Kazuyuki Hirayama

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str., Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.

Molecular systematics of the marine Dothideomycetes

Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicola guatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity.

Fungal diversity notes 1–110: taxonomic and phylogenetic contributions to fungal species

This paper is a compilation of notes on 110 fungal taxa, including one new family, 10 new genera, and 76 new species, representing a wide taxonomic and geographic range. The new family, Paradictyoarthriniaceae is introduced based on its distinct lineage in Dothideomycetes and its unique morphology. The family is sister to Biatriosporaceae and Roussoellaceae. The new genera are Allophaeosphaeria (Phaeosphaeriaceae), Amphibambusa (Amphisphaeriaceae), Brunneomycosphaerella (Capnodiales genera incertae cedis), Chaetocapnodium (Capnodiaceae), Flammeascoma (Anteagloniaceae), Multiseptospora (Pleosporales genera incertae cedis), Neogaeumannomyces (Magnaporthaceae), Palmiascoma (Bambusicolaceae), Paralecia (Squamarinaceae) and Sarimanas (Melanommataceae). The newly described species are the Ascomycota Aliquandostipite manochii, Allophaeosphaeria dactylidis, A. muriformia, Alternaria cesenica, Amphibambusa bambusicola, Amphisphaeria sorbi, Annulohypoxylon thailandicum, Atrotorquata spartii, Brunneomycosphaerella laburni, Byssosphaeria musae, Camarosporium aborescentis, C. aureum, C. frutexensis, Chaetocapnodium siamensis, Chaetothyrium agathis, Colletotrichum sedi, Conicomyces pseudotransvaalensis, Cytospora berberidis, C. sibiraeae, Diaporthe thunbergiicola, Diatrype palmicola, Dictyosporium aquaticum, D. meiosporum, D. thailandicum, Didymella cirsii, Dinemasporium nelloi, Flammeascoma bambusae, Kalmusia italica, K. spartii, Keissleriella sparticola, Lauriomyces synnematicus, Leptosphaeria ebuli, Lophiostoma pseudodictyosporium, L. ravennicum, Lophiotrema eburnoides, Montagnula graminicola, Multiseptospora thailandica, Myrothecium macrosporum, Natantispora unipolaris, Neogaeumannomyces bambusicola, Neosetophoma clematidis, N. italica, Oxydothis atypica, Palmiascoma gregariascomum, Paraconiothyrium nelloi, P. thysanolaenae, Paradictyoarthrinium tectonicola, Paralecia pratorum, Paraphaeosphaeria spartii, Pestalotiopsis digitalis, P. dracontomelon, P. italiana, Phaeoisaria pseudoclematidis, Phragmocapnias philippinensis, Pseudocamarosporium cotinae, Pseudocercospora tamarindi, Pseudotrichia rubriostiolata, P. thailandica, Psiloglonium multiseptatum, Saagaromyces mangrovei, Sarimanas pseudofluviatile, S. shirakamiense, Tothia spartii, Trichomerium siamensis, Wojnowicia dactylidicola, W. dactylidis and W. lonicerae. The Basidiomycota Agaricus flavicentrus, A. hanthanaensis, A. parvibicolor, A. sodalis, Cantharellus luteostipitatus, Lactarius atrobrunneus, L. politus, Phylloporia dependens and Russula cortinarioides are also introduced. Epitypifications or reference specimens are designated for Hapalocystis berkeleyi, Meliola tamarindi, Pallidocercospora acaciigena, Phaeosphaeria musae, Plenodomus agnitus, Psiloglonium colihuae, P. sasicola and Zasmidium musae while notes and/or new sequence data are provided for Annulohypoxylon leptascum, A. nitens, A. stygium, Biscogniauxia marginata, Fasciatispora nypae, Hypoxylon fendleri, H. monticulosum, Leptosphaeria doliolum, Microsphaeropsis olivacea, Neomicrothyrium, Paraleptosphaeria nitschkei, Phoma medicaginis and Saccotheciaceae. A full description of each species is provided with light micrographs (or drawings). Molecular data is provided for 90 taxa and used to generate phylogenetic trees to establish a natural classification for species.

