Early-diverging fungal phyla:taxonomy,species concept,ecology,distribution,anthropogenic impact,and novel phylogenetic proposals

The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa,has dramatically changed the classification system of early-diverging fungi over the past several decades.The number of phyla established for non-Dikarya fungi has increased from 2 to 17.However,to date,both the classification and phylogeny of the basal fungi are still unresolved.In this article,we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla.We also provide information on the ecology and distribu-tion in Mucoromycota and highlight the impact of chytrids on amphibian populations.Species concepts in Chytridiomycota,Aphelidiomycota,Rozellomycota,Neocallimastigomycota are discussed in this paper.To preserve the current application of the genus Nephridiophaga(Chytridiomycota:Nephridiophagales),a new type species,Nephridiophaga blattellae,is proposed.

Fungal diversity notes 1387-1511:taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 13th contribution in the Fungal Diversity Notes series,wherein 125 taxa from four phyla,ten classes,31 orders,69 families,92 genera and three genera incertae sedis are treated,demonstrating worldwide and geographic distri-bution.Fungal taxa described and illustrated in the present study include three new genera,69 new species,one new com-bination,one reference specimen and 51 new records on new hosts and new geographical distributions.Three new genera,Cylindrotorula(Torulaceae),Scolecoleotia(Leotiales genus incertae sedis)and Xenovaginatispora(Lindomycetaceae)are introduced based on distinct phylogenetic lineages and unique morphologies.Newly described species are Aspergillus lan-naensis,Cercophora dulciaquae,Cladophialophora aquatica,Coprinellus punjabensis,Cortinarius alutarius,C.mammil-latus,C.quercoflocculosus,Coryneum fagi,Cruentomycena uttarakhandina,Cryptocoryneum rosae,Cyathus uniperidiolus,Cylindrotorula indica,Diaporthe chamaeropicola,Didymella azollae,Diplodia alanphillipsii,Dothiora coronicola,Efibula rodriguezarmasiae,Erysiphe salicicola,Fusarium queenslandicum,Geastrum gorgonicum,G.hansagiense,Helicosporium sexualis,Helminthosporium chiangraiensis,Hongkongmyces kokensis,Hydrophilomyces hydraenae,Hygrocybe boertmannii,Hyphoderma australosetigerum,Hyphodontia yunnanensis,Khaleijomyces umikazeana,Laboulbenia divisa,Laboulbenia triarthronis,Laccaria populina,Lactarius pallidozonarius,Lepidosphaeria strobelii,Longipedicellata megafusiformis,Lophiotrema lincangensis,Marasmius benghalensis,M.jinfoshanensis,M.subtropicus,Mariannaea camelliae,Mel-anographium smilaxii,Microbotryum polycnemoides,Mimeomyces digitatus,Minutisphaera thailandensis,Mortierella solitaria,Mucor harpali,Nigrograna jinghongensis,Odontia huanrenensis,O.parvispina,Paraconiothyrium ajrekarii,Par-afuscosporella niloticus,Phaeocytostroma yomensis,Phaeoisaria synnematicus,Phanerochaete hainanensis,Pleopunctum thailandicum,Pleurotheciella dimorphospora,Pseudochaetosphaeronema chiangraiense,Pseudodactylaria albicolonia,Rhexoacrodictys nigrospora,Russula paravioleipes,Scolecoleotia eriocamporesi,Seriascoma honghense,Synandromyces makranczyi,Thyridaria aureobrunnea,Torula lancangjiangensis,Tubeufia longihelicospora,Wicklowia fusiformispora,Xenovaginatispora phichaiensis and Xylaria apiospora.One new combination,Pseudobactrodesmium stilboideus is pro-posed.A reference specimen of Comoclathris permunda is designated.New host or distribution records are provided for Acrocalymma fici,Aliquandostipite khaoyaiensis,Camarosporidiella laburni,Canalisporium caribense,Chaetoscutula juniperi,Chlorophyllum demangei,C.globosum,C.hortense,Cladophialophora abundans,Dendryphion hydei,Diaporthe foeniculina,D.pseudophoenicicola,D.pyracanthae,Dictyosporium pandanicola,Dyfrolomyces distoseptatus,Ernakula-mia tanakae,Eutypa flavovirens,E.lata,Favolus septatus,Fusarium atrovinosum,F.clavum,Helicosporium luteosporum,Hermatomyces nabanheensis,Hermatomyces sphaericoides,Longipedicellata aquatica,Lophiostoma caudata,L.clematidis-vitalbae,Lophiotrema hydei,L.neoarundinaria,Marasmiellus palmivorus,Megacapitula villosa,Micropsalliota globocys-tis,M.gracilis,Montagnula thailandica,Neohelicosporium irregulare,N.parisporum,Paradictyoarthrinium diffractum,Phaeoisaria aquatica,Poaceascoma taiwanense,Saproamanita manicata,Spegazzinia camelliae,Submersispora variabi-lis,Thyronectria caudata,T.mackenziei,Tubeufia chiangmaiensis,T.roseohelicospora,Vaginatispora nypae,Wicklowia submersa,Xanthagaricus necopinatus and Xylaria haemorrhoidalis.The data presented herein are based on morphological examination of fresh specimens,coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Forecasting the number of species of asexually reproducing fungi(Ascomycota and Basidiomycota)

Asexually reproducing fungi play a significant role in essential processes in managed and wild ecosystems such as nutrients cycling and multitrophic interactions.A large number of such taxa are among the most notorious plant and animal pathogens.In addition,they have a key role in food production,biotechnology and medicine.Taxa without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based taxonomy.The number,variation and diversity of asexually reproducing taxa are insufficiently known,even though fungi capable of asexual reproduction may provide an untapped,rich biological resource for future exploitation.Currently,ca.30,000 asexual species belonging to ca.3800 genera have been reported(including 1388 coelomycetous and 2265 hyphomycetous genera).Recent reports(2017–2020)reiterate that the number of asexually producing fungi is higher than the number of frequently sexually-reproducing fungi.With the advent of molecular tools and the abandonment of the dual nomenclature system for pleomorphic fungi,priority criteria were established and revisited in the latest outline of fungi and fungus-like taxa.However,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be addressed.The number of species of speciose genera(e.g.Alternaria,Aspergillus,Cercospora,Fusarium,Phoma and Pseudocercospora),cryptic species,species of pleomorphic genera,less studied life modes(such as lichenicolous taxa,taxa from extreme environments)and species from biodiversity-rich areas still need evaluation to achieve more reliable estimates of their diversity.This paper discusses the current knowledge on the matter,with diversity estimates,and potential obstacles in several chapters on(1)speciose genera;(2)pleomorphic genera;(3)cryptic species;(4)well-studied but insufficiently resolved taxa,e.g.leaf inhabiting species,marine fungi,(5)less studied life modes,e.g.lichenicolous,rock-inhabiting fungi,insect-associated and yeast-forming taxa and(6)species from biodiversity-rich areas.

Taming the beast:a revised classification of Cortinariaceae based on genomic data

Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.