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Notes,outline and divergence times of Basidiomycota

Fungal Diversity 2019年第6期99卷 105-367页

作者： Mao-Qiang He Rui-Lin Zhao Kevin D.Hyde Dominik Begerow Martin Kemler Andrey Yurkov Eric H.C.McKenzie Olivier Raspe Makoto Kakishima Santiago Sanchez-Ramırez Else C.Vellinga Roy Halling Viktor Papp Ivan V.Zmitrovich Bart Buyck Damien Ertz Nalin N.Wijayawardene Bao-Kai Cui Nathan Schoutteten Xin-Zhan Liu Tai-Hui Li Yi-Jian Yao Xin-Yu Zhu An-Qi Liu Guo-Jie Li Ming-Zhe Zhang Zhi-Lin Ling Bin Cao Vladimir Antonin Teun Boekhout Bianca Denise Barbosa da Silva Eske De Crop Cony Decock Balint Dima Arun Kumar Dutta Jack W.Fell Jozsef Geml Masoomeh Ghobad-Nejhad Admir J.Giachini Tatiana B.Gibertoni Sergio P.Gorjon Danny Haelewaters Shuang-Hui He Brendan P.Hodkinson Egon Horak Tamotsu Hoshino Alfredo Justo Young Woon Lim Nelson Menolli Jr Armin Mesic Jean-Marc Moncalvo Gregory M.Mueller La szlo G.Nagy RHenrik Nilsson Machiel Noordeloos Jorinde Nuytinck Takamichi Orihara Cheewangkoon Ratchadawan Mario Rajchenberg Alexandre G.S.Silva-Filho Marcelo Aloisio Sulzbacher Zdenko Tkalcec Ricardo Valenzuela Annemieke Verbeken Alfredo Vizzini Felipe Wartchow Tie-Zheng Wei Michael WeiB Chang-Lin Zhao Paul M.Kirk State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101People’s Republic of China Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand College of Life Sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408People’s Republic of China Ruhr-Universitat Bochum AG GeobotanikND03UniversitatsstraBe 15044801 BochumGermany Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures InhoffenstraBe 7B38124 BrunswickGermany Manaaki Whenua-Landcare Research Private Bag 92170AucklandNew Zealand Research Department Meise Botanic GardenNieuwelaan 381860 MeiseBelgium Service General de l'Enseignement superieur et de la Recherche scientifique Federation Wallonie-BruxellesLavallee 11080 BrusselsBelgium University of Tsukuba TsukubaIbaraki 305-8572Japan Department of Ecology and Evolutionary Biology University of Toronto25 Willcocks St.TorontoON M5S 3B2Canada Berkeley USA Institute of Systematic Botany The New York Botanical GardenBronxNY 10458-5126USA Department of Botany Szent Istvan University1518 BudapestHungary Komarov Botanical Institute Russian Academy of SciencesProfessor Popov st.2Saint PetersburgRussia 197376 Institut pour Systematique Ecologie Biodiversite(ISYEB UMR 7205) Sorbonne universiteMuseum National d’Histoire Naturelle CP 39CNRSDepartement Origines et Evolution12 Rue Buffon75005 ParisFrance Institute of Microbiology Beijing Forestry UniversityBeijing 100083People’s Republic of China Department of Biology Research Group MycologyGhent UniversityK.L.Ledeganckstraat 359000 GhentBelgium State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Institute of MicrobiologyGuangzhou 510070People’s Republic of China Department of Botany Moravian Mu

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota.The present work provides an overview of all validly published,currently used basidiomycete genera to date in a single document.An outline of all genera of Basidiomycota is provided,which includes 1928 currently used genera names,with 1263 synonyms,which are distributed in 241 families,68 orders,18 classes and four subphyla.We provide brief notes for each accepted genus including information on classification,number of accepted species,type species,life mode,habitat,distribution,and sequence information.Furthermore,three phylogenetic analyses with combined LSU,SSU,5.8s,rpb1,rpb2,and ef1 datasets for the subphyla Agaricomycotina,Pucciniomycotina and Ustilaginomycotina are conducted,respectively.Divergence time estimates are provided to the family level with 632 species from 62 orders,168 families and 605 genera.Our study indicates that the divergence times of the subphyla in Basidiomycota are 406-430 Mya,classes are 211-383 Mya,and orders are 99-323 Mya,which are largely consistent with previous studies.In this study,all phylogenetically supported families were dated,with the families of Agaricomycotina diverging from 27-178 Mya,Pucciniomycotina from 85-222 Mya,and Ustilaginomycotina from 79-177 Mya.Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system,and also provide a better understanding of their phylogeny and evolution.

