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One stop shop Ⅱ:taxonomic update with molecular phylogeny for important phytopathogenic genera:26–50(2019)

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Fungal Diversity 2019年第1期 41-129页

作者： ruvishika S.Jayawardena Kevin D.Hyde rajesh Jeewon Masoomeh ghobad-Nejhad Dhanushka N.Wanasinghe Ningguo Liu Alan J.L.Phillips Jose ribamar COliveira-Filho gladstone Ada Silva Tatiana B.gibertoni P.Abeywikrama L.M.Carris K.W.T.Chethana A.J.Dissanayake S.Hongsanan S.C.Jayasiri A.r.McTaggart r.H.Perera K.Phutthacharoen K.g.Savchenko r.g.shivas Naritsada Thongklang Wei Dong DePing Wei Nalin NWijayawardena Ji-Chuan Kang The Engineering research Center of Southwest Biopharmaceutical resources Ministry of EducationGuizhou UniversityGuiyang 550025People’s Republic of China Center of Excellence in Fungal research Mae Fah Luang UniversityChiang RaiThailand Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Department of Biotechnology Iranian Research Organization for Science and Technology(IROST)P.O.Box 15815-3538Tehran 15819Iran World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Universidade de Lisboa Faculdade de CienciasBiosystems and Integrative Sciences Institute(BioISI)Campo Grande1749-016 LisbonPortugal Departamento de Micologia Universidade Federal de PernambucoAvenida da EngenhariaS/N-Cidade UniversitariaRecifePE 50740-600Brazil Beijing Key Laboratory of Environmet Friendly Management on Fruit Disease and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Department of Plant Pathology Washington State UniversityPullmanWA 99164USA College of Life Science and Oceanography ShenZhen University1068Nanhai AvenueNanshanShenzhen 518055China Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbaneQLD 4001Australia Department of Biological Sciences Butler UniversityIndianapolisIN 46208USA Centre for Crop Health University of Southern QueenslandToowoombaQLD 4350Australia Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Faculty of Agriculture National Resources and EnvironmentNaresuan UniversityPhitsanulok 65000Thailand

This paper is the second in a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi.It focuses on 25 phytopathogenic genera:Alternaria,Bipolaris,Boeremia,Botryosphaeria,Calonectria,Coniella,Corticiaceae,Curvularia,Elsinoe,Entyloma,Erythricium,Fomitiporia,Fulviformes,Laetisaria,Limonomyces,Neofabraea,Neofusicoccum,Phaeoacremonium,Phellinotus,Phyllosticta,Plenodomus,Pseudopyricularia,Tilletia,Venturia and Waitea,using recent molecular data,up to date names and the latest taxonomic insights.For each genus a taxonomic background,diversity aspects,species identification and classification based on molecular phylogeny and recommended genetic markers are provided.In this study,varieties of the genus Boeremia have been elevated to species level.Botryosphaeria,Bipolaris,Curvularia,Neofusicoccum and Phyllosticta that were included in the One Stop Shop 1 paper are provided with updated entries,as many new species have been introduced to these genera.

关键词： Boeremia DNA barcodes Endophytes Plant pathology Systematics Taxonomy

Species diversity of Basidiomycota

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Fungal Diversity 2022年第3期114卷 281-325页

作者： Mao-Qiang He rui-Lin Zhao Dong-Mei Liu Teodor T.Denchev Dominik Begerow Andrey Yurkov Martin Kemler Ana M.Millanes Mats Wedin A.r.McTaggart roger.g.shivas Bart Buyck Jie Chen Alfredo Vizzini Viktor Papp Ivan V.Zmitrovich Naveed Davoodian Kevin D.Hyde State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101People’s Republic of China College of Life Sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408People’s Republic of China Institute of Ecology Chinese Reserach Academy of Environmental SciencesBeijing 100012People’s Republic of China Institute of Biodiversity and Ecosystem research Bulgarian Academy of Sciences2 Gagarin St.1113 SofiaBulgaria Evolution der Pflanzen und Pilze Ruhr-Universität BochumND 03Universitätsstr.15044801 BochumGermany Leibniz Institute DSMZ-german Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B38124 BraunschweigGermany Departamento de Biología y geología Física y Química InorgánicaUniversidad Rey Juan Carlos28933 MóstolesSpain Department of Botany Swedish Museum of Natural HistoryP.O.Box 5000710405 StockholmSweden Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbane 4001Australia Centre for Crop Health University of Southern QueenslandToowoomba 4350Australia Institut pour Systematique EcologieBiodiversite(ISYEBUMR 7205)Sorbonne universitéMuséum National d’Histoire Naturelle CP 39CNRSDépartement Origines et Evolution12 Rue Buffon75005 ParisFrance Facultad de Ciencias Biológicas y Agropecuarias PeñuelaUniversidad VeracruzanaAmatlán de los Reyes94945 VeracruzMéxico Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale P.A.Mattioli 2510125 TorinoItaly Department of Botany Hungarian University of Agriculture and Life Sciences1518 BudapestHungary Komarov Botanical Institute Russian Academy of SciencesProfessor Popov st.2Saint PetersburgRussia 197376 royal Botanic gardens Victoria Birdwood AvenueMelbourneVIC 3004Australia Center of Excellence in Fungal research Mae Fah Luang UniversityChiang Rai 57100Thailand CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia(KLPB) Kunming Institute of BotanyChinese Academy of Science

