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Trends in yeast diversity discovery

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Fungal Diversity 2022年第3期114卷 491-537页

作者： teun boekhout Anthony S.Amend Fouad El Baidouri Toni Gabaldón József Geml Moritz Mittelbach Vincent Robert Chen Shuhui Tan Benedetta Turchetti Duong Vu Qi-Ming Wang Andrey Yurkov Westerdijk Institute of Fungal Biodiversity Uppsalalaan 83584CT UtrechtThe Netherlands Institute of Biodiversity and Ecosystems Dynamics(IBED) University of AmsterdamSciencepark 9041098 XH AmsterdamThe Netherlands School of Life Sciences University of Hawaii at Manoa2538 McCarthy MallEdmonson 216HonoluluHI 96822USA Barcelona Supercomputing Centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain MTA-EKE Lendület Environmental Microbiome Research Group Eszterházy Károly UniversityLeányka u.6.3300 EgerHungary Senate Department for the Environment Transport and Climate ProtectionBerlinGermany The Yeasts Foundation UtrechtThe Netherlands Department of Agriculture Food and Environmental SciencesUniversity of PerugiaPerugiaItaly Industrial Yeasts Collection DBVPG University of PerugiaPerugiaItaly College of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071002HebeiChina Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures BrunswickGermany

Yeasts,usually defined as unicellular fungi,occur in various fungal ***,they are not a taxonomic unit,but rather represent a fungal lifestyle shared by several unrelated *** the discovery of new yeast species occurs at an increasing speed,at the current rate it will likely take hundreds of years,if ever,before they will all be *** parts of the earth,including many threatened habitats,remain unsampled for yeasts and many others are only superficially *** habitats,such as glaciers,are home to a specific community of cold-adapted yeasts,and,hence,there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate *** same is true for yeast communities in various natural forests that are impacted by deforestation and forest *** countries of the so-called Global South have not been sampled for yeasts,despite their economic ***,extensive research activity in Asia,especially China,has yielded many taxonomic *** genomics stud-ies have demonstrated the presence of yeast species with a hybrid origin,many of them isolated from clinical or industrial ***-metabarcoding studies have demonstrated the prevalence,and in some cases dominance,of yeast species in soils and marine waters worldwide,including some surprising distributions,such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.

关键词： Yeasts Ascomycota Basidiomycota Diversity CBD Nagoya protocol Soil DNA-metabarcoding Marine Malassezia Cold environments China

Phylogeny of the industrial relevant,thermophilic genera Myceliophthora and Corynascus

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Fungal Diversity 2012年第1期52卷 197-207页

作者： Joost van den Brink Robert A.Samson Ferry Hagen teun boekhout Ronald P.de Vries CBS-KNAW Fungal Biodiversity Centre P.O.Box 851673508 AD UtrechtThe Netherlands

Species of the genus Myceliophthora and its teleomorph Corynascus have attracted increasing interest due to their potential to produce thermostable *** study re-assessed the phylogenetic relationship of 49 isolates of nine species belonging to Myceliophthora and *** species,***,was shown not to belong to the genus Myceliophthora and should be placed in the genus *** other species belonged to two phylogenetic clusters:mesophilic fungi with the type species *** and ***,and thermophilic fungi with ***,*** and *** phylogenetic data provides no clear separation of the two genera Corynascus and *** avoid confusion in future taxonomic studies,it is proposed that all existing Corynascus species be renamed to Myceliophthora,which is the old name and the one more frequently ***,this study identified two groups within the isolates listed as *** and assigned one group(five isolates)to *** based on AFLP analysis and mating *** study provides new insights into the genetic differences within the genus Myceliophthora and will therefore be essential for the interpretation of future genomic and physiological studies of these species.

关键词： Myceliophthora Corynascus Thermophiles M.heterothallica M.thermophila.Thermophilic fungi Multigene phylogeny AFLP analysis Mating behavior

Classification of marine Ascomycota,Basidiomycota,Blastocladiomycota and Chytridiomycota

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Fungal Diversity 2015年第4期73卷 1-72页

作者： E.B.Gareth Jones Satinee Suetrong Jariya Sakayaroj Ali H.Bahkali Mohamed A.Abdel-Wahab teun boekhout Ka-Lai Pang Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia Fungal Biodiversity Laboratory BIOTECNational Science and Technology Development Agency(NSTDA)113 Thailand Science ParkThanon PhahonyothinTombon Khlong NuengAmphoe Khlong LuangPathum Thani 12120Thailand Department of Botany Faculty of ScienceSohag UniversitySohagEgypt CBS Fungal Biodiversity Centre(KNAW) Uppsalalaan 83584CT UtrechtThe Netherlands Institute of Marine Biology and Center of Excellence for the Oceans Taiwan Ocean University2 Pei-Ning RoadKeelung 20224TaiwanRepublic of China

This paper lists the accepted names and classification of marine fungi,updating the scheme presented in *** classification includes 1,112 species(in 472 genera):Ascomycota 805(in 352 genera),Basidiomycota 21 species(in 17 genera),Chytridiomycota and related phyla 26 species(in 13 genera),Zygomycota three(in two genera),Blastocladiomycota one species(one genus),asexual morphs of filamentous fungi 43(in 26 genera);and marine yeasts:Ascomycota 138 species(in 35 genera),Basidiomycota 75 species(in 26 genera).These fungi belong to 129 families and 65 *** Halosphaeriaceae remains the largest family of marine fungi with 141 species in 59 genera,while the most specious genera are Aspergillus(47 species),Penicillium(39 species)and the yeast genus Candida(64 species).The review includes details of recent higher order nomenclature changes,and accounts of new families,genera and species described over the past 5 years.

关键词： Fungal classification Marine fungi Molecular phylogeny New taxa Praelongicaulis gen nov Tirisporellales Torpedosporales ordo nov

黑粉菌亚门（Ustilaginomycotina）无性型真菌研究

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黑粉菌亚门（Ustilaginomycotina）无性型真菌研究

中国菌物学会第六届会员代表大会（2014年学术年会）暨...

作者：王启明白逢彦 teun boekhout 中国科学院微生物研究所

黑粉菌亚门（Ustilaginomycotina）除了包括植物病原真菌黑粉菌（smuts）夕卜,还包括一些无性型酵母菌和类酵母菌’例如Acaromyces spp.,Pseiidozyma spp.,Meira spp"Tilletiopsis spp.和Malassezia spp.o该类酵母在工农业生产、人类健康、资源与环境保护等领域中具有重要的应用价值。近期国外学者根据多基因序列分析和形态学数据对黑粉菌亚门进行了重新修订,但是仍然有些问题没有解决,例如和属在该亚门内的系统学位置任然不清楚。我们用18SrDNA,26S rDNADl/D2,ITS,RPB1,RPB2和EFl-a六个基因片段对以上两个属的系统学地位进行了研究。研究结果表明Maktssezict和MonilieHa位于黑粉菌亚门内,它们是黑粉菌纲（Ustilaginomycetes）和外担子菌纲（Exobasidiomycetes）的姊妹群。Moniliellomycetes class nov.和Malasseziomycetes class nov.两个新纲被创建,分别来容纳和Malassezia两个类群。

关键词：黑粉菌亚门系统进化 Moniliellomycetes Malasseziomycetes

The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

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Fungal Diversity 2021年第4期109卷 27-55页

作者： teun boekhout M.Catherine Aime Dominik Begerow Toni Gabaldón Joseph Heitman Martin Kemler Kantarawee Khayhan Marc-AndréLachance Edward J.Louis Sheng Sun Duong Vu Andrey Yurkov Westerdijk Fungal Biodiversity Institute UtrechtThe Netherlands Institute of Biodiversity and Ecosystem Dynamics(IBED) University of AmsterdamAmsterdamThe Netherlands Dept Botany and Plant Pathology College of AgriculturePurdue UniversityWest LafayetteIN 47907USA Evolution of Plants and Fungi Ruhr-University Bochum44801 BochumGermany Barcelona Supercomputing Centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain Department of Molecular Genetics and Microbiology Duke University Medical CenterDurhamNC 27710USA Department of Microbiology and Parasitology Faculty of Medical SciencesUniversity of PhayaoPhayao 56000Thailand Department of Biology University of Western OntarioLondonON N6A 5B7Canada Department of Genetics and Genome Biology Genetic Architecture of Complex TraitsUniversity of LeicesterLeicester LE17RHUK German Collection of Microorganisms and Cell Cultures Leibniz Institute DSMZBrunswickGermany

Here we review how evolving species concepts have been applied to understand yeast ***,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth *** the biological species concept was added,which applied data from mating *** 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 *** 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 *** 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 *** genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they *** seems a relatively common phenomenon and has been observed in all major fungal lineages that contain *** that hybrids may greatly differ in their post-hybridization *** 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.

