Systematic arrangement within the family Clitocybaceae (Tricholomatineae, Agaricales): phylogenetic and phylogenomic evidence, morphological data and muscarine-producing innovation

The Clitocybaceae is a recently established family.Currently,the infrafamilial divisions and relationships within the family are vague due to limited sampling and genes employed for phylogenetic analysis.Some mushrooms of the family contain the neurotoxic muscarine,which has caused many severe and even deadly poisonings worldwide.However,the taxonomic distribution and evolution of the toxin within the family is largely unknown.In this study,phylogenetic analyses based on nucleotide sequences of ITS and of six molecular loci(ITS,LSU,TEF1,RPB1,RPB2 and ATP6),plus a phylogenomic analysis based on 485 single-copy orthologous genes,were performed to reconstruct the framework of Clitocybaceae.BEAST analysis was used to estimate the divergence times within the family.Additionally,biochemical analysis for muscarine was conducted of 32 representative species.Based on these analyses,an updated classification of Clitocybaceae into six genera(Clitocybe,Collybia,Dendrocollybia,Lepista,Pseudolyophyllum,and Singerocybe)is proposed.The genus Collybia is emended to accommodate four subgenera(Collybia,Crassicybe,Leucocalocybe,and Macrosporocybe).Seventeen new Chinese species and 15 new combinations are proposed.Keys to the genera of Clitocybaceae and the subgenera of Collybia,as well as to the known species of Clitocybe and Collybia subgen.Collybia in China,are presented.In addition,muscarine was detected in 18 species,and these muscarine-containing species formed a major monophyletic clade within Collybia subgen.Collybia.Finally,our phylogenetic,phylogenomic,chemotaxonomic and molecular dating results indicate that the Clitocybaceae is a natural group estimated to have arisen some 60 million years ago,and in this family,muscarine has evolved only once circa 20 million years ago without later losses.

The family Amanitaceae: molecular phylogeny, higher-rank taxonomy and the species in China

Mushrooms in the basidiomycete family Amanitaceae are very important both economically and ecologically.However,the delimitation of the family is still controversial,in part due to limited taxon sampling and in part because of insufficient gene fragment employed for molecular phylogenetic analyses.Furthermore,species diversity in the family is likely to have been largely underestimated,due to morphological similarity between taxa and phenotypic plasticity.In this study,we examined 1190 collections,including 1008 Chinese and 182 external ones,and performed the first comprehensive phylogenetic analyses of Amanitaceae using multi-locus sequence data.To test the monophyly of the Amanitaceae,a concatenated(nrLSU,rpb1,and rpb2)dataset of 200 taxa of the order Agaricales was analyzed.To infer the phylogeny of Amanitaceae,a concatenated nrLSU,tef1-a,rpb2 and b-tubulin dataset(3010 sequences from ca.890 samples with 2309 newly generated sequences)was used.In this dataset,252 sequences from the types of 77 species were provided.Our results indicate that Amanitaceae is a monophyletic group,and consists of five genera,namely Amanita,Catatrama,Limacella,Limacellopsis and Myxoderma.It is clear that Catatrama is closely related to Limacella,however,the phylogenetic relationships among these genera remain largely unresolved.Amanita contains 95%of the species in the family,and is here divided into three subgenera and eleven sections(subgen.Amanita,containing:sect.Amanita,sect.Amarrendiae,sect.Caesareae and sect.Vaginatae;subgen.Amanitina,containing:sect.Amidella,sect.Arenariae,sect.Phalloideae,sect.Roanokenses,sect.Strobiliformes and sect.Validae;and subgen.Lepidella,containing sect.Lepidella).Subgen.Lepidella occupies the basal position in the genus.One-hundred and sixty-two species of Amanitaceae known from China are treated in this study,including 50 novel species and 112 known taxa.Amanita gleocystidiosa,A.pyriformis,A.atrofusca,A.subjunquillea var.alba and A.areolata are treated as synonyms of A.sychnopyramis f.subannulata,A.orientigemmata,A.umbrinolutea,A.subjunquillea and A.zangii,respectively.26 extralimital taxa including a novel species,namelyCatatrama indica,were included in our study to allow us to make comparisons between these and the Chinese taxa.DNA sequence data for all the species of Amanitaceae in China and keys for identification of the species are provided.