关键词： Classification Molecular clock Fungi systematics Taxonomy

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Towards standardizing taxonomic ranks using divergence times-a case study for reconstruction of the Agaricus taxonomic system

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Fungal Diversity 2016年第3期78卷 239-292页

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li Jean-Marc Moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in Fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada Department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S 3B2Canada Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunming 650201China INRA-UR1264 Mycologie et Sécuritédes AlimentsCS 2003233882 Villenave d’Ornon cedexFrance Avda.Padre Claret n°7 5°G09400 Aranda de DueroBurgosSpain

The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary.Some authors have proposed the use of divergence time as a universally standardized criterion.Agaricus(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial value.Recent studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional taxonomy.In this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and sections.Many monophyletic groups were recognized,but most basal relationships were unresolved.One hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence data.Divergence times within the multi-gene phylogeny were estimated using BEAST v1.8.Based on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic ranks.We propose to segregate Agaricus into five subgenera and 20 sections.Subgenus Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are introduced.Within Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are introduced.Section Laeticolores is placed in the subgenus Minores and sections Rarolentes and Subrutilescentes are placed in the subge

关键词： Agaricaceae Divergence times Multi-gene phylogenetics systematics Taxonomy

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Endophytic Colletotrichum species from Bletilla ochracea (Orchidaceae), with descriptions of seven new speices

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Fungal Diversity 2013年第4期61卷 139-164页

作者： Gang Tao Zuo-Yi Liu Fang Liu Ya-Hui Gao Lei Cai State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101People’s Republic of China Guizhou Institute of Plant Protection Guiyang 550006People’s Republic of China Guizhou Key Laboratory of Agricultural Biotechnology Guiyang 550006People’s Republic of China

Thirty-six strains of endophytic Colletotrichum species were isolated from leaves of Bletilla ochracea Schltr.(Orchidaceae)collected from 5 sites in Guizhou,China.Seventeen different species,including 7 new species(namely C.bletillum,C.caudasporum,C.duyunensis,C.endophytum,C.excelsum-altitudum and C.guizhouensis and C.ochracea),8 previously described species(C.boninense,C.cereale,C.destructivum,C.karstii,C.liriopes,C.miscanthi,C.parsonsiae and C.tofieldiae)and 2 sterile mycelia were identified.All of the taxa were identified based on morphology and phylogeny inferred from multi-locus sequences,including the nuclear ribosomal internal transcribed spacer(ITS)region,partial genes ofβ-tubulin(TUB2),actin(ACT)and glyceraldehyde-3-phosphate dehydrogenase(GAPDH).Comprehensive morphological descriptions and illustrations are provided for new species.Our investigation indicates a high diversity of Colletotrichum species in B.ochracea.

关键词： Fungal diversity Phylogeny systematics Taxonomy

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The sequestrate genus Rosbeeva T.Lebel&Orihara gen.nov.(Boletaceae)from Australasia and Japan:new species and new combinations

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Fungal Diversity 2012年第1期52卷 49-71页

作者： Teresa Lebel Takamichi Orihara Nitaro Maekawa National Herbarium of Victoria Royal Botanic Gardens MelbournePrivate Bag 2000Birdwood AveSouth YarraVIC 3141Australia The United Graduate School of Agriculture Sciences Tottori University4–101 Koyama-cho-minamiTottori 680–8553Japan Fungus/Mushroom Resource and Research Center Faculty of AgricultureTottori University4–101 Koyama-cho-minamiTottori 680–8553Japan Kanagawa Prefectural Museum of Natural History 499 IriudaOdawara-shiKanagawa 250–0031Japan