关键词： Fungi Species concepts Comparative genomics Hybrids Nomenclature Taxonomy

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格特隐球菌感染病例临床特征分析

格特隐球菌感染病例临床特征分析

2012年中国菌物学会学术年会

作者：陈敏潘炜华邓淑文 teun boekhout 廖万清上海市医学真菌分子生物学重点实验室上海长征医院皮肤科

最近十年来,格特隐球菌因突然在地处温带的加拿大温哥华岛及美国部分地区引发人与动物感染的爆发性流行事件而广受国际医学真菌学界的关注。目前,关于我国格特隐球菌感染临床特征的研究匮乏,但已有的分子流行病学研究显示我国患者感染... 详细信息

最近十年来,格特隐球菌因突然在地处温带的加拿大温哥华岛及美国部分地区引发人与动物感染的爆发性流行事件而广受国际医学真菌学界的关注。目前,关于我国格特隐球菌感染临床特征的研究匮乏,但已有的分子流行病学研究显示我国患者感染的格特隐球菌除1株VGIIb型菌株外,全部为VGI型菌株。我们对收集自我院及上海华山医院(1993年-2011年)共147株隐球菌临床分离株进行了CGB培养基与ITS序列分析,共发现了11株格特隐球菌,以此这11例患者病例进行了回顾性分析,发现我国格特隐球菌感染主要分布在江苏、上海、浙江、福建、广东、海南等热带、亚热带地区,HIV均为为阴性,平均颅内压达(349+47 mmHO),较新生隐球菌感染组(300+56 mmHO)偏高(P=0.007),神经系统尤其是视神经系统后遗症较多见(54.5%,n=11),CD4T计数与易感性尚需进一步研究。

关键词：格特隐球菌感染中国

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

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Fungal Diversity 2022年第3期114卷 463-490页

作者： Nalin N.Wijayawardene Alan J.L.Phillips Diana Santos Pereira Dong-Qin Dai AndréAptroot Josiane S.Monteiro Irina S.Druzhinina Feng Cai Xinlei Fan Laura Selbmann Claudia Coleine Rafael F.Castañeda-Ruiz Martin Kukwa Adam Flakus Patricia Oliveira Fiuza Paul M.Kirk Kunhiraman C.Rajesh Kumar Ilesha S.leperuma Arachchi Nakarin Suwannarach Li-Zhou Tang teun boekhout Chen Shuhui Tan R.P.Prabath K.Jayasinghe Marco Thines Centre for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujing 655011YunnanPeople’s Republic of China Section of Genetics Institute for Research and Development in Health and Social CareNo:393/3Lily AvenueOff Robert Gunawardane MawathaBattaramulla 10120Sri Lanka Faculdade de Ciências Biosystems and Integrative Sciences Institute(BioISI)Universidade de LisboaCampo Grande1749-016 LisbonPortugal Laboratório de Botânica/Liquenologia Instituto de BiociênciasUniversidade Federal de Mato Grosso do SulAvenida Costa e Silva S/NBairro UniversitárioCampo GrandeMS CEP 79070-900Brazil Coordination of Botany Museu Paraense Emílio GoeldiBelémPA 66077830Brazil Fungal Genomics Laboratory(FungiG) College of Resources and Environmental SciencesNanjing Agricultural UniversityWeigang 1Nanjing 210095JiangsuPeople’s Republic of China The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing 100083People’s Republic of China Department of Ecological and Biological Sciences University of TusciaViterboItaly Italian National Antarctic Museum(MNA) Mycological SectionGenoaItaly Alejandro de Humboldt’(INIFAT) Instituto de Investigaciones Fundamentales en AgriculturaTropicalSantiago de Las VegasHavanaCuba Department of Plant Taxonomy and Nature Conservation Faculty of BiologyUniversity of GdańskWita Stwosza 5980-308 GdańskPoland W.Szafer Institute of Botany Polish Academy of SciencesLubicz 4631-512 KrakowPoland Universidade Federal do Rio Grande do Norte(UFRN) Programa de Pós-Graduação em Sistemática e EvoluçãoCentro de BiociênciasCampus UniversitárioAv.Senador Salgado Filho3000Lagoa NovaNatalRN 59078-970Brazil Biodiversity Informatics and Spatial Analysis Jodrell LaboratoryRoyal Botanic GardensKewRichmond TW93DSSurreyUK National Fungal Culture Collection of India(NFCCI) Biodiversity and Palaeobiology GroupMACS Agharkar Research InstituteG.G.

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 *** addition,they have a key role in food production,biotechnology and *** without or rare sexual reproduction are distinguished based on their sporulating structures and conidiomata in traditional morphology-based *** 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 ***,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 *** 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 ***,species numbers and taxonomic boundaries of pleomorphic taxa and their synanamorphs or synasexual morphs have yet to be *** number of species of speciose genera(***,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 *** 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,*** inhabiting species,marine fungi,(5)less studied life modes,e.g.

关键词： Cryptic species DNA sequences Morphology Pleomorphism Speciose genera Species identificat

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黑粉菌亚门进化基因组学

黑粉菌亚门进化基因组学

中国菌物学会2016年学术年会

作者：王启明章小灵李宽 teun boekhout Dominik Begerow 白逢彦中国科学院微生物研究所真菌学国家重点实验室 CBS-KNAW Fungal Biodiversity Centre Yeast Division Ruhr-Universit?t Bochum

黑粉菌亚门内的类群具有多样的生活方式和生态位点,在人类活动和生态系统中担当着重要的角色:如植物寄生菌能够造成小麦、玉米、大麦和甘蔗等重要经济作物的病害,动物寄生菌能造成动物及人类浅度或深度的感染,有些无性型类群可以用作植... 详细信息

黑粉菌亚门内的类群具有多样的生活方式和生态位点,在人类活动和生态系统中担当着重要的角色:如植物寄生菌能够造成小麦、玉米、大麦和甘蔗等重要经济作物的病害,动物寄生菌能造成动物及人类浅度或深度的感染,有些无性型类群可以用作植物病害的生物防治剂。该亚门内大部分物种与寄主植物和动物协同进化,而且还会在不同尺度上进行寄主的跨越和转移,具有重要的科学研究价值。本研究将对该亚门内4个纲、10个目和28个科内的代表性的属种进行系统性的全基因组的测定和分析。截至目前为止,已经完成了分布在黑粉菌亚门10个目的 30个种的基因组草图。初步分析表明黑粉菌亚门物种的基因组大小在9-34M之间。分泌性效应因子的初步预测结果显示Moniliela属的分泌性蛋白数目明显比植物病原菌少,并且没有发现该属模式种与***同源的交配型基因。由于该属其大部分种的基因组还未测定,所以不清楚是否是整个属的种都缺失了交配型基因。我们还发现Golubevia pallescens有两个紧连的信息素受体Pra基因,多拷贝Pra基因除了在伞菌纲内的某些类群中发现外,在其它担子菌的类群中还没有发现。根据现有数据的初步分析,我们已经发现了一些有意思的现象,随着更多物种的测序和深入的分析将会彻底阐明黑粉菌遗传多样性及其适应进化机制。

关键词：黑粉菌基因组进化

擔子菌酵母的多基因系統發育分析與分類系統更新

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擔子菌酵母的多基因系統發育分析與分類系統更新

第十二届海峡两岸真菌学学术研讨会

作者：白逢彥王啟明劉新展 Bart Theelen Marizeth Groenewald teun boekhout 中國科學院微生物研究所

主要以單細胞形式存在和繁殖的擔子菌稱為擔子菌酵母,目前包括約70餘屬700餘種。由於形態簡單,擔子菌酵母與其它酵母菌一樣擁有一套獨立於絲狀真菌的分類系統,其主要分類依據為形態和生理生化等表型性狀。但是,分子系統學研究發現,擔子...

主要以單細胞形式存在和繁殖的擔子菌稱為擔子菌酵母,目前包括約70餘屬700餘種。由於形態簡單,擔子菌酵母與其它酵母菌一樣擁有一套獨立於絲狀真菌的分類系統,其主要分類依據為形態和生理生化等表型性狀。但是,分子系統學研究發現,擔子菌酵母並不是一個獨立的演化類群,而是與絲狀擔子菌一起分散在傘菌（Agaricomycotina）、鏽菌（Pucciniomycotina）和黑粉菌（Ustilaginomycotina）等3個亞門中不同的類群中。現行的擔子菌酵母分類系統卻與絲狀擔子菌分類系統不相容,而且許多科、屬都是非常異源的。隨著大量擔子菌酵母新種的發現,使一些科屬的異源性進一步增加,更加凸顯了現行分類系統的不合理性。為了適應真菌系統學和生物多樣性研究的發展,迫切需要對現行擔子菌酵母分類系統進行更新。為此,我們完成了絕大多數擔子菌酵母已知種的多基因序列分析,所測基因包括3個rRNA基因（18S、ITS+5.8S、26S D1/D2區）,3個單拷貝蛋白基因（EF-1α、RPBl、RPB2）和1個線粒體基因（CYTB）。用不同演算法,包括Bayesian inference、maximum likelihood和neighbour-joining等進行了單基因樹和多基因樹構建,比較清楚地揭示了絕大多數種間的系統發育關係。同時,應用數量分析方法,包括phylogenetic rank boundary optimization（PRBO）和general mixed Yule coalescent（GMYC）等,對根據系統樹界定的目、科和屬進行了量化評估,以檢驗各個等級分類單元劃分的合理性。再結合形態和生理生化等表型特徵,並遵循"一種真菌一個名稱"的新命名法規,我們對整個擔子菌酵母的分類系統進行了更新。在傘菌亞門中,酵母菌分佈在銀耳綱（Tremellomycetes）中的5個目,17個科和54個屬中,其中新科7個,新屬18個,新組合種191個。鏽菌類酵母分佈在5個綱,10個目,20個科和51個屬中,其中新綱1個,新科7個,新屬23個,新組合種122個。黑粉菌類酵母歸屬於4個綱,12目,21個科和58個屬中,其中新綱2個,新目3個,新科3個,新屬6個,新組合種28個。

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