Multigene phylogeny of the family Cordycipitaceae (Hypocreales): new taxa and the new systematic position of the Chinese cordycipitoid fungus Paecilomyces hepiali

The phylogeny and systematics of cordycipitoid fungi have been extensively studied in the last two decades.However,systematic positions of some taxa in the family Cordycipitaceae have not yet been thoroughly resolved.In this study,a new phylogenetic framework of Cordycipitaceae is reconstructed using multigene(nrSSU,nrLSU,tef-1α,rpb1 and rpb2)sequence data with large-scale taxon sampling.In addition,ITS sequence data of species belonging to the Lecanicillium lineage in the family Cordycipitaceae are used to further determine their phylogenetic placements.Based on molecular phylogenetic data together with morphological evidence,two new genera(Flavocillium and Liangia),16 new species and four new combina-tions are introduced.In the new genus Flavocillium,one new species F.bifurcatum and three new combinations previously described as Lecanicillium,namely F.acerosium,F.primulinium and F.subprimulinium,are proposed.The genus Liangia is built by the new species Lia.sinensis with Lecanicillium-like asexual morph,isolated from an entomopathogenic fungus Beauveria yunnanensis.Due to the absence of Paecilomyces hepiali,an economically and medically significant fungus,in the earlier phylogenetic analyses,its systematic position has been puzzling in both business and academic communities for a long time.Here,P.hepiali is recharacterized using the holotype material along with seven additional samples.It is assigned to the genus Samsoniella(Cordycipitaceae,Hypocreales)possessing Cordyceps-like sexual morph and Isaria-like asexual morph,and thus a new combination,namely S.hepiali is proposed.An additional nine new species in Samsoniella are described:S.alpina,S.antleroides,S.cardinalis,S.cristata,S.lanmaoa,S.kunmingensis,S.ramosa,S.tortricidae and S.yunnanensis.Four new species in Cordyceps are described:C.chaetoclavata,C.cocoonihabita,C.shuifuensis and C.sub-tenuipes.Simplicillium yunnanense,isolated from synnemata of Akanthomyces waltergamsii,is described as a new species.

Molecular phylogenetic analyses redefine seven major clades and reveal 22 new generic clades in the fungal family Boletaceae

Mushrooms in the basidiomycete family Boletaceae are ecologically and economically very important.However,due to the morphological complexity and the limited phylogenetic information on the various species and genera of this fungal family,our understanding of its systematics and evolution remains rudimentary.In this study,DNA sequences of four genes(nrLSU,tef1-α,rpb1,and rpb2)were newly obtained from ca.200 representative specimens of Boletaceae.Our phylogenetic analyses revealed seven major clades at the subfamily level,namely Austroboletoideae,Boletoideae,Chalciporoideae,Leccinoideae,Xerocomoideae,Zangioideae,and the Pulveroboletus Group.In addition,59 genus-level clades were identified,of which 22 were uncovered for the first time.These 22 clades were mainly placed in Boletoideae and the Pulveroboletus Group.The results further indicated that the characters frequently used in the morphology-based taxonomy of Boletaceae,such as basidiospore ornamentation,the form of the basidioma,and the stuffed pores each had multiple origins within the family,suggesting that the use of such features for high-level classification of Boletaceae should be de-emphasized and combined with other characters.

