Species diversity, updated classification and divergence times of the phylum Mucoromycota

Zygomycetes are phylogenetically early diverging,ecologically diverse,industrially valuable,agriculturally beneficial,and clinically pathogenic fungi.Although new phyla and subphyla have been constantly established to accommodate spe-cific members and a subkingdom Mucoromyceta,comprising Calcarisporiellomycota,Glomeromycota,Mortierellomycota and Mucoromycota,was erected to unite core zygomycetous fungi,phylogenetic relationships within phyla have not been well resolved.Taking account of the information of monophyly and divergence time estimated from ITS and LSU rDNA sequences,the present study updates the classification framework of the phylum Mucoromycota from the class down to the generic rank:three classes,three orders,20 families(including five new families Circinellaceae,Protomycocladaceae,Rhizomucoraceae,Syzygitaceae and Thermomucoraceae)and 64 genera.The taxonomic hierarchy was calibrated with estimated divergence times:phylum earlier than 617 Mya,classes and orders earlier than 547 Mya,families earlier than 199 Mya,and genera earlier than 12 Mya.Along with this outline,all genera of Mucoromycota are annotated and 58 new species are described.In addition,three new combinations are proposed.In this study,we update the taxonomic backbone of the phylum Mucoromycota and reinforce its phylogeny.We also contribute numerous new taxa and enrich the diversity of Mucoromycota.

Species diversity,taxonomy and phylogeny of Polyporaceae(Basidiomycota)in China

Polyporaceae is one of the most important families of Basidiomycota.Investigations on the species diversity,taxonomy and phylogeny of Polyporaceae in China are carried out.So far 217 species belonging to 42 genera are reported from China.Two new genera:Amylosporia gen.nov.and Murinicarpus gen.nov.,twelve new species:Coriolopsis dendriformis sp.nov.,C.hainanensis sp.nov.,Funalia cystidiata sp.nov.,Haploporus microsporus sp.nov.,Perenniporia citrinoalba sp.nov.,P.yinggelingensis sp.nov.,Picipes hainanensis sp.nov.,P.jiajinensis sp.nov.,P.pseudovarius sp.nov.,Trametes duplexa sp.nov.,T.ellipsoidea sp.nov.and T.stiptica sp.nov.,and six new combinations,Amylosporia hattorii comb.nov.,Hornodermoporus latissimus comb.nov.,Murinicarpus subadustus comb.nov.,Picipes pumilus comb.nov.,Vanderbylia delavayi comb.nov.and Vanderbylia robiniophila comb.nov.,are proposed.All the species are described based on the Chinese collections.Keys to genera of Polyporaceae occurring in China and keys to species of each genus are provided.This monograph provides a revised classification of Polyporaceae in China according to the modern taxonomy.The phylogeny of Polyporaceae from China are reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene(nLSU),the small subunit nuclear ribosomal RNA gene(nSSU),the small subunit mitochondrial rRNA gene sequences(mtSSU),the translation elongation factor 1-αgene(TEF1),theβ-tubulin gene(TBB1),the RNA polymerase II largest subunit(RPB1)and second largest subunit(RPB2)genes.In addition,full morphological descriptions,illustrations,color photographs,taxonomic notes,ecology and all the available sequences of Polyporaceae species found from China are provided.

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.

