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.

Fungal diversity notes 929-1035:taxonomic and phylogenetic contributions on genera and species of fungi

This article is the ninth in the series of Fungal Diversity Notes,where 107 taxa distributed in three phyla,nine classes,31 orders and 57 families are described and illustrated.Taxa described in the present study include 12 new genera,74 new species,three new combinations,two reference specimens,a re-circumscription of the epitype,and 15 records of sexualasexual morph connections,new hosts and new geographical distributions.Twelve new genera comprise Brunneofusispora,Brunneomurispora,Liua,Lonicericola,Neoeutypella,Paratrimmatostroma,Parazalerion,Proliferophorum,Pseudoastrosphaeriellopsis,Septomelanconiella,Velebitea and Vicosamyces.Seventy-four new species are Agaricus memnonius,A.langensis,Aleurodiscus patagonicus,Amanita flavoalba,A.subtropicana,Amphisphaeria mangrovei,Baorangia major,Bartalinia kunmingensis,Brunneofusispora sinensis,Brunneomurispora lonicerae,Capronia camelliaeyunnanensis,Clavulina thindii,Coniochaeta simbalensis,Conlarium thailandense,Coprinus trigonosporus,Liua muriformis,Cyphellophora filicis,Cytospora ulmicola,Dacrymyces invisibilis,Dictyocheirospora metroxylonis,Distoseptispora thysanolaenae,Emericellopsis koreana,Galiicola baoshanensis,Hygrocybe lucida,Hypoxylon teeravasati,Hyweljonesia indica,Keissleriella caraganae,Lactarius olivaceopallidus,Lactifluus midnapurensis,Lembosia brigadeirensis,Leptosphaeria urticae,Lonicericola hyaloseptispora,Lophiotrema mucilaginosis,Marasmiellus bicoloripes,Marasmius indojasminodorus,Micropeltis phetchaburiensis,Mucor orantomantidis,Murilentithecium lonicerae,Neobambusicola brunnea,Neoeutypella baoshanensis,Neoroussoella heveae,Neosetophoma lonicerae,Ophiobolus malleolus,Parabambusicola thysanolaenae,Paratrimmatostroma kunmingensis,Parazalerion indica,Penicillium dokdoense,Peroneutypa mangrovei,Phaeosphaeria cycadis,Phanerochaete australosanguinea,Plectosphaerella kunmingensis,Plenodomus artemisiae,P.lijiangensis,Proliferophorum thailandicum,Pseudoastrosphaeriellopsis kaveriana,Pseudohelicomyces menglunicus,Pseudoplagiostoma mangiferae,Robillarda mangiferae,Roussoella elaeicola,Russula choptae,R.uttarakhandia,Septomelanconiella thailandica,Spencermartinsia acericola,Sphaerellopsis isthmospora,Thozetella lithocarpi,Trechispora echinospora,Tremellochaete atlantica,Trichoderma koreanum,T.pinicola,T.rugulosum,Velebitea chrysotexta,Vicosamyces venturisporus,Wojnowiciella kunmingensis and Zopfiella indica.Three new combinations are Baorangia rufomaculata,Lanmaoa pallidorosea and Wojnowiciella rosicola.The reference specimens of Canalisporium kenyense and Tamsiniella labiosa are designated.The epitype of Sarcopeziza sicula is re-circumscribed based on cyto-and histochemical analyses.The sexual-asexual morph connection of Plenodomus sinensis is reported from ferns and Cirsium for the first time.In addition,the new host records and country records are Amanita altipes,A.melleialba,Amarenomyces dactylidis,Chaetosphaeria panamensis,Coniella vitis,Coprinopsis kubickae,Dothiorella sarmentorum,Leptobacillium leptobactrum var.calidus,Muyocopron lithocarpi,Neoroussoella solani,Periconia cortaderiae,Phragmocamarosporium hederae,Sphaerellopsis paraphysata and Sphaeropsis eucalypticola.

Can we use environmental DNA as holotypes?

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community.The idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(i.e.sequence based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,i.e.can we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to mgDNA.There has been much debate,through several publications on the considerable problems of using mgDNA as holotypes.The proponents have tried to debate the virtues of using mgDNA as holotypes.Those against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with mgDNA.Different disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar ideas.In this paper we explore the use of mgDNA as holotypes.We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences.In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal taxonomy.In fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological roles.We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes.The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed.We provide evidence from case studies on Botryosphaeria,Colletotrichum,Penicillium and Xylaria.The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing.We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species.If this approach adopted,it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes.We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.