One hundred noteworthy boletes from China

Fungi of the family Boletaceae are of great importance in both ecology and economy.Our previous molecular phylogenetic studies have shown this family to have an extremely high species diversity in China.To further document the Chinese boletes,morphological studies and phylogenetic analyses were conducted including species of Boletaceae from China and other parts of the world.The results indicate that seven subfamily-level major clades and 62 generic clades can be retrieved,52 of which are found in China.Furthermore,100 species(comprising 32 genera)common in China are illustrated and described here in detail.Among them,four genera and 46 species are new to science,and 26 new combinations are proposed.To interpret the species concepts consistently,epitypes for five species are designated based on collections made from or near the type localities.Notes on eight extralimital species are also provided.Among the species reported here,most of the species are known only from East Asia.Only Leccinum scabrum(Bull.)Gray,Porphyrellus porphyrosporus(Fr.&Hok)E.-J.Gilbert and Tylopilus felleus(Bull.)P.Karst.are widely distributed in the Holarctic,and Buchwaldoboletus lignicola(Kallenb.)Pila´t;Strobilomyces strobilaceus(Scop.)Berk.are in Eurasia;while Aureoboletus mirabilis(Murrill)Halling,Harrya chromapes(Frost)Halling et al.,and Sutorius eximius(Peck)Halling et al.are found throughout East Asia-North America based on morphological and molecular phylogenetic evidences.

Fungal diversity notes 111-252-taxonomic and phylogenetic contributions to fungal taxa