Fungi are eukaryotes that play essential roles in ecosystems.Among fungi,Basidiomycota is one of the major phyla with more than 40,000 described species.We review species diversity of Basidiomycota from five groups with different lifestyles or habitats:saprobic in grass/forest litter,wood-decaying,yeast-like,ectomycorrhizal,and plant parasitic.Case studies of Agaricus,Cantharellus,ganoderma,gyroporus,russula,Tricholoma,and groups of lichenicolous yeast-like fungi,rust fungi,and smut fungi are used to determine trends in discovery of biodiversity.In each case study,the number of new species published during 2009–2020 is analysed to determine the rate of discovery.Publication rates differ between taxa and reflect different states of progress for species discovery in different genera.The results showed that lichenicolous yeast-like taxa had the highest publication rate for new species in the past two decades,and it is likely this trend will continue in the next decade.The species discovery rate of plant parasitic basidiomycetes was low in the past ten years,and remained constant in the past 50 years.We also found that the establishment of comprehensive and robust taxonomic systems based on a joint global initiative by mycologists could promote and standardize the recognition of taxa.We estimated that more than 54,000 species of Basidiomycota will be discovered by 2030,and estimate a total of 1.4–4.2 million species of Basidiomycota glob-ally.These numbers illustrate a huge gap between the described and yet unknown diversity in Basidiomycota.

关键词： Biodiversity Fungi Species number Taxonomy

A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex

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Fungal Diversity 2012年第5期56卷 131-144页

作者： Dimuthu S.Manamgoda Lei Cai Eric H.C.McKenzie Pedro W.Crous Hugo Madrid Ekachai Chukeatirote roger.g.shivas Yu Pei Tan Kevin D.Hyde Institute of Excellence in Fungal research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100190People’s Republic of China Landcare research Private Bag 92170AucklandNew Zealand CBS-KNAW Fungal Biodiversity Centre Uppsalalaan 83584 CT UtrechtNetherlands Department of Agriculture Fisheries and ForestryPlant Pathology Herbarium(BRIP)Plant Biosecurity ScienceGPO Box 267BrisbaneQLD 4001Australia

Three genera,Cochliobolus,Bipolaris and Curvularia form a complex that contains many plant pathogens,mostly on grasses(Poaceae)with a worldwide distribution.The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred.There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia,and some species show intermediate morphology.We investigated this complex based on a set of ex-type cultures and collections from northern Thailand.Combined gene analysis of rDNA ITS(internal transcribed spacer),gPDH(glyceraldehyde 3-phosphate dehydrogenase),LSU(large subunit)and EF1-α(translation elongation factor 1-α)shows that this generic complex divides into two groups.Bipolaris and Cochliobolus species clustered in group 1 along with their type species,whereas Curvularia species(including species named as Bipolaris,Cochliobolus and Curvularia)clustered in group 2,with its generic type.The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia.Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.

关键词： Anamorph generic complex Neotype Nomenclature Pathogens Pseudocochliobolus

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J2ME游戏优化揭密

程序员 2003年第11期 73-76页

作者： Mike shivas

速度永远是游戏开发追求目标之一,更何况是在资源和处理能力有限的手机环境里。优化、优化、再优化,游戏开发者永不停止的脚步。

关键词： J2ME 程序设计程序代码优化游戏软件优化

Speciation of Macalpinomyces eriachnes,a complex of 11 host specific species

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Speciation of Macalpinomyces eriachnes,a complex of 11 host ...

