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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles  ( SCI-EXPANDED收录)   被引量:105

文献类型:期刊文献

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

作者:Polme, Sergei Abarenkov, Kessy Henrik Nilsson, R. Lindahl, Bjorn D. Clemmensen, Karina Engelbrecht Kauserud, Havard Nguyen, Nhu Kjoller, Rasmus Bates, Scott T. Baldrian, Petr Froslev, Tobias Guldberg Adojaan, Kristjan Vizzini, Alfredo Suija, Ave Pfister, Donald Baral, Hans-Otto Jarv, Helle Madrid, Hugo Norden, Jenni Liu, Jian-Kui Pawlowska, Julia Poldmaa, Kadri Partel, Kadri Runnel, Kadri Hansen, Karen Larsson, Karl-Henrik Hyde, Kevin David Sandoval-Denis, Marcelo Smith, Matthew E. Toome-Heller, Merje Wijayawardene, Nalin N. Menolli, Nelson, Jr. Reynolds, Nicole K. Drenkhan, Rein Maharachchikumbura, Sajeewa S. N. Gibertoni, Tatiana B. Laessoe, Thomas Davis, William Tokarev, Yuri Corrales, Adriana Soares, Adriene Mayra Agan, Ahto Machado, Alexandre Reis Arguelles-Moyao, Andres Detheridge, Andrew de Meiras-Ottoni, Angelina Verbeken, Annemieke Dutta, Arun Kumar Cui, Bao-Kai Pradeep, C. K. Marin, Cesar Stanton, Daniel Gohar, Daniyal Wanasinghe, Dhanushka N. Otsing, Eveli Aslani, Farzad Griffith, Gareth W. Lumbsch, Thorsten H. Grossart, Hans-Peter Masigol, Hossein Timling, Ina Hiiesalu, Inga Oja, Jane Kupagme, John Y. Geml, Jozsef Alvarez-Manjarrez, Julieta Ilves, Kai Loit, Kaire Adamson, Kalev Nara, Kazuhide Kungas, Kati Rojas-Jimenez, Keilor Bitenieks, Kriss Irinyi, Laszlo Nagy, Laszlo Laszlo Soonvald, Liina Zhou, Li-Wei Wagner, Lysett Aime, M. Catherine opik, Maarja Mujica, Maria Isabel Metsoja, Martin Ryberg, Martin Vasar, Martti Murata, Masao Nelsen, Matthew P. Cleary, Michelle Samarakoon, Milan C. Doilom, Mingkwan Bahram, Mohammad Hagh-Doust, Niloufar Dulya, Olesya Johnston, Peter Kohout, Petr Chen, Qian Tian, Qing Nandi, Rajasree Amiri, Rasekh Perera, Rekhani Hansika dos Santos Chikowski, Renata Mendes-Alvarenga, Renato L. Garibay-Orijel, Roberto Gielen, Robin Phookamsak, Rungtiwa Jayawardena, Ruvishika S. Rahimlou, Saleh Karunarathna, Samantha C. Tibpromma, Saowaluck Brown, Shawn P. Sepp, Siim-Kaarel Mundra, Sunil Luo, Zhu-Hua Bose, Tanay Vahter, Tanel Netherway, Tarquin Yang, Teng May, Tom Varga, Torda Li, Wei Coimbra, Victor Rafael Matos de Oliveira, