Obba and Sebipora, new polypore genera related to Cinereomyces and Gelatoporia (Polyporales, Basidiomycota)

A re-assessment of Taxomyces andreanae, the alleged taxol-producing fungus, using comparative genomics

The monotypic "bulbilliferous hyphomycete" genus Taxomyces was erected in 1993 for a fungal endophyte isolated from the Yew tree Taxus brevifolia and named Taxomyces andreanae. This fungus was reported to produce the plant-derived anti-cancer drug taxol. The original description of the fungus was not conclusive as to its taxonomic position because no sporulation or other salient morphological features were reported. Consequently, the taxonomic affinities of this fungus have remained obscure. However, a full genome sequence of this strain was generated by a German research group in 2013, in an unsuccessful attempt to detect the biosynthesis genes encoding for taxol. This prompted us to search for phylogenetic marker genes and compare those with the data that recently have become available from state-of-the-art polyphasic taxonomic studies. Surprisingly, the strain turned out to belong to the phlebioid clade of wood-destroying Basidiomycota as inferred from a comparison of its partial ITS, the 28S rDNA (LSU), the RNA polymerase II largest subunit (rpb1), the RNA polymerase II second largest subunit (rpb2), and the translation elongation factor 1-α (tef1) sequences. A multi gene genealogy based on these loci revealed that the closest relative is Ceriporiopsis (syn. Mycoacia) gilvescens. Even though such wood-destroying Basidiomycota are regularly encountered among the endophytic isolates after surface-disinfection of plant organs, the vast majority of the reported endophytic fungi belong to the Ascomycota. Nevertheless, the data available now allow for synonymizing Taxomyces with Ceriporiopsis, and the necessary new combination is made.

Cinereomyces wuliangshanensis sp. nov. from China

A new poroid wood-inhabiting fungal species, Cinereomyces wuliangshanensis, is proposed based on morphological and molecular characters. The species is characterized by resupinate brittle basidiomata with a white pore surface, a dimitic hyphal system with clamped generative hyphae, and subglobose to broadly ellipsoid hyaline thin-walled smooth basidiospores (4.2–5.1 × 2.9–3.8 μm). Sequences were generated from the internal transcribed spacer (ITS) region of nuclear ribosomal RNA gene and phylogenetically analyzed using maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogeny strongly (100% BS, 100% BT, 1.00 BPP) supports C. wuliangshanensis in a monophyletic lineage grouping with C. lindbladii and a clade comprising Obba rivulosa and O. valdiviana.

Two new species of <i>Steccherinum</i> (<i>Polyporales, Basidiomycota</i>) from southern China based on morphology and DNA sequence data

Two new wood-inhabiting fungal species, Steccherinum hirsutum and S. yunnanense spp. nov., are proposed based on a combination of morphological features and molecular evidence. Sequences of internal transcribed spacer and large subunit region of nuculear ribosomal RNA gene of the studied samples were generated, and phylogenetic analyses were performed using maximum likelihood, maximum parsimony and bayesian inference methods. Steccherinum hirsutum is characterized by an annual growth habit, stipitate basidiocarps with scarlet to red, odontioid hymenial surface, a dimitic hyphal system with clamped generative hyphae negative in Melzer's reaction, and acyanophilous basidiospores measuring 2.5-3.5 × 1.5-2.5 µm. Steccherinum yunnanense is distinguished by resupinate basidiomata with odontioid hymenial surface, a dimitic hyphal system with clamped generative hyphae, strongly encrusted cystidia and ellipsoid, hyaline, thin-walled, smooth basidiospores (3.5-4.5 × 2-3.5 µm). The phylogenetic analyses comfirmed that two new species nest in Steccherinum, in the residual polyporoid clade.

Steccherinum tenuissimum and S. xanthum spp. nov. (Polyporales, Basidiomycota): New species from China

Two new wood-inhabiting fungal species, Steccherinum tenuissimum and S. xanthum spp. nov. are described based on a combination of morphological features and molecular evidence. Steccherinum tenuissimum is characterized by an annual growth habit, resupinate basidiomata with an odontioid hymenial surface, a dimitic hyphal system with clamped generative hyphae, strongly encrusted cystidia and basidiospores measuring 3-5 × 2-3.5 μm. Steccherinum xanthum is characterized by odontioid basidiomata and a monomitic hyphal system with generative hyphae bearing clamp connections and covering by crystals, colourless, thin-walled, smooth, IKI-, CB-and has basidiospores measuring 2.7-5.5 × 1.8-4.0 μm. Sequences of the ITS and nLSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS + nLSU sequences showed that two new Steccherinum species felled into the residual polyporoid clade. Further investigation was obtained for more representative taxa in Steccherinum based on ITS + nLSU sequences, which demonstrated that S. tenuissimum and S. xanthum were sister to S. robustius with high support (100% BP, 100% BS and 1.00 BPP).