Macalpinomyces eriachnes represents a complex of cryptic species

第十二届海峡两岸真菌学学术研讨会

作者： Li,Ying-Ming Chen,Qian shivas,r.g. Cai,Lei State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences

＜正＞Macalpinomyces eriachnes,the type species of Macalpinomyces,was a smut fungus endemic to Australia.In this study,morphological characterization,multi-locus phylogenetic analysis and the general Mixed Yule-Coalescent（gMYC）analyses were conducted for 26 morphologically indistinguishable specimens of M.eriachnes from 11 host species of Eriachne.The results revealed a

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Macalpinomyces eriachnes represents a complex of cryptic spe...

Epitypification and neotypification:guidelines with appropriate and inappropriate examples

中国菌物学会第六届会员代表大会（2014年学术年会）暨...

作者： Yingming Li roger.g.shivas Alistair r.McTaggart Lei Cai Key Laboratory of Systematic Mycology Institute of MicrobiologyChinese Academy of Sciences

Macalpinomyces eriachnes,is a monotypic species of smut fungus endemic to Australia.It is the type species of Macalpinomyces.In our study,combined morphological and multi-locus phylogenetic analysis of 31 specimens of M.eriachnes from 14 species of Eriachne revealed a complex of host specific cryptic species.Our result showed that specimens from same host but in different region were genetically similar than the specimens from same geographic region but in different host.Diversification of M.eriachnes complex is clearly linked with the host,suggesting the importance host-adaption in the process of speciation.The taxonomy of this complex is partly resolved by the descriptions of 9 new species restricted to certain species of Eriachne.Further,Macalpinomyces was confirmed as belonging to the Ustilaginaceae.

关键词： phylogeny morphology Ustilaginaceae species complex

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Fungal Diversity 2014年第6期69卷 57-91页

作者： Hiran A.Ariyawansa David L.Hawksworth Kevin D.Hyde E.B.gareth Jones Sajeewa S.N.Maharachchikumbura Dimuthu S.Manamgoda Kasun M.Thambugala Dhanushka Udayanga Erio Camporesi Anupama Daranagama ruvishika Jayawardena Jian-Kui Liu Eric H.C.McKenzie rungtiwa Phookamsak Indunil C.Senanayake roger.g.shivas Qing Tian Jian-Chu Xu Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina World Agroforestry Centre East and Central AsiaKunming 650201YunnanChina Institute of Excellence in Fungal research School of ScienceMae Fah Luang UniversityChiang Rai 57100Thailand Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de MadridPlaza Ramón y CajalMadrid 28040Spain Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Mycology Section Royal Botanic GardensKewRichmond Surrey TW93DSUK Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia A.M.B.gruppo Micologico Forlivese“Antonio Cicognani” Via Roma18ForlìItaly Manaaki Whenua Landcare research Private Bag 92170 AucklandNew Zealand Plant Pathology Herbarium Agri-Science Queensland40 Boggo RoadDutton ParkQld 4102Australia

review of phylogenetic studies carried out together with morphological ones shows that a major problem with most early studies is that they concentrated on techniques and used material or strains of fungi that in most cases were not carefully reference,and in a worrying number of cases wrongly named.Most classical species,particularly of microfungi,are not represented by adequate type material,or other authoritatively identified cultures or specimens,that can serve as DNA sources for phylogenetic study,or for developing robust identification systems.Natural classifications of fungi therefore suffer fromthe lack of reference strains in resultant phylogenetic trees.In some cases,epitypification and neotypification can solve this problem and these tools are increasingly used to resolve taxonomic confusion and stabilize the understanding of species,genera,families,or orders of fungi.This manuscript discusses epitypification and neotypification,describes how to epitypify or neotypify species and examines the importance of this process.A set of guidelines for epitypification is presented.Examples where taxa have been epitypified are presented and the benefits and problems of epitypification are discussed.As examples of epitypification,or to provide reference specimens,a new epitype is designated for Paraphaeosphaeria michotii and reference specimens are provided for Astrosphaeriella stellata,A.bakeriana,Phaeosphaeria elongata,Ophiobolus cirsii,and O.erythrosporus.In this way we demonstrate how to epitypify taxa and its importance,and also illustrate the value of proposing reference specimens if epitypification is not advisable.Although we provided guidelines for epitypification,the decision to epitypify or not lies with the author,who should have experience of the fungus concerned.This responsibility is to be taken seriously,as once a later typification is made,it may not be possible to undo that,particularly in the case of epitypes,without using the lengthy and tedious formal conservation and rejection processes.