The sequestrate genus Chamonixia has been shown to have affinities to the Boletales,in particular the genus Leccinum.Australasian and Japanese species of Chamonixia were examined using morphological and molecular(ITS and nLSU rDNA)data and found to also have affinities with Leccinum and Leccinellum,however they form a distinct clade separate from the European type species C.caespitosa Rolland and North American species.A new genus,Rosbeeva T.Lebel&Orihara gen.nov.,is proposed for the Australasian,Japanese and Chinese taxa.The species R.mucosa(Petri)T.Lebel comb.***.is restricted in distribution to Singapore and Borneo,and R.pachyderma(Zeller&C.W.Dodge)T.Lebel comb.***.to New Zealand,with Australian collections considered to belong to a revised R.vittatispora(G.W.Beaton,Pegler&T.W.K.Young)T.Lebel comb.***.or a new species R.westraliensis T.Lebel sp.nov.The Chinese species R.bispora(B.C.Zhang&Y.N.Yu)T.Lebel&Orihara comb.nov is transferred to the new genus based upon morphological data.Two new species from Japan,Rosbeeva eucyanea Orihara and R.griseovelutina Orihara,are also described and illustrated.A key to all species of Rosbeeva is provided.Due to the highly modified gastroid sporocarp forms of both Chamonixia and Rosbeeva,many macroscopic characters of use in agaricoid taxonomy are difficult to interpret.However,color change and texture of sporocarps are of some use to distinguish genera and species.Microscopic characters such as spore shape,dimensions,and ornamentation,and pileipellis and hymenophoral trama structure,are essential for determining genera and species.

关键词： Chamonixia Sequestrate fungi Leccinum systematics Octaviania

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What is a species in fungal plant pathogens?

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Fungal Diversity 2021年第4期109卷 239-266页

作者： Ruvishika S.Jayawardena Kevin D.Hyde Antonio Roberto Gomes de Farias Chitrabhanu S.Bhunjun Himashi S.Ferdinandez Dimuthu S.Manamgoda Dhanushka Udayanga Indunil S.Herath Kasun M.Thambugala Ishara S.Manawasinghe Achala J.Gajanayake Binu C.Samarakoon Digvijayini Bundhun Deecksha Gomdola Naruemon Huanraluek Ya-ru Sun Xia Tang Itthayakorn Promputtha Marco Thines Innovative Institute of Plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Departamento de Genética Universidade Federal de PernambucoAv.Prof.Moraes Rego1235Cidade UniversitáriaRecifePE 50670-901Brazil Department of Botany Faculty of Applied SciencesUniversity of Sri JayewardenepuraNugegodaSri Lanka Department of Biosystems Technology Faculty of TechnologyUniversity of Sri JayewardenepuraPitipanaHomagama 10200Sri Lanka Genetics and Molecular Biology Unit Faculty of Applied SciencesUniversity of Sri JayewardenepuraGangodawilaNugegodaSri Lanka School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Department of Biological Sciences Institute of EcologyEvolution and DiversityGoethe UniversityMax-von-Laue-Str.1360486 Frankfurt am MainGermany Senckenberg Biodiversity and Climate Research Centre Senckenberganlage 2560325 Frankfurt am MainGermany

Scientific names are crucial for communicating knowledge concerning fungi and fungus-like organisms.In plant pathology,they link information regarding biology,host range,distribution and potential risk to agriculture and food security.In the past,delimitation among pathogenic taxa was primarily based on morphological characteristics.Due to distinct species sharing overlapping characteristics,the morphological identification of species is often neither straightforward nor reliable.Hence,the phylogenetic species concept based on molecular phylogenetic reconstructions gained importance.The present opinion discusses what a fungal species is and how identification of species in plant pathology has changed over the past decades.In this context,host-specialization and species complexes are discussed.Furthermore,species concepts in plant pathology are examined using case studies from Bipolaris,Colletotrichum,Curvularia,Diaporthe,Diplodia,Meliola,Plasmopara,rust fungi and Trichoderma.Each entry contains a brief introduction to the genus,concepts used in species identification so far and the problems in describing a species followed by recommendations.The importance of correctly naming and identifying a species is addressed in the context of recent introductions,and we also discuss whether the introduction of new species in pathogenic genera has been overestimated.We also provide guidelines to be considered when introducing a new species in a plant pathogenic genus.

