SEM) of Pesotum anamorph; c. SEM of conidia of Pesotum; d. conidia of Pesotum; e. Sporothrix-like anamorph with conidia; f. SEM of Sporothrix anamorph with conidia.-Scale bars: a = 100 μm; b, d, e = 10 μm; c = 1 μm; f = 3 μm. 
Ophiostomatoid fungi were isolated from Scolytus ratzeburgi infesting Betula pendula and B. pubescens in Norway. Fungi were identified based on morphology, DNA sequence comparison for two gene regions and phylogenetic analyses. The most abundant fungus was Ophiostoma karelicum, suggesting a specific relationship between the fungus, the vector insect and the host tree. Our results suggest that O. karelicum occurs across the geographic range of S. ratzeburgi and its close relatedness to the Dutch elm disease fungi suggests that it could be important if introduced into other parts of the world. Other fungi, only occasionally isolated from S. ratzeburgi, were identified as O. quercus and a novel taxon, described here as O. denticiliatum sp. nov.
The timber and pulp industries of Finland rely heavily on importations from Russia as source of raw timber. These imports raise the risk of accidentally importing forest pests and pathogens, especially bark beetles and their associated fungi, into Finland. Although ophiostomatoid fungi have previously been reported from Finland and Russia, the risks of accidentally moving these fungi has prompted a first survey to compare the diversity of conifer-infesting bark beetles and associated fungi from boreal forests on both sides of the Finnish-Russian border. The aim of the present study was to identify and characterise Ophiostoma species isolated in association with 11 bark beetle species infesting Pinus sylvestris and Picea abies during this survey in the eastern parts of Finland and neighbouring Russia. Fungal isolates were grouped based on morphology and representatives of each morphological group were subjected to DNA sequence comparisons of the internal transcribed spaced region (ITS1, 5.8S, ITS2) and β-tubulin gene region. A total of 15 species of Ophiostoma were identified, including seven known species, five new species, and three species for which the identity remains uncertain. In the O. piceae-complex we identified O. canum, O. floccosum, O. karelicum and O. rachisporum sp. nov., and related to these, some isolates belonging to the European clade of O. minus in the O. minus-complex. Ophiostoma bicolor and O. fuscum sp. nov. were identified in the O. ips-complex, while O. ainoae, O. brunneo-ciliatum, O. tapionis sp. nov. and O. pallidulum sp. nov. were shown to group close to, but not in a strict monophyletic lineage with species of the O. ips-complex. Together with a single O. abietinum-like isolate, the only species that grouped close to the Sporothrix schenckii- O. stenoceras complex, was O. saponiodorum sp. nov.
Single most parsimonious tree resulting from maximum parsimony analysis of combined ITS and EF1-α sequence data. MP bootstrap values are given at the nodes. The tree was rooted to two isolates of Pseudofusicoccum stromaticum. The new species are in bold face.  
Barriopsis iraniana holotype. a. Conidiomata on pine needles in culture; b, c. conidia developing on conidiogenous cells between paraphyses; d. young conidium showing longitudinal striations while attached to a conidiogenous cell; e. hyaline, striate conidia; f-i. hyaline and brown, striate conidia, 1-and 3septate conidia can be seen in f and g; j. catenulate chlamydospores.-Scale bars: a = 250 μm; b, c, e-i = 10 μm; d= 5 μm; j = 40 μm.
Phaeobotryon cupressi holotype. a. Conidiomata formed on pine needles in culture; b. sectioned conidioma; c. paraphyses and developing conidia; d, e. microconidiogenous cells; f. microconidia; g. conidia and conidiogenous cells; h. hyaline conidia; i, j. brown, aseptate conidia; k. germinating conidia; l. chlamydospores and a hyaline conidium. — Scale bars: a = 250 μm; b = 100 μm; c, h, i, k, l = 10 μm; d, e = 2.5 μm; f, g, j = 5 μm.  
Species in the Botryosphaeriaceae are well known as pathogens and saprobes of woody hosts, but little is known about the species that occur in Iran. In a recent survey of this family in Iran two fungi with diplodia-like anamorphs were isolated from various tree hosts. These two fungi were fully characterised in terms of morphology of the anamorphs in culture, and sequences of the ITS1/ITS2 regions of the ribosomal DNA operon and partial sequences of the translation elongation factor 1-alpha. Phylogenetic analyses placed them within a clade consisting of Barriopsis and Phaeobotryon species, but they were clearly distinct from known species in these genera. Therefore, they are described here as two new species, namely Barriopsis iraniana on Citrus, Mangifera and Olea, and Phaeobotryon cupressi on Cupressus sempervirens.
Top-cited authors
Pedro W Crous
  • Westerdijk Fungal Biodiversity Institute
J.Z. Groenewald
  • Westerdijk Fungal Biodiversity Institute
Treena I Burgess
  • Murdoch University
Roger Shivas
  • University of Southern Queensland 
María P. Martín
  • Real Jardín Botánico-CSIC, Consejo Superior de Investigaciones Científicas