Notes, outline and divergence times of Basidiomycota

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

Elaphroporia ailaoshanensis gen. et sp. nov. in Polyporales (Basidiomycota)

A new poroid wood-inhabiting fungal genus, Elaphroporia, typified by E. ailaoshanensissp. nov., is proposed based on a combination of morphological features and molecular evidence. The genus is characterised by an annual growth habit, resupinate basidiocarps, becoming rigid and light-weight up on drying, a monomitic hyphal system with thick-walled generative hyphae bearing both clamp connections and simple septa, slightly amyloid, CB+ and ellipsoid, hyaline, thin-walled, smooth and IKI-, CB- basidiospores. Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on molecular data of ITS+nLSU sequences showed that Elaphroporia belonged to the residual polyporoid clade and was closely related to Junghuhnia crustacea. Further investigation was obtained for more representative taxa in the Meruliaceae based on ITS+nLSU sequences, in which the result demonstrated that the genus Elaphroporia formed a monophyletic lineage with a strong support (100 % BS, 100 % BP, 1.00 BPP) and then grouped with Flaviporus and Steccherinum.

Resolution of phylogenetic position of Nigrofomitaceae within Hymenochaetales (Basidiomycota) and Nigrofomes sinomelanoporus sp. nov. (Nigrofomitaceae) from China

The family Nigrofomitaceae has been considered to be a member of Polyporales and a synonym of Polyporaceae for a long time. However, no molecular evidence supports this taxonomic opinion. For the first time, Nigrofomitaceae is included in a phylogenetic analysis, which shows that this family is separated from Polyporales and nested within Hymenochaetales as a distinct lineage from four well-known families, viz. Hymenochaetaceae, Neoantrodiellaceae, Oxyporaceae and Schizoporaceae. Therefore, Nigrofomitaceae is treated as the fifth family of Hymenochaetales. Nigrofomes melanoporus, the type species of Nigrofomitaceae, was considered to have a pantropical distribution. However, from both morphological and phylogenetic perspectives, the Chinese specimens labelled as N. melanoporus are found not to be conspecific with the specimens of N. melanoporus from Costa Rica, close to the type locality in Cuba. These Chinese specimens are thus described as a new species Nigrofomes sinomelanoporus. The species diversity of Nigrofomes in pantropical region is discussed.

A revised family-level classification of the Polyporales (Basidiomycota)

Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia + amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea, and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological, and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.

Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

Phylogenetic and phylogenomic overview of the Polyporales

We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.

Morphological and molecular identification of four new resupinate species of Perenniporia (Polyporales) from southern China

Four new resupinate species, Perenniporia hainaniana, P. macropora, P. russeimarginata and P. subtephropora, are described as new from southern China on the basis of morphological and molecular examination. Perenniporia hainaniana is characterized by a perennial growth habit, cream to buff pore surface, a dimitic to trimitic hyphal system with amyloid skeletal hyphae and presence of dendrohyphidia. Perenniporia macropora is distinguished by an annual growth habit, large pores (2-3 per mm), a dimitic hyphal system with branched skeletal hyphae and presence of dendrohyphidia. Perenniporia russeimarginata differs from other species in the genus by a perennial growth habit, white to cream pore surface and reddish to reddish brown sterile margin. Perenniporia subtephropora is characterized by a perennial growth habit, cream-buff to grayish buff pore surface, hymenophoral trama becoming black in KOH and a dimitic hyphal system with branched skeletal hyphae. Phylogenetic analysis inferred from the ITS and LSU-rDNA regions revealed eight clades for Perenniporia sensu lato with the four new species recognized in Perenniporia sensu stricto. The Perenniporia ochroleuca group, P. vicina group, P. martia group, P. subacida, Microporellus, Perenniporiella and Abundisporus, formed monophyletic entities respectively, and they are not related to P. medulla-panis (generic type), which belongs to Perenniporia sensu stricto. Abundisporus, Microporellus and Perenniporiella were widely applied as generic names. Other generic or clade names, Hornodermoporus, Truncospora, Vanderbylia and the P. subacida clade, have not been widely applied, but they are valid higher level taxa containing former species of Perenniporia. A key to genera and clades allied with Perennioporia sensu stricto and a key to species of Perennioporia are provided.