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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

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 distribution.This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and macroecology.The 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 continents.The plots are supplied with geographical and edaphic metadata.The OTUs are taxonomically and functionally assigned to guilds and other functional groups.The entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential contamination.The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data.The GSMc dataset is available over the PlutoF repository.

关键词： Soil fungi Global dataset PacBio sequencing Fungal richness

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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 studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,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 challenging.In 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 levels.Combining 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,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In 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 sequences.On 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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