This paper is a compilation of notes on 142 fungal taxa,including five new families,20 new genera,and 100 new species,representing a wide taxonomic and geographic range.The new families,Ascocylindricaceae,Caryosporaceae and Wicklowiaceae(Ascomycota)are introduced based on their distinct lineages and unique morphology.The new Dothideomycete genera Pseudomassariosphaeria(Amniculicolaceae),Heracleicola,Neodidymella and Pseudomicrosphaeriopsis(Didymellaceae),Pseudopithomyces(Didymosphaeriaceae),Brunneoclavispora,Neolophiostoma and Sulcosporium(Halotthiaceae),Lophiohelichrysum(Lophiostomataceae),Galliicola,Populocrescentia and Vagicola(Phaeosphaeriaceae),Ascocylindrica(Ascocylindricaceae),Elongatopedicellata(Roussoellaceae),Pseudoasteromassaria(Latoruaceae)and Pseudomonodictys(Macrodiplodiopsidaceae)are introduced.The newly described species of Dothideomycetes(Ascomycota)are Pseudomassariosphaeria bromicola(Amniculicolaceae),Flammeascoma lignicola(Anteagloniaceae),Ascocylindrica marina(Ascocylindricaceae),Lembosia xyliae(Asterinaceae),Diplodia crataegicola and Diplodia galiicola(Botryosphaeriaceae),Caryospora aquatica(Caryosporaceae),Heracleicola premilcurensis and Neodidymella thailandicum(Didymellaceae),Pseudopithomyces palmicola(Didymosphaeriaceae),Floricola viticola(Floricolaceae),Brunneoclavispora bambusae,Neolophiostoma pigmentatum and Sulcosporium thailandica(Halotthiaceae),Pseudoasteromassaria fagi(Latoruaceae),Keissleriella dactylidicola(Lentitheciaceae),Lophiohelichrysum helichrysi(Lophiostomataceae),Aquasubmersa japonica(Lophiotremataceae),Pseudomonodictys tectonae(Macrodiplodiopsidaceae),Microthyrium buxicola and Tumidispora shoreae(Microthyriaceae),Alloleptosphaeria clematidis,Allophaeosphaeria cytisi,Allophaeosphaeria subcylindrospora,Dematiopleospora luzulae,Entodesmium artemisiae,Galiicola pseudophaeosphaeria,Loratospora luzulae,Nodulosphaeria senecionis,Ophiosphaerella aquaticus,Populocrescentia forlicesenensis and Vagicola vagans(Phaeosphaeriaceae),Elongatopedicellata lignicola,Roussoella magnatum and Roussoella angustior(Roussoellaceae)and Shrungabeeja longiappendiculata(Tetraploasphaeriaceae).The new combinations Pseudomassariosphaeria grandispora,Austropleospora archidendri,Pseudopithomyces chartarum,Pseudopithomyces maydicus,Pseudopithomyces sacchari,Vagicola vagans,Punctulariopsis cremeoalbida and Punctulariopsis efibulata Dothideomycetes.The new genera Dictyosporella(Annulatascaceae),and Tinhaudeus(Halosphaeriaceae)are introduced in Sordariomycetes(Ascomycota)while Dictyosporella aquatica(Annulatascaceae),Chaetosphaeria rivularia(Chaetosphaeriaceae),Beauveria gryllotalpidicola and Beauveria loeiensis(Cordycipitaceae),Seimatosporium sorbi and Seimatosporium pseudorosarum(Discosiaceae),Colletotrichum aciculare,Colletotrichum fusiforme and Colletotrichum hymenocallidicola(Glomerellaceae),Tinhaudeus formosanus(Halosphaeriaceae),Pestalotiopsis subshorea and Pestalotiopsis dracaenea(Pestalotiopsiceae),Phaeoacremonium tectonae(Togniniaceae),Cytospora parasitica and Cytospora tanaitica(Valsaceae),Annulohypoxylon palmicola,Biscogniauxia effusae and Nemania fusoideis(Xylariaceae)are introduced as novel species to order Sordariomycetes.The newly described species of Eurotiomycetes are Mycocalicium hyaloparvicellulum(Mycocaliciaceae).Acarospora septentrionalis and Acarospora castaneocarpa(Acarosporaceae),Chapsa multicarpa and Fissurina carassensis(Graphidaceae),Sticta fuscotomentosa and Sticta subfilicinella(Lobariaceae)are newly introduced in class Lecanoromycetes.In class Pezizomycetes,Helvella pseudolacunosa and Helvella rugosa(Helvellaceae)are introduced as new species.The new families,Dendrominiaceae and Neoantrodiellaceae(Basidiomycota)are introduced together with a new genus Neoantrodiella(Neoantrodiellaceae),here based on both morphology coupled with molecular data.In the class Agaricomycetes,Agaricus pseudolangei,Agaricus haematinus,Agaricus atrodiscus and Agaricus exilissimus(Agaricaceae),Amanita melleialba,Amanita pseudosychnopyramis and Amanita subparvipantherina(Amanitaceae),Entoloma calabrum,Cora barbulata,Dictyonema gomezianum and Inocybe granulosa(Inocybaceae),Xerocomellus sarnarii(Boletaceae),Cantharellus eucalyptorum,Cantharellus nigrescens,Cantharellus tricolor and Cantharellus variabilicolor(Cantharellaceae),Cortinarius alboamarescens,Cortinarius brunneoalbus,Cortinarius ochroamarus,Cortinarius putorius and Cortinarius seidlii(Cortinariaceae),Hymenochaete micropora and Hymenochaete subporioides(Hymenochaetaceae),Xylodon ramicida(Schizoporaceae),Colospora andalasii(Polyporaceae),Russula guangxiensis and Russula hakkae(Russulaceae),Tremella dirinariae,Tremella graphidis and Tremella pyrenulae(Tremellaceae)are introduced.Four new combinations Neoantrodiella gypsea,Neoantrodiella thujae(Neoantrodiellaceae),Punctulariopsis cremeoalbida,Punctulariopsis efibulata(Punctulariaceae)are also introduced here for the division Basidiomycota.Furthermore Absidia caatinguensis,Absidia koreana and Gongronella koreana(Cunninghamellaceae),Mortierella pisiformis and Mortierella formosana(Mortierellaceae)are newly introduced in the Zygomycota,while Neocallimastix cameroonii and Piromyces irregularis(Neocallimastigaceae)are introduced in the Neocallimastigomycota.Reference specimens or changes in classification and notes are provided for Alternaria ethzedia,Cucurbitaria ephedricola,Austropleospora,Austropleospora archidendri,Byssosphaeria rhodomphala,Lophiostoma caulium,Pseudopithomyces maydicus,Massariosphaeria,Neomassariosphaeria and Pestalotiopsis montellica.

Four new genera of the fungal family Boletaceae

Based on our previous molecular phylogenetic analyses,four new genera are described,namely Baorangia,Lanmaoa,Parvixerocomus,and Rugiboletus,and one known genus,Neoboletus,is re-delimitated.Four new species and nine new combinations are proposed.Morphological characters of each genus and related eleven species are described and illustrated.Most of species in the genera described from southwestern China are wild edible mushrooms and can be found in free markets.

