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 i...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.展开更多
Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae.The phylogenetically supported genera we re...Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae.The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are:Acantholichen,Ampulloclitocybe,Arrhenia,Cantharellula,Cantharocybe,Chromosera,Chrysomphalina,Cora,Corella,Cuphophyllus,Cyphellostereum,Dictyonema,Eonema,Gliophorus,Haasiella,Humidicutis,Hygroaster,Hygrocybe,Hygrophorus,Lichenomphalia,Neohygrocybe,Porpolomopsis and Pseudoarmillariella.A new genus that is sister to Chromosera is described as Gloioxanthomyces.Revisions were made at the ranks of subfamily,tribe,genus,subgenus,section and subsection.We present three new subfamilies,eight tribes(five new),eight subgenera(one new,one new combination and one stat.nov.),26 sections(five new and three new combinations and two stat.nov.)and 14 subsections(two new,two stat.nov.).Species of Chromosera,Gliophorus,Humidicutis,and Neohygrocybe are often treated within the genus Hygrocybe;we therefore provide valid names in both classification systems.We used a minimalist approach in transferring genera and creating new names and combinations.Consequently,we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus,Ampulloclitocybe andCantharocybe,despite weak phylogenetic support.We include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are lacking.The lower hygrophoroid clade is basal to Hygrophoraceae s.s.,comprising the genera Aphroditeola,Macrotyphula,Phyllotopsis,Pleurocybella,Sarcomyxa,Tricholomopsis and Typhula.展开更多
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 a...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.展开更多
Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,an...Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.展开更多
The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corr...The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.展开更多
基金Estonian Science Foundation grants PSG136,PRG632,PUT1170the University of Tartu(PLTOM20903)the European Regional Development Fund(Centre of Excellence EcolChange).
文摘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.
基金This work was not directly supported by grants,but the following grants were essential in obtaining collections and some sequences used in this work:US NSF Biodiversity Surveys and Inventories Program grants to the Research Foundation of the State University of New York,College at Cortland(DEB-9525902 and DEB-0103621),in collaboration with the USDA-Forest Service,Center for Forest Mycology Research,Forest Products Laboratory in Madison supported collecting in Belize,the Dominican Republic and Puerto Rico.US NSF grant DBI 6338699 to K.W.Hughes and R.H.Peterson at the University of Tennessee,Knoxville supported collecting by E.Lickey,D.J.Lodge,K.W.Hughes,R.Kerrigan,A.Methven,V.P.Hustedt,P.B.Matheny and R.H.Petersen in the Great Smoky Mountain National Park,and sequencing by K.W.Hughes and Lickey.A National Geographic Society’s Committee for Research and Exploration grant to T.J.Baroni(SUNY Cortland)supported the 2007 expedition to Doyle’s Delight in Belize by M.C.Aime,T.J.Baroni and D.J.Lodge.An Explorer’s Club,Washington Group Exploration and Field Research Grant to M.C.Aime and a National Geographic Society’s Committee for Research and Exploration grant to T.Henkel supported collecting in Guyana.
文摘Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae.The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are:Acantholichen,Ampulloclitocybe,Arrhenia,Cantharellula,Cantharocybe,Chromosera,Chrysomphalina,Cora,Corella,Cuphophyllus,Cyphellostereum,Dictyonema,Eonema,Gliophorus,Haasiella,Humidicutis,Hygroaster,Hygrocybe,Hygrophorus,Lichenomphalia,Neohygrocybe,Porpolomopsis and Pseudoarmillariella.A new genus that is sister to Chromosera is described as Gloioxanthomyces.Revisions were made at the ranks of subfamily,tribe,genus,subgenus,section and subsection.We present three new subfamilies,eight tribes(five new),eight subgenera(one new,one new combination and one stat.nov.),26 sections(five new and three new combinations and two stat.nov.)and 14 subsections(two new,two stat.nov.).Species of Chromosera,Gliophorus,Humidicutis,and Neohygrocybe are often treated within the genus Hygrocybe;we therefore provide valid names in both classification systems.We used a minimalist approach in transferring genera and creating new names and combinations.Consequently,we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus,Ampulloclitocybe andCantharocybe,despite weak phylogenetic support.We include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are lacking.The lower hygrophoroid clade is basal to Hygrophoraceae s.s.,comprising the genera Aphroditeola,Macrotyphula,Phyllotopsis,Pleurocybella,Sarcomyxa,Tricholomopsis and Typhula.
文摘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.
基金SS and JH were supported by NIH/NIAID R37 MERIT Award AI39115-23NIH/NIAID R01 Award AI50113-16+1 种基金and NIH/NIAID R01 Award AI133654-03EJL was supported by BBSRC Award BB/L022508/1.DB was supported by DFG Award BE 2201/23-1 and BE 2201/28-1.JH is also co-director and fellow of the CIFAR program Fungal Kingdom:Threats&Opportunities.MCA acknowledges USDA Hatch project 1010662.
文摘Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.
文摘The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.
