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Improving ITS sequence data for identification of plant pathogenic fungi

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Fungal Diversity 2014年第4期67卷 11-19页

作者： R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias Artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna Friberg Tobias Guldberg Froslev Bettina Halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov Department of Biological and Environmental Sciences University of GothenburgBox 46140530 GothenburgSweden Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Plant Systematics and Geography Faculty of BiologyUniversity of WarsawAl.Ujazdowskie 400-478 WarsawPoland Department of Organismal Biology Uppsala UniversityNorbyvagen 18D75236 UppsalaSweden Institute of Ecology and Earth Sciences University of TartuLai 40Tartu 51005Estonia Microbial Evolution Research Group University of OsloBlindernveien 310371 OsloNorway Institute of Biological Sciences University of Malaya50603 Kuala LumpurMalaysia Department of Biology CESAMUniversity of Aveiro3810-193 AveiroPortugal School of Plant Sciences The University of Arizona1140 E South Campus DriveForbes 303TucsonAZ 85721USA Laboratory of Environmental Microbiology Institute of Microbiology ASCRVídeňská108314220 Prague 4Czech Republic Department of Infectious Diseases Institute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGuldhedsgatan 1041346 GoteborgSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden University of California at Berkeley 321 Koshland Hall University of CaliforniaBerkeleyCA 94720-3102USA Agriculture and Forestry Sciences Beijing 100097China Institute of Forestry and Rural Engineering Estonian University of Life SciencesKreutzwaldi551014 TartuEstonia Natural History Museum of Denmark Øster Voldgade 5-71350 København KDenmark Institute for Genomics and Bioinformatics Graz University of Technology8010 GrazAustria Core Facility Bioinformatics Austrian Centre of Industrial Biotechnology8010 GrazAustria Forest Soils and Biogeochemistry Swiss Federal Research Institute WSLZuercherstrasse 1118903 BirmensdorfSwitzerland Molecular Ecology Institute for Sustainability SciencesAgroscopeReckenholzstrasse 191

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human *** taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro *** a result,species identification is frequently ***(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular ***,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi *** we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological *** results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://***),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related *** present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.

关键词： Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

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Fungal Diversity 2021年第6期111卷 573-588页

作者： Leho Tedersoo Vladimir Mikryukov Sten Anslan Mohammad bahram Abdul Nasir Khalid Adriana Corrales Ahto Agan Aída-M.Vasco-Palacios Alessandro Saitta Alexandre Antonelli Andrea C.Rinaldi Annemieke Verbeken Bobby P.Sulistyo Boris Tamgnoue Brendan Furneaux Camila Duarte Ritter Casper Nyamukondiwa Cathy Sharp César Marín D.Q.Dai Daniyal Gohar Dipon Sharmah Elisabeth Machteld Biersma Erin K.Cameron Eske De Crop Eveli Otsing Evgeny A.Davydov Felipe E.Albornoz Francis Q.Brearley Franz Buegger Genevieve Gates Geoffrey Zahn Gregory Bonito Indrek Hiiesalu Inga Hiiesalu Irma Zettur Isabel C.Barrio Jaan Pärn Jacob Heilmann-Clausen Jelena Ankuda John Y.Kupagme Joosep Sarapuu Jose G.Maciá-Vicente Joseph Djeugap Fovo József Geml Juha M.Alatalo Julieta Alvarez-Manjarrez Jutamart Monkai Kadri Põldmaa Kadri Runnel Kalev Adamson Kari A.Bråthen Karin Pritsch Kassim I.Tchan Kęstutis Armolaitis Kevin D.Hyde Kevin K.Newsham Kristel Panksep Lateef A.Adebola Louis J.Lamit Malka Saba Marcela Eda Silva Cáceres Maria Tuomi Marieka Gryzenhout Marijn Bauters Miklós Bálint Nalin Wijayawardene Niloufar Hagh-Doust Nourou S.Yorou Olavi Kurina Peter E.Mortimer Peter Meidl RHenrik Nilsson Rasmus Puusepp Rebeca Casique-Valdés Rein Drenkhan Roberto Garibay-Orijel Roberto Godoy Saleh Alfarraj Saleh Rahimlou Sergei Põlme Sergey V.Dudov Sunil Mundra Talaat Ahmed Tarquin Netherway Terry W.Henkel Tomas Roslin Vladimir E.Fedosov Vladimir G.Onipchenko WAErandi Yasanthika Young Woon Lim Meike Piepenbring Darta Klavina Urmas Kõljalg Kessy Abarenkov Mycology and Microbiology Center University of TartuTartuEstonia Institute of Ecology and Earth Sciences TartuEstonia Department of Ecology Swedish University of Agricultural SciencesUppsalaSweden Department of Botany University of the PunjabQuaid-e-Azam CampusLahorePakistan Centro de Investigaciones en Microbiología y Biotecnología-UR(CIMBIUR) Facultad de Ciencias NaturalesUniversidad del RosarioBogotáColombia Grupo de Microbiología Ambiental y BioMicro Escuela de MicrobiologíaUniversidad de Antioquia UdeAMedellínColombia Department of Agricultural Food and Forest SciencesUniversity of PalermoPalermoItaly Royal Botanic Gardens SurreyUK Department of Biomedical Sciences University of CagliariCagliariItaly Research Group Mycology Department of BiologyGhent UniversityGhentBelgium Department of Biomedicine Indonesia International Institute for Life SciencesJakartaIndonesia Plant Pathology and Agricultural Zoology Research Unit Department of Plant ProtectionFaculty of Agronomy and Agricultural SciencesUniversity of DschangDschangCameroon Department of Ecology and Genetics Uppsala UniversityUppsalaSweden Eukaryotic Microbiology University of Duisburg-EssenEssenGermany Department of Biological Sciences and Biotechnology Botswana International University of Science and TechnologyPalapyeBotswana Natural History Museum of Zimbabwe BulawayoZimbabwe Institute of Botany Czech Academy of SciencesPrůhoniceCzech Republic Center for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujingPeople’s Republic of China Department of Botany Jawaharlal Nehru Rajkeeya MahavidyalayaPondicherry UniversityPort BlairIndia British Antarctic Survey NERCCambridgeUK Natural History Museum of Denmark University of CopenhagenCopenhagenDenmark Department of Environmental Science Saint Mary’s UniversityHalifaxNSCanada Altai State University BarnaulRussia CSIRO Land and Water WembleyWAAustralia Department of N

Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and *** data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and *** dataset comprises 722,682 fungal operational taxonomic units(OTUs)derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all *** plots are supplied with geographical and edaphic *** OTUs are taxonomically and functionally assigned to guilds and other functional *** entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential *** dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published *** GSMc dataset is available over the PlutoF repository.

关键词： Soil fungi Global dataset PacBio sequencing Fungal richness

FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

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Fungal Diversity 2020年第2期107卷 I0001-I0016页

作者： Sergei Põlme Kessy Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hyde Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli Jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis Yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John Y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad bahram Niloufar Hagh-Doust Olesya Dulya Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.Jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay Bose Tanel Vahter Tarquin Netherway Teng Yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov Yongzhong Lu Yosuke Matsuda Yumiko Miyamoto Urm Institute of Ecology and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global Biodiversity Centre Box 46140530 GothenburgSweden Department of Biological and Environmental Sciences University of GothenburgGothenburgSweden Department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary Biology(EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA Department of Biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLOBE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly Department of Organismic and Evolutionary Biology and Farlow Library and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA Blaihofstr.42 72074 TübingenGermany SYNLAB Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile Centro de Genómica y Bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary Biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland Department of Botany Swedish Museum of

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and ***,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 *** 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 *** 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,*** resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** 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 *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

关键词： Fungal traits Trophic modes Function Guild Bioinformatics High-throughput sequencing Community ecology

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全球表层土壤中微生物群落的结构及功能

家电科技 2018年第8期 8-8页

作者： Mohammad bahram Falk Hildebrand Sofia K. Forslund Jennifer L. Anderson Nadejda A. Soudzilovskaia Peter M. Bodegom Johan Bengtsson-Patme Sten Anslan Luis Pedro Coelho Helery Harend Jaime Huerta-Cepas Marnix H. Medema Mia R. Maltz Sunil Mundra Pal Axel Olsson Mari Pent Sergei Polme Shinichi Sunagawa Martin Ryberg Leho Tedersoo Peer Bork 李巧红(编译)

土壤中存在着地球上最多样化的微生物群落,它们对地球养分循环和碳储存都至关重要。为了更好的了解土壤功能,对土壤微生物的全球分布模式和功能基因序列进行建模,并了解土壤中细菌和真菌群落的多样性和结构之间的生物、环境联系是很有... 详细信息

土壤中存在着地球上最多样化的微生物群落,它们对地球养分循环和碳储存都至关重要。为了更好的了解土壤功能,对土壤微生物的全球分布模式和功能基因序列进行建模,并了解土壤中细菌和真菌群落的多样性和结构之间的生物、环境联系是很有必要的。

关键词：微生物群落表层土壤土壤功能结构土壤微生物基因序列分布模式真菌群落