关键词： Epitype generic types Molecular data Nomenclature Systematics Taxonomy Typification

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names

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Fungal Diversity 2014年第6期69卷 1-55页

作者： Nalin N.Wijayawardene Pedro W.Crous Paul M.Kirk David L.Hawksworth Saranyaphat Boonmee Uwe Braun Dong-Qin Dai Melvina J.D’souza Paul Diederich Asha Dissanayake Mingkhuan Doilom Singang Hongsanan E.B.gareth Jones Johannes Z.groenewald ruvishika Jayawardena James D.Lawrey Jian-Kui Liu robert Lücking Hugo Madrid Dimuthu S.Manamgoda Lucia Muggia Matthew P.Nelsen rungtiwa Phookamsak Satinee Suetrong Kazuaki Tanaka Kasun M.Thambugala Dhanushka N.Wanasinghe Saowanee Wikee Ying Zhang Andre Aptroot H.A.Ariyawansa Ali H.Bahkali D.Jayarama Bhat Cécile gueidan Putarak Chomnunti g.Sybren De Hoog Kerry Knudsen Wen-Jing Li Eric H.C.McKenzie Andrew N.Miller Alan J.L.Phillips Marcin Piatek Huzefa A.raja roger S.shivas Bernad Slippers Joanne E.Taylor Qing Tian Yong Wang Joyce H.C.Woudenberg Lei Cai Walter M.Jaklitsch Kevin D.Hyde Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Institute of Excellence in Fungal research Chiang Rai 57100Thailand Forestry and Agricultural Biotechnology Institute(FABI) University of PretoriaPretoria 0002South Africa CBS-KNAW Fungal Biodiversity Centre Uppsalalaan 83584 CT UtrechtThe Netherlands State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing100101People_s Republicof China Mycology Section Royal Botanic GardensKewRichmondSurrey TW93DSUK Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Departamento de Biología VegetalⅡ Facultad de FarmaciaUniversidad Complutense de MadridPlaza Ramón y CajalMadrid 28040Spain School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Institut Für Biologie Martin-Luther-UniversitatBereich Geobotanik Und Botanischer GartenHerbariumNeuwerk 2106099 Halle(Saale)Germany Musée National d'histoire Naturelle 25 Rue MunsterL-2160 LuxembourgLuxembourg Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box 2455Riyadh 11451Kingdom of Saudi Arabia Department of Environmental Science and Policy George Mason University4400 University DriveFairfaxVA 22030-4444USA Science and Education Integrative Research(Botany)The Field Museum1400 South Lake Shore DriveChicagoIL 60605-2496USA Institute of Plant Sciences University of GrazHolteigasse 68010GrazAustria Department of Life Science University of TriesteVia L.Giorgieri 10TriesteItaly Committee on Evolutionary Biology University of Chicago1025 E.57th StreetChicagoIL 60637USA Fungal Biodiversity Laboratory(BFBD) National Center for Gen

Article 59.1,of the International Code of Nomenclature for Algae,Fungi,and Plants(ICN;Melbourne Code),which addresses the nomenclature of pleomorphic fungi,became effective from 30 July 2011.Since that date,each fungal species can have one nomenclaturally correct name in a particular classification.All other previously used names for this species will be considered as synonyms.The older generic epithet takes priority over the younger name.Any widely used younger names proposed for use,must comply with Art.57.2 and their usage should be approved by the Nomenclature Committee for Fungi(NCF).In this paper,we list all genera currently accepted by us in Dothideomycetes(belonging to 23 orders and 110 families),including pleomorphic and nonpleomorphic genera.In the case of pleomorphic genera,we follow the rulings of the current ICN and propose single generic names for future usage.The taxonomic placements of 1261 genera are listed as an outline.Protected names and suppressed names for 34 pleomorphic genera are listed separately.Notes and justifications are provided for possible proposed names after the list of genera.Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes.A phylogenetic tree based on four gene analyses supported 23 orders and 75 families,while 35 families still lack molecular data.