The molecular phylogeny of freshwater Dothideomycetes

The freshwater Dothideomycetes species are an ecological rather than taxonomic group and comprise approximately 178 meiosporic and mitosporic species. Due to convergent or parallel morphological adaptations to aquatic habitats, it is difficult to determine phylogenetic relationships among freshwater taxa and among freshwater, marine and terrestrial taxa based solely on morphology. We conducted molecular sequence-based phylogenetic analyses using nuclear ribosomal sequences (SSU and/or LSU) for 84 isolates of described and undescribed freshwater Dothideomycetes and 85 additional taxa representative of the major orders and families of Dothideomycetes. Results indicated that this ecological group is not monophyletic and all the freshwater taxa, except three aeroaquatic Tubeufiaceae, occur in Pleosporomycetidae as opposed to Dothideomycetidae. Four clades comprised of only freshwater taxa were recovered. The largest of these is the Jahnulales clade consisting of 13 species, two of which are the anamorphs Brachiosphaera tropicalis and Xylomyces chlamydosporus. The second most speciose clade is the Lindgomycetaceae clade consisting of nine taxa including the anamorph Taeniolella typhoides. The Lindgomycetaceae clade consists of taxa formerly described in Massarina, Lophiostoma, and Massariosphaeria e.g., Massarina ingoldiana, Lophiostoma breviappendiculatum, and Massariosphaeria typhicola and several newly described and undescribed taxa. The aquatic family Amniculicolaceae, including three species of Amniculicola, Semimassariosphaeria typhicola and the anamorph, Anguillospora longissima, was well supported. A fourth clade of freshwater species consisting of Tingoldiago graminicola, Lentithecium aquaticum, L. arundinaceum and undescribed taxon A-369-2b was not well supported with maximum likelihood bootstrap and Bayesian posterior probability. Eight freshwater taxa occurred along with terrestrial species in the Lophiostoma clades 1 and 2. Two taxa lacking statistical support for their placement with any taxa included in this study are considered singletons within Pleosporomycetidae. These singletons, Ocala scalariformis, and Lepidopterella palustris, are morphologically distinct from other taxa in Pleosporomycetidae. This study suggests that freshwater Dothideomycetes are related to terrestrial taxa and have adapted to freshwater habitats numerous times. In some cases (Jahnulales and Lindgomycetaceae), species radiation appears to have occurred. Additional collections and molecular study are required to further clarify the phylogeny of this interesting ecological group.

Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs.

A new pleosporalean family Tetraplosphaeriaceae is established to accommodate five new genera; 1) Tetraplosphaeria with small ascomata and anamorphs belonging to Tetraploa s. str., 2) Triplosphaeria characterised by hemispherical ascomata with rim-like side walls and anamorphs similar to Tetraploa but with three conidial setose appendages, 3) Polyplosphaeria with large ascomata surrounded by brown hyphae and anamorphs producing globose conidia with several setose appendages, 4) Pseudotetraploa, an anamorphic genus, having obpyriform conidia with pseudosepta and four to eight setose appendages, and 5) Quadricrura, an anamorphic genus, having globose conidia with one or two long setose appendages at the apex and four to five short setose appendages at the base. Fifteen new taxa in these genera mostly collected from bamboo are described and illustrated. They are linked by their Tetraploa s. l. anamorphs. To infer phylogenetic placement in the Pleosporales, analyses based on a combined dataset of small- and large-subunit nuclear ribosomal DNA (SSU+LSU nrDNA) was carried out. Tetraplosphaeriaceae, however, is basal to the main pleosporalean clade and therefore its relationship with other existing families was not completely resolved. To evaluate the validity of each taxon and to clarify the phylogenetic relationships within this family, further analyses using sequences from ITS-5.8S nrDNA (ITS), transcription elongation factor 1-α (TEF), and β-tubulin (BT), were also conducted. Monophyly of the family and that of each genus were strongly supported by analyses based on a combined dataset of the three regions (ITS+TEF+BT). Our results also suggest that Tetraplosphaeria (anamorph: Tetraploa s. str.) is an ancestral lineage within this family. Taxonomic placement of the bambusicolous fungi in Astrosphaeriella, Kalmusia, Katumotoa, Massarina, Ophiosphaerella, Phaeosphaeria, Roussoella, Roussoellopsis, and Versicolorisporium, are also discussed based on the SSU+LSU phylogeny.

