The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications.However,the genomic era also brings new challenges,as phylogenetic incongruenc...The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications.However,the genomic era also brings new challenges,as phylogenetic incongruences make the appearance of monophyly in some phylogenetic trees questionable.Existing criteria for constructing taxonomic systems,such as diagnostic characters and divergence time,become insufficient to address this challenge.Through order-level analyses of genomic data of the Subkingdom Dikarya within the Kingdom Fungi,we introduce the extended quadripartition internode certainty(EQP-IC)value as a novel criterion for constructing high-level fungal classifications,with a recommended threshold of 0.1 for each taxonomic rank.Suprageneric taxa with an EQP-IC value exceeding 0.1 exhibit reduced topological variation,suggesting a stronger correspondence with natural taxonomic category.This new criterion was also put into practice to investigate the derived suborders of mushroom-forming Agaricales,including three suborders,Agaricineae,Pluteineae,and Tricholomatineae(APT),that had been long-standing problems in phylogenetic analyses.In total,142 genomes,including 64 newly generated ones,were utilized to reconstruct the phylogenetic relationships and delve into the phylogenetic incongruencies and evolutionary histories of APT.Our data suggested widespread and high-level incomplete lineage sorting(ILS)and introgression/hybridization(IH)present among suborders within the APT.Therefore,a dichotomous phylogenetic tree may not reflect the real relationships among the clades within the APT.Instead,their natural relationships may be reticulate.Three newly named suborders,Amanitineae,Macrocystidiineae,and Omphalinineae are added to the clade including APT.The new combination Baisuzhenia humphreyi,new genus Baisuzhenia,new family Baisuzheniaceae,and new suborder Baisuzheniineae are proposed to accommodate Stereopsis humphreyi,which shows an independent,but close relationship,with the clade formed by the six above-mentioned derived suborders of Agaricales.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
Basidiomycota is one of the major phyla in the fungal tree of life.The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology.In this study,we present a time-framed p...Basidiomycota is one of the major phyla in the fungal tree of life.The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology.In this study,we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families,47 orders,14 classes and four subphyla;we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019;and we provide notes for each order and discuss the history,defining characteristics,evolution,justification of orders,problems,significance,and plates.Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443-490 Myr(million years),classes in a time range of 312-412 Myr,and orders in a time range of 102-361 Myr.Families diverged in a time range of 50-289 Myr,76-224 Myr,and 62-156 Myr in Agaricomycotina,Pucciniomycotina,and Ustilaginomycotina,respectively.Based on the phylogenomic relationships and divergence times,we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae.In the current outline of Basidiomycota,there are four subphyla,20 classes,77 orders,297 families,and 2134 genera accepted.When building a robust taxonomy of Basidiomycota in the genomic era,the generation of molecular phylogenetic data has become relatively easier.Finding phenotypical characters,especially those that can be applied for identification and classification,however,has become increasingly challenging.展开更多
基金supported by the Joint Funds of the National Natural Science Foundation of China and Yunnan Provincial Government(U2202205)Yunnan Revitalization Talent Support Program:Science&Technology Champion Project(202305AB350004)+1 种基金the Science and Technology Fundamental Resources Investigation Program of the Ministry of Science and Technology of China(2023FY101303)the National Natural Science Foundation of China(no.31670024).
文摘The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications.However,the genomic era also brings new challenges,as phylogenetic incongruences make the appearance of monophyly in some phylogenetic trees questionable.Existing criteria for constructing taxonomic systems,such as diagnostic characters and divergence time,become insufficient to address this challenge.Through order-level analyses of genomic data of the Subkingdom Dikarya within the Kingdom Fungi,we introduce the extended quadripartition internode certainty(EQP-IC)value as a novel criterion for constructing high-level fungal classifications,with a recommended threshold of 0.1 for each taxonomic rank.Suprageneric taxa with an EQP-IC value exceeding 0.1 exhibit reduced topological variation,suggesting a stronger correspondence with natural taxonomic category.This new criterion was also put into practice to investigate the derived suborders of mushroom-forming Agaricales,including three suborders,Agaricineae,Pluteineae,and Tricholomatineae(APT),that had been long-standing problems in phylogenetic analyses.In total,142 genomes,including 64 newly generated ones,were utilized to reconstruct the phylogenetic relationships and delve into the phylogenetic incongruencies and evolutionary histories of APT.Our data suggested widespread and high-level incomplete lineage sorting(ILS)and introgression/hybridization(IH)present among suborders within the APT.Therefore,a dichotomous phylogenetic tree may not reflect the real relationships among the clades within the APT.Instead,their natural relationships may be reticulate.Three newly named suborders,Amanitineae,Macrocystidiineae,and Omphalinineae are added to the clade including APT.The new combination Baisuzhenia humphreyi,new genus Baisuzhenia,new family Baisuzheniaceae,and new suborder Baisuzheniineae are proposed to accommodate Stereopsis humphreyi,which shows an independent,but close relationship,with the clade formed by the six above-mentioned derived suborders of Agaricales.
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.
基金provided by National Natural Science Foundation of China(Grant nos.32100011,31961143010,31970010,31470152)China Postdoctoral Science Foundation(Grant no.2021M693361)+3 种基金National Key R&D Program of China project”Accurate identification and innovative utilization of germplasm resources of edible mushrooms suitable for factory cultivation(Grant no.2022YFD1200605)Beijing Innovation Consortium of Agriculture Research System(Grant no.BAIC03-01)Biological Resources Programme,Chinese Academy of Sciences(Grant no.KFJ-BRP-009-003)Survey of Wildlife Resources in Key Areas of Tibet(Grant no.ZL202203601).
文摘Basidiomycota is one of the major phyla in the fungal tree of life.The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology.In this study,we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families,47 orders,14 classes and four subphyla;we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019;and we provide notes for each order and discuss the history,defining characteristics,evolution,justification of orders,problems,significance,and plates.Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443-490 Myr(million years),classes in a time range of 312-412 Myr,and orders in a time range of 102-361 Myr.Families diverged in a time range of 50-289 Myr,76-224 Myr,and 62-156 Myr in Agaricomycotina,Pucciniomycotina,and Ustilaginomycotina,respectively.Based on the phylogenomic relationships and divergence times,we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae.In the current outline of Basidiomycota,there are four subphyla,20 classes,77 orders,297 families,and 2134 genera accepted.When building a robust taxonomy of Basidiomycota in the genomic era,the generation of molecular phylogenetic data has become relatively easier.Finding phenotypical characters,especially those that can be applied for identification and classification,however,has become increasingly challenging.