Porcini mushrooms(Boletus sect.Boletus)from China

Porcini mushrooms(Boletus sect.Boletus)have both economic and ecological importance.Recent molecular phylogenetic study has uncovered rich species diversity of this group of fungi from China.In this study,the Chinese porcini were characterized by both morphological andmolecular phylogenetic evidence.15 species were recognized,including nine new species,namely B.botryoides,B.fagacicola,B.griseiceps,B.monilifer,B.sinoedulis,B.subviolaceofuscus,B.tylopilopsis,B.umbrinipileus and B.viscidiceps.Three previously described species,viz.B.bainiugan,B.meiweiniuganjun and B.shiyong,were revised,and B.meiweiniuganjun is treated as a synonym of B.bainiugan.A key to the Chinese porcini mushrooms was provided.

The genus Phylloporus (Boletaceae, Boletales) from China: morphological and multilocus DNA sequence analyses

Species of the genus Phylloporus in China were investigated based on morphology and molecular phylogenetic analysis of a three-locus(nrLSU,ITS and tef-1a)DNA sequence dataset.Twenty-one phylogenetic species were recognized among the studied collections.Seven of them are described as new:P.brunneiceps,P.imbricatus,P.maculatus,P.pachycystidiatus,P.rubeolus,P.rubrosquamosus,and P.yunnanensis.In addition,four of them correspond with the previous morphology-based taxa:P.bellus,P.luxiensis,P.parvisporus,and P.rufescens.The remaining ten phylogenetic species were not described due to the paucity of the materials.A key to the Chinese morphologically recognizable taxa was provided.A preliminary biogeographical analysis showed that(1)Pylloporus species in East Asia and Southeast Asia are mostly closely related,(2)species pairs or closely related species of Phylloporus between East Asia and North/Central America are relatively common,and(3)the biogeographic relationship of Phylloporus between East Asia and Europe was supported by only a single species pair.Unexpectedly,no taxa common either to both Europe and East Asia,or to both East Asia and North/Central America,were uncovered.Clades look to have taxa from both sides of the Pacific and Europe/Asia though.

Occultocarpon,a new monotypic genus of Gnomoniaceae on Alnus nepalensis from China

Microfungi in the Gnomoniaceae(Diaporthales,Ascomycetes)comprise species commonly reported as pathogens and endophytes on trees and herbaceous hosts primarily from temperate forests of North America,Europe,and Japan.The diversity of Gnomoniaceae in China is poorly known,although several plant families that occur there specifically the Betulaceae are considered important hosts.An exploratory trip to Yunnan,China,resulted in the discovery of several members of the Gnomoniaceae.In this paper a new monotypic genus,Occultocarpon and its species,O.ailaoshanense,are described and illustrated.A phylogeny based on three genes(LSU,rpb2,tef1-α)reveals that O.ailaoshanense belongs to the Gnomoniaceae and forms a branch distinct from the currently known genera.Occultocarpon ailaoshanense is characterized by perithecia with thin,central to eccentric necks in groups embedded in a stroma and oblong elliptical-elongated,one-septate ascospores.Occultocarpon ailaoshanense occurs on the bark of branches of Alnus nepalensis(Betulaceae)in Yunnan,China.

Borofutus, a new genus of Boletaceae from tropical Asia: phylogeny, morphology and taxonomy

A new monotypic genus in the Boletaceae,Borofutus,typified by B.dhakanus,is described using morphological and molecular evidence.This is a putatively ectomycorrhizal fungus associated with Shorea robusta.Borofutus is characterized by the combination of the following characters:basidiomata small to medium-sized;pileus grayish brown to cocoa brown;hymenophore subdecurrent,cream then golden brown,with broad,nearly hexagonal pores;basidiospores purple to purplish red in H2O,ornamented with irregular to regular shallow pits;cystidia lageniform,thick-walled.Borofutus is sister to Spongiforma in molecular phylogenetic analyses using DNA nucleotide sequences of single or multiple loci.A description,line drawings,phylogenetic placement and comparison with allied taxa are presented herein.