关键词： Article 59.1 Ascomycota One name Phylogeny Pleomorphism

One stop shop:backbones trees for important phytopathogenic genera:Ⅰ(2014)

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Fungal Diversity 2014年第4期 21-125页

作者： Kevin D.Hyde r.Henrik Nilsson S.Aisyah Alias Hiran A.Ariyawansa Jaime E.Blair Lei Cai Arthur W.A.M.de Cock Asha J.Dissanayake Sally L.glockling Ishani D.goonasekara Michal gorczak Matthias Hahn ruvishika S.Jayawardena Jan A.L.van Kan Matthew H.Laurence C.AndréLévesque Xinghong Li Jian-Kui Liu Sajeewa S.N.Maharachchikumbura Dimuthu S.Manamgoda Frank N.Martin Eric H.C.McKenzie Alistair r.McTaggart Peter E.Mortimer Prakash V.r.Nair Julia Pawlowska Tara L.rintoul roger.g.shivas Christoffel F.J.Spies Brett A.Summerell Paul W.J.Taylor razak B.Terhem Dhanushka Udayanga Niloofar Vaghefi grit Walther Mateusz Wilk Marta Wrzosek Jian-Chu Xu JiYe Yan Nan Zhou Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China World Agroforestry Centre East Asia NodeHeilongtanKunming 650201People’s Republic of China Institute of Excellence in Fungal research and School of ScienceMae Fah Luang UniversityChiang Rai 57100Thailand Botany and Microbiology Department College of ScienceKing Saud UniversityRiyadh 1145Saudi Arabia Department of Biological and Environmental Sciences University of GothenburgBox 46140530 GöteborgSweden Institute of Ocean and Earth Sciences(IOES) C308Institute of Postgraduate Studies BuildingUniversity of Malaya50603 Kuala LumpurMalaysia Department of Biology Franklin&Marshall CollegeLancasterPAUSA State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101 People’s Republic of China CBS-KNAW Fungal Biodiversity Centre Uppsalalaan 83584CT UtrechtThe Netherlands Beijing Academy of Agriculture and Forestry Sciences Institute of Plant and Environment ProtectionNo.9 of ShuguanghuayuanzhongluHaidian DistrictBeijing 100097People’s Republic of China 135 Brodrick road Eastbourne BN229RAEast SussexUK Department of Plant Systematics and geography Faculty of BiologyUniversity of WarsawAl.Ujazdowskie 400-478WarsawPoland Department of Biology TU KaiserslauternErwin-Schrodinger-StraBe67663 KaiserslauternGermany Laboratory of Phytopathology Wageningen UniversityDroevendaalsesteeg 16708 PB WageningenThe Netherlands royal Botanic gardens and Domain Trust Mrs Macquaries RdSydneyNew South Wales 2000Australia Agriculture and Agri-Food Canada Central Experimental FarmOttawaONCanada United States Department of Agriculture Agriculture Research ServiceSalinasCAUSA Landcare research Private Bag92170 AucklandNew Zealand Department of Agriculture Fisheries and ForestryEcosciences PrecinctDutton ParkQueensland 4102Australia Faculty of Veterinary and Agricultural Sciences The University of

Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry.They are also part of the natural ecosystem and may play a role in regulating plant numbers/density.Morphological identification and analysis of plant pathogenic fungi,while important,is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi.Molecular(DNA sequence)data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies,although hampered in part by non-standard laboratory practices and analytical methods.To facilitate current and future research,this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota,Basidiomycota,Mucormycotina(Fungi),and Oomycota,using recent molecular data,up-to-date names,and the latest taxonomic insights.Lineagespecific laboratory protocols together with advice on their application,as well as general observations,are also provided.We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge.researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort.Bipolaris,Botryosphaeriaceae,Botryosphaeria,Botrytis,Choanephora,Colletotrichum,Curvularia,Diaporthe,Diplodia,Dothiorella,Fusarium,gilbertella,Lasiodiplodia,Mucor,Neofusicoccum,Pestalotiopsis,Phyllosticta,Phytophthora,Puccinia,Pyrenophora,Pythium,rhizopus,Stagonosporopsis,Ustilago and Verticillium are dealt with in this paper.

关键词： Ascomycota Basidiomycota Endophytes Mucormycotina Molecular identification Oomycota Plant pathogens Protozoa