A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective

In this paper,we provide a phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in 2007.We selected 529 species to address phylogenetic relationships of higher-level taxa using a maximumlikelihood framework and sequence data from six genes traditionally used in fungal molecular systematics(nrLSU,nrSSU,5.8S,tef1-a,rpb1 and rpb2).These species represent 18 classes,62 orders,183 families,and 392 genera from the phyla Basidiomycota(including the newly recognized subphylum Wallemiomycotina)and Entorrhizomycota,and 13 species representing 13 classes of Ascomycota as outgroup taxa.We also conducted a molecular dating analysis based on these six genes for 116 species representing 17 classes and 54 orders of Basidiomycota and Entorrhizomycota.Finally we performed a phyloproteomics analysis from 109 Basidiomycota species and 6 outgroup taxa using amino-acid sequences retrieved from 396 orthologous genes.Recognition of higher taxa follows the criteria in Zhao et al(Fungal Divers 78:239–292,2016):(i)taxa must be monophyletic and statistically well-supported in molecular dating analyses,(ii)their respective stem ages should be roughly equivalent,and(iii)stem ages of higher taxa must be older than those of lower level taxa.The time-tree indicates that the mean of stem ages of Basidiomycota and Entorrhizomycota are ca.530 Ma;subphyla of Basidiomycota are 406–490 Ma;most classes are 358–393 Ma for those of Agaricomycotina and 245–356 Ma for those of Pucciniomycotina and Ustilaginomycotina;most orders of those subphyla split 120–290 Ma.Monophyly of most higherlevel taxa of Basidiomycota are generally supported,especially those taxa introduced in the recent ten years:phylum Entorrhizomycota,classes Malasseziomycetes,Moniliellomycetes,Spiculogloeomycetes,Tritirachiomycetes and orders Amylocorticiales,Golubeviales,Holtermanniales,Jaapiales,Lepidostromatales,Robbauerales,Stereopsidales and Trichosporonales.However,the younger divergence times of Leucosporidiales(Microbotryomycetes)indicate that its order status is not supported,thus we propose combining it under Microbotryales.On the other hand,the families Buckleyzymaceae and Sakaguchiaceae(Cystobasidiomycetes)are raised to Buckleyzymales and Sakaguchiales due to their older divergence times.Cystofilobasidiales(Tremellomycetes)has an older divergence time and should be amended to a higher rank.We however,do not introduce it as new class here for Cystofilobasidiales,as DNA sequences from these taxa are not from their respective types and thus await further studies.Divergence times for Exobasidiomycetes,Cantharellales,Gomphales and Hysterangiales were obtained based on limited species sequences in molecular dating study.More comprehensive phylogenetic studies on those four taxa are needed in the future because our ML analysis based on wider sampling,shows they are not monophyletic groups.In general,the six-gene phylogenies are in agreement with the phyloproteomics tree except for the placements of Wallemiomycotina,orders Amylocorticiales,Auriculariales,Cantharellales,Geastrales,Sebacinales and Trechisporales from Agaricomycetes.These conflicting placements in the six-gene phylogeny vs the phyloproteomics tree are discussed.This leads to future perspectives for assessing gene orthology and problems in deciphering taxon ranks using divergence times.

Fungal diversity notes 367-490:taxonomic and phylogenetic contributions to fungal taxa