关键词： Dual nomenclature Host-specificity Polyphasic approach Pathology Phylogeny Species delimitation systematics

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The Colletotrichum orbiculare species complex: Important pathogens of field crops and weeds

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Fungal Diversity 2013年第4期61卷 29-59页

作者： Ulrike Damm Paul F.Cannon Fang Liu Robert W.Barreto Eduardo Guatimosim Pedro W.Crous CBS-KNAW Fungal Biodiversity Centre Uppsalalaan 83584 CT UtrechtThe Netherlands Royal Botanic Gardens KewRichmond TW93ABUK State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Departamento de Fitopatologia Universidade Federal de ViçosaViçosaMinas Gerais 36570-000Brazil Laboratory of Phytopathology Wageningen University and Research Centre(WUR)Droevendaalsesteeg 16708 PB WageningenThe Netherlands

Colletotrichum orbiculare causes anthracnose of Cucurbitaceae and is phylogenetically closely related to pathogens of several other herbaceous hosts belonging to the Asteraceae,Fabaceae and Malvaceae.Most of them are known for their hemibiotrophic infection strategy and as destructive pathogens either of field crops or weeds.In order to study the phylogenetic relationships of these fungi,a multilocus analysis(ITS,GAPDH,CHS-1,HIS3,ACT,TUB2,GS)of 42 strains of C.orbiculare and related species was conducted.The analysis resulted in nine clades that confirmed the four species previously known as belonging to this species complex,C.lindemuthianum,C.malvarum,C.orbiculare and C.trifolii,and recognised four new species from weeds,namely C.bidentis,C.sidae,C.spinosum and C.tebeestii.The name C.orbiculare itself is widely used in plant pathology and science,but is invalid according to current nomenclatural rules.Therefore we described a new species with the same epithet and a type specimen that agrees with our current understanding of this species,and is linked to a living culture.Following the recent epitypification of C.lindemuthianum,we chose appropriate specimens with associated strains to serve as epitypes of C.malvarum and C.trifolii,and selected an authentic specimen of C.trifolii as lectotype.

关键词： Ascomycota Host specificity Morphology Phylogeny systematics

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Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae

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Fungal Diversity 2013年第4期61卷 89-105页

作者： Fang Liu Ulrike Damm Lei Cai Pedro W.Crous State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Department of Biology MicrobiologyUtrecht UniversityPadualaan 83584 CH UtrechtThe Netherlands CBS-KNAW Fungal Biodiversity Centre Uppsalalaan 83584 CT UtrechtThe Netherlands Laboratory of Phytopathology Wageningen University and Research Centre(WUR)Droevendaalsesteeg 16708 PB WageningenThe Netherlands

Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C.acutatum,C.boninense and C.gloeosporioides.In the present study,a multi-locus phylogenetic analysis(ACT,CAL,CHS-1,GAPDH,GS,ITS,TUB2)revealed that strains of the C.gloeosporioides complex associated with Proteaceae belong to at least six species.These include C.alienum,C.aotearoa,C.kahawae(subsp.ciggaro),C.siamense,and two new taxa,C.proteae and C.grevilleae.The most economically important pathogen of Proteaceae seems to be C.alienum,and not C.gloeosporioides as previously reported.All taxa associated with Proteaceae are morphologically described on different media in culture,except strains of C.siamense,which proved to be sterile.Furthermore,C.populi is synonymised with C.aenigma.

关键词： Ascomycota Colletotrichum Morphology Phylogeny systematics

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High levels of endemism among Galapagos basidiolichens

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Fungal Diversity 2017年第4期85卷 45-73页

作者： Manuela Dal Forno Frank Bungartz Alba Yanez-Ayabaca Robert Lücking James D.Lawrey Department of Botany Smithsonian InstitutionNational Museum of Natural History10th St&Constitution Ave NWWashingtonDC 20560USA Department of Environmental Science and Policy George Mason UniversityFairfaxVA 22030-4444USA Charles Darwin Foundation for the Galapagos Islands Puerto AyoraGalapagosEcuador School of Life Sciences Arizona State UniversityPO Box 874501TempeAZ 85287-4501USA Facultad de Ciencias Agricolas Universidad Central del EcuadorCiudadela UniversitariaQuitoEcuador Botanical Garden and Botanical Museum Berlin KoniginLuise-Straße 6–814195 BerlinGermany Science&Education The Field Museum1400 South Lake ShoreChicagoIL 60605USA