A molecular phylogenetic assessment of Massarina ingoldiana sensu lato

Massarina ingoldiana occurs worldwide on a variety of dead plant substrates in aquatic habitats. This species has been accommodated in Massarina or Lophiostoma in Pleosporales, Dothideomycetes, but the validity of either of these taxonomic placements has not been confirmed with molecular data. In addition morphological variations occur among different populations of this species causing problems in identification. To evaluate the generic placement and monophyly of M. ingoldiana and the taxonomic usefulness of variable morphological features, phylo-genetic analyses based on SSU and LSU sequences of ribosomal DNA were conducted for 10 putative strains of this species and its relatives. Phylogenies revealed that M. ingoldiana sensu lato is polyphyletic and comprises two distinct lineages within Pleosporales. Neither lineage was congeneric with either Massarina or Lophiostoma. Based on molecular data and a reevaluation of morphology, two new genera, Lindgomyces and Tingoldiago, are established for the two lineages of M. ingoldiana sensu lato. Lindgomyces includes four species, L. ingoldianus comb. nov. (= M. ingoldiana sensu stricto), L. rotundatus sp. nov. (= M. ingoldiana sensu lato), L. cinctosporae sp. nov. and L. breviappendiculatus comb. nov. (= Lophiostoma breviappendiculatum). A new aquatic family, Lindgomycetaceae, is proposed for Lindgomyces and its sister taxon, Massariosphaeria typhicola. Isolates of a fungus from submerged Phragmites, with ascospores similar to those of M. ingoldiana, occurred in an additional single species lineage distant from that of M. ingoldiana (Lindgomyces). This fungus is described as Tingoldiago graminicola gen. & sp. nov. The discovery that Tingoldiago, which occurs in a lineage distantly related to Lindgomyces but has morphologically similar ascospores and ascospore sheaths, suggests that the elaborate ascospore sheath in M. ingoldiana has arisen in two separate lineages as a result of convergent evolution in response to the aquatic environment. The large gelatinous sheath previously was considered one of the most distinctive and stable features for species identification of M. ingoldiana.

Phylogeny of Discosia and Seimatosporium, and introduction of Adisciso and Immersidiscosia genera nova

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.

Towards a natural classification and backbone tree for Lophiostomataceae , Floricolaceae , and Amorosiaceae fam. nov .

The genera Lophiostoma, Misturatosphaeria and several other allied taxa in Lophiostomataceae are revisited. Accounts of these taxa, including their history, morphology, and family placement, based on molecular phylogeny, are provided. Type or representative specimens of Lophiostoma and Misturatosphaeria were examined and fresh specimens were obtained from Germany, Italy, Japan and Thailand. A multi-gene phylogenetic analysis of the lophiostomataceous genera Floricola, Lophiostoma, Misturatosphaeria and related taxa is provided. Sixteen genera including Lophiostoma, Lophiohelichrysum, Dimorphiopsis, Platystomum and Vaginatispora, plus eleven newly introduced genera Biappendiculispora, Alpestrisphaeria, Capulatispora, Coelodictyosporium, Guttulispora, Lophiopoacea, Neotrematosphaeria, Paucispora, Pseudolophiostoma, Pseudoplatystomum and Sigarispora are accepted in Lophiostomataceae based on morphology and phylogeny. Lophiostoma caulium, Lophiostoma arundinis and Lophiostoma caudatum are accommodated in Sigarispora. Lophiostoma winteri and Lophiostoma fuckelii are placed in the genera Lophiopoacea and Vaginatispora respectively. Three Curreya species and Misturatosphaeria claviformis are transferred to a new genus, Neocurreya. All other Misturatosphaeria species except Misturatosphaeria aurantiinotata and M. uniseptata are separated in the new genera Asymmetrispora, Aurantiascoma, Magnibotryascoma, Pseudoaurantiascoma and Pseudomisturatosphaeria based on their morphological and phylogenetic affinities. Another new genus, Ramusculicola is introduced for a new collection from Thailand. These seven new genera are accommodated in a new family Floricolaceae, together with Floricola and Misturatosphaeria. Several massarina-like species clustered as a sister clade to Amorosia littoralis and are accommodated in a new genus Angustimassarina. A new family Amorosiaceae is proposed to accommodate the genera Amorosia and Angustimassarina. The putatively named species Decaisnella formosa and Thyridaria macrostomoides form a separate clade together with a new genus Lignosphaeria which is placed in Dothideomycetes, genera incertae sedis.