This is a continuity of a series of taxonomic papers where materials are examined,described and novel combinations are proposed where necessary to improve our traditional species concepts and provide updates on their classification.In addition to extensive morphological descriptions and appropriate asexual and sexual connections,DNA sequence data are also analysed from concatenated datasets(rDNA,TEF-a,RBP2 and b-Tubulin)to infer phylogenetic relationships and substantiate systematic position of taxa within appropriate ranks.Wherever new species or combinations are being proposed,we apply an integrative approach(morphological and molecular data as well as ecological features wherever applicable).Notes on 125 fungal taxa are compiled in this paper,including eight new genera,101 new species,two new combinations,one neotype,four reference specimens,new host or distribution records for eight species and one alternative morphs.The new genera introduced in this paper are Alloarthopyrenia,Arundellina,Camarosporioides,Neomassaria,Neomassarina,Neotruncatella,Paracapsulospora and Pseudophaeosphaeria.The new species are Alfaria spartii,Alloarthopyrenia italica,Anthostomella ravenna,An.thailandica,Arthrinium paraphaeospermum,Arundellina typhae,Aspergillus koreanus,Asterina cynometrae,Bertiella ellipsoidea,Blastophorum aquaticum,Cainia globosa,Camarosporioides phragmitis,Ceramothyrium menglunense,Chaetosphaeronema achilleae,Chlamydotubeufia helicospora,Ciliochorella phanericola,Clavulinopsis aurantiaca,Colletotrichum insertae,Comoclathris italica,Coronophora myricoides,Cortinarius fulvescentoideus,Co.nymphatus,Co.pseudobulliardioides,Co.tenuifulvescens,Cunninghamella gigacellularis,Cyathus pyristriatus,Cytospora cotini,Dematiopleospora alliariae,De.cirsii,Diaporthe aseana,Di.garethjonesii,Distoseptispora multiseptata,Dis.tectonae,Dis.tectonigena,Dothiora buxi,Emericellopsis persica,Gloniopsis calami,Helicoma guttulatum,Helvella floriforma,H.oblongispora,Hermatomyces subiculosa,Juncaceicola italica,Lactarius dirkii,Lentithecium unicellulare,Le.voraginesporum,Leptosphaeria cirsii,Leptosphaeria irregularis,Leptospora galii,Le.thailandica,Lindgomyces pseudomadisonensis,Lophiotrema bambusae,Lo.fallopiae,Meliola citri-maximae,Minimelanolocus submersus,Montagnula cirsii,Mortierella fluviae,Muriphaeosphaeria ambrosiae,Neodidymelliopsis ranunculi,Neomassaria fabacearum,Neomassarina thailandica,Neomicrosphaeropsis cytisi,Neo.cytisinus,Neo.minima,Neopestalotiopsis cocoe¨s,Neopestalotiopsis musae,Neoroussoella lenispora,Neotorula submersa,Neotruncatella endophytica,Nodulosphaeria italica,Occultibambusa aquatica,Oc.chiangraiensis,Ophiocordyceps hemisphaerica,Op.lacrimoidis,Paracapsulospora metroxyli,Pestalotiopsis sequoiae,Peziza fruticosa,Pleurotrema thailandica,Poaceicola arundinis,Polyporus mangshanensis,Pseudocoleophoma typhicola,Pseudodictyosporium thailandica,Pseudophaeosphaeria rubi,Purpureocillium sodanum,Ramariopsis atlantica,Rhodocybe griseoaurantia,Rh.indica,Rh.luteobrunnea,Russula indoalba,Ru.pseudoamoenicolor,Sporidesmium aquaticivaginatum,Sp.olivaceoconidium,Sp.pyriformatum,Stagonospora forlicesenensis,Stagonosporopsis centaureae,Terriera thailandica,Tremateia arundicola,Tr.guiyangensis,Trichomerium bambusae,Tubeufia hyalospora,Tu.roseohelicospora and Wojnowicia italica.New combinations are given for Hermatomyces mirum and Pallidocercospora thailandica.A neotype is proposed for Cortinarius fulvescens.Reference specimens are given for Aquaphila albicans,Leptospora rubella,Platychora ulmi and Meliola pseudosasae,while new host or distribution records are provided for Diaporthe eres,Di.siamensis,Di.foeniculina,Dothiorella iranica,Do.sarmentorum,Do.vidmadera,Helvella tinta and Vaginatispora fuckelii,with full taxonomic details.An asexual state is also reported for the first time in Neoacanthostigma septoconstrictum.This paper contributes to a more comprehensive update and improved identification of many ascomycetes and basiodiomycetes.