This study is a re-assessment of basidiolichen diversity in the Galapagos Islands.We present a molecular phylogenetic analysis,based on 92 specimens from Galapagos,using two nuclear ribosomal DNA markers(ITS and nuLSU).We also re-examined the morphology and anatomy of all sequenced material.The molecular results confirm our previous assessment that all Galapagos basidiolichens belong to the Dictyonema clade,which in Galapagos is represented by four genera:Acantholichen,Cora,Cyphellostereum,and Dictyonema.Most species previously reported from Galapagos in these genera were at the time believed to represent widely distributed taxa.This conclusion,however,has changed with the inclusion of molecular data.Although almost the same number of species is distinguished,the phylogenetic data now suggest that all are restricted to the Galapagos Islands.Among them,six species are proposed here as new to science,namely Cora galapagoensis,Cyphellostereum unoquinoum,Dictyonema barbatum,D.darwinianum,D.ramificans,and D.subobscuratum;and four species have already been described previously,namely Acantholichen galapagoensis,Cora santacruzensis,Dictyonema pectinatum,and D.galapagoense,here recombined as Cyphellostereum galapagoense.Our analysis is set on a very broad phylogenetic framework,which includes a large number of specimens(N=826)mainly from Central and South America,and therefore strongly suggests an unusually high level of endemism previously not recognized.This analysis also shows that the closest relatives of half of the basidiolichens now found in Galapagos are from mainland Ecuador,implying that they reached the islands through the shortest route,with all species arriving on the islands through independent colonization events.

关键词： Lichens systematics Biodiversity Evolution Lichenizedbasidiomycetes Galapagos

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Sm-Nd isotope dating of hydrothermal calcites from the Xikuangshan antimony deposit,Central Hunan

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Chinese Science Bulletin 2002年第13期47卷 1134-1137页

作者： PENG Jiantang HU Ruizhong LIN Yuanxian ZHAO Junhong Institute of Geochemistry Chinese Academy of SciencesGuiyang 550002China Tianjin Institute of Geology&Mineral Resources Chinese Academy of Geological SciencesTianjin 300170China

The research on Samarium-Neodymium isotope systematics of hydrothermal calcites from the Xi-kuangshan antimony deposit, Central Hunan, places precise timing constraints on the Sb mineralization in this area. It is revealed that the Xikuangshan deposit formed during the late Jurassic-early Cretaceous Period, the early- and late-stage mineralization took place at (155.5±1.1) Ma and (124.1±3.7) Ma, respectively. The accurate age determination of mineralization is very crucial for revealing the super-enrichment mechanism of the element Sb at the Xikuangshan mine, and lays some foundations for the further understandings of its ore genesis and mineralization mechanism.

关键词： mineralization epoch Sm-Nd isotope systematics hydro-thermal calcites Xikuangshan antimony deposit.

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Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning

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Chinese Science Bulletin 2001年第8期46卷 661-665页

作者： HE Shunping CHEN Yiyu Nakajiama Tsuneo Institute of Hydrobiology Chinese Academy of SciencesWuhan 430072China Lake Biwa Museum 10910 OroshimoKusatsuShiga 525Japan

1140 bp of cytochrome b gene were amplified and sequenced from 14 species of primitive cyprinid fishes in East Asia. Aligned with other ten cytochrome b gene sequences of cyprinid fish from Europe and North America retrieved from Gene bank, we obtained a matrix of 24 DNA sequences. A cladogram was generated by the method of Maximum likelihood for the primitive cyprinid fishes. The result indicated that subfamily Leuciscinae and Danioninae do not form a monophyletic group. In the subfamily Danioninae, Opsariichthys biden and Zacco platypus are very primitive and form a natural group and located at the root. But the genera in subfamily Danioninae are included in different groups and have not direct relationship. Among them, Aphyocypris chinensis and Yaoshanicus arcus form a monophyletic group. Tanichthys albonubes and Gobiocypris rarus have a close relation to Gobioninae. The genus Danio is far from other genera in Danioninae. In our cladogram, the genera in Leuciscinae were divided into two groups that

关键词： cyprinidae molecular systematics cytochrome b gene phylogeny.

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