Fungal diversity notes 1277-1386:taxonomic and phylogenetic contributions to fungal taxa

This is the twelfth contribution to the Fungal Diversity Notes series on fungal taxonomy,based on materials collected from many countries which were examined and described using the methods of morphology,anatomy,and strain culture,combined with DNA sequence analyses.110 taxa are described and illustrated,including five new genera,92 new species,eight new combinations and other taxonomic contributions(one new sequenced species,one new host and three new records)which are accommodated in 40 families and 1 incertae sedis in Dothideomycetes.The new genera are Amyloceraceomyces,Catenuliconidia,Hansenopezia,Ionopezia and Magnopulchromyces.The new species are Amyloceraceomyces angustisporus,Amylocorticium ellipsosporum,Arthrinium sorghi,Catenuliconidia uniseptata,Clavulina sphaeropedunculata,Colletotrichum parthenocissicola,Coniothyrium triseptatum,Cortinarius indorusseus,C.paurigarhwalensis,C.sinensis,C.subsanguineus,C.xiaojinensis,Diaporthe pimpinel-lae,Dictyosporella guizhouensis,Diplodia torilicola,Fuscoporia marquesiana,F.semiarida,Hansenopezia decora,Helicoarcta-tus thailandicus,Hirsutella hongheensis,Humidicutis brunneovinacea,Lentaria gossypina,L.variabilis,Lycoperdon lahorense,L.pseudocurtisii,Magnopulchromyces scorpiophorus,Moelleriella gracilispora,Neodevriesia manglicola,Neodidymelliopsis salvia,N.urticae,Neoroussoella magnoliae,Neottiella gigaspora,Ophiosphaerella chiangraiensis,Phaeotremella yunnanensis,Podosphaera yulii,Rigidoporus juniperinus,Rhodofomitopsis pseudofeei,Russula benghalensis,Scleroramularia vermispora,Scytinopogon minisporus,Sporormurispora paulsenii,Thaxteriellopsis obliqus,Tomentella asiae-orientalis,T.atrobadia,T.atrocastanea,T.aureomarginata,T.brevis,T.brunneoflava,T.brunneogrisea,T.capitatocystidiata,T.changbaiensis,T.citri-nocystidiata,T.coffeae,T.conclusa,T.cystidiata,T.dimidiata,T.duplexa,T.efibulata,T.efibulis,T.farinosa,T.flavidobadia,T.fuscocrustosa,T.fuscofarinosa,T.fuscogranulosa,T.fuscopelliculosa,T.globospora,T.gloeocystidiata,T.griseocastanea,T.griseofusca,T.griseomarginata,T.inconspicua,T.incrustata,T.interrupta,T.liaoningensis,T.longiaculeifera,T.longiechinuli,T.megaspora,T.olivacea,T.olivaceobrunnea,T.pallidobrunnea,T.pallidomarginata,T.parvispora,T.pertenuis,T.qingyuanensis,T.segregata,T.separata,T.stipitata,T.storea,Trichoderma ceratophylletum,Tyromyces minutulus,Umbelopsis heterosporus and Xylolentia reniformis.The new combinations are Antrodiella descendena,Chloridium macrocladum,Hansenopezia retrocurvata,Rhodofomitopsis monomitica,Rh.oleracea,Fuscoporia licnoides,F.scruposa and Ionopezia gerardii.A new sequenced species(Graphis supracola),one new host(Aplosporella prunicola)and three new geographical records(Golovinomyces monardae,Paradictyoarthrinium diffractum and Prosthemium betulinum),are reported.

Taxonomy and phylogeny of the brown-rot fungi:Fomitopsis and its related genera

Taxonomic and phylogenetic studies on the brown-rot fungi,Fomitopsis and its related genera,are carried out.On the basis of morphological characters and phylogenetic evidence of DNA sequences of multiple loci including the internal transcribed spacer(ITS)regions,the large subunit nuclear ribosomal RNA gene(nLSU),the small subunit nuclear ribosomal RNA gene(nSSU),the small subunit mitochondrial rRNA gene sequences(mtSSU),the translation elongation factor 1-αgene(tef1)and the second subunit of RNA polymerase II(rpb2),six new genera,Fragifomes,Niveoporofomes,Piptoporellus,Rhodofomitopsis,Rubellofomes and Ungulidaedalea are established.Four new species,Buglossoporus eucalypticola,Daedalea allantoidea,Piptoporellus hainanensis and P.triqueter are descibed from China.Illustrated descriptions of the novel species are provided.Identification keys to Fomitopsis and its related genera,as well as keys to the species of each genus are provided.

Phylogeny,divergence time estimation,and biogeography of the genus Heterobasidion(Basidiomycota,Russulales)

There have been several investigations into the genus Heterobasidion,however,differentiation of species in these studies have depended on the gene regions analyzed.Reliable defining of species,establishing species divergence times and establishing species biogeographical distributions have been challenging.Here,we used a multilocus phylogenetic approach and maximum parsimony,maximum likehood,and Bayesian analyses to infer the phylogenetic relationships of Heterobasidion species.In addition,we focused on a fungus fossil-based approach and used the largest subunit of RNA polymerase II-the second subunit of RNA polymerase II(RPB1-RPB2)dataset to perform maximum likelihoodbased estimation and Bayesian binary analyses,to assess the divergence and biogeographical distributions of Heterobasidion species.The Heterobasidion annousum/H.insulare species complex clusters in three groups in the phylogenetic analyses.Molecular dating suggests that ancestral Heterobasidion species originated in Eurasia during the Early Miocene,followed by dispersal and speciation to other continents during the Middle Miocene and Early Pliocene.Our data are compatible with the previous viewpoint that H.irregulare and H.occidentale colonized North America via different routes,which has been interpreted as Beringian and Thulean North Atlantic vicariance.In addition,we propose that the occurrence of H.araucariae in the southern Hemisphere was probably due to recent human-mediated introductions.Plate tectonics and long-distance dispersal are the most likely factors that influenced Heterobasidion speciation and biogeography.

FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

New species and phylogeny of Perenniporia based on morphological and molecular characters

Three new resupinate,poroid,wood-inhabiting fungi,Perenniporia aridula,P.bannaensis and P.substraminea,are introduced on the basis of morphological and molecular characters.Molecular study based on sequence data from the ribosomal ITS and LSU regions supported the three new species’positions in Perenniporia s.s.,and all of them formed monophyletic lineages with strong support(100%BP,1.00 BPP).Phylogenetic analysis revealed seven clades for the 31 species of Perenniporia s.l.used in this study.Among them,Perenniporiella clustered with Perenniporia ochroleuca group,and then subsequently grouped with Abundisporus.In addition,the P.ochroleuca group,the P.vicina group,the P.martia group and P.subacida formed well supported monophyletic entities,which could be recognized as distinct genera,and they are not related to P.medulla-panis which belongs to Perenniporia s.s.clade.An identification key to 38 species of Perenniporia occurring in China is provided.

Fragiliporiaceae,a new family of Polyporales(Basidiomycota)

Fragiliporiaceae fam.nov.,a new poroid wood-inhabiting family,is introduced based on the combination of molecular and morphological data,and is typified by Fragiliporia gen.nov.The phylogenetic analysis shows that Fragiliporia fragilis sp.nov.forms a monophyletic group within Polyporales and warrants the introduction of a new fragiliporia clade based on molecular data of ITS+nLSU rRNA gene regions.Combined ITS,nLSU,mtSSU,TEF1 and RPB2 sequence data also demonstrated that the new family Fragiliporiaceae also formed a monophyletic lineage(70%BS,57%BP,0.99 BPP),and grouped with the phlebioid clade,residual polyporoid clade and core polyporoid clade.Fragiliporiaceae has unique macromorphological characters in having resupinate basidiocarps with very soft tubes when fresh,which become brittle when dry(becoming almost powdery when bruised);a monomitic hyphal system with thick-walled generative hyphae,clamp connections,and frequently H-,W-or Y-shaped hyphae branching from the clamp connections.

Correction to:FungalTraits:a user friendly traits database of fungi and fungus-like stramenopiles

Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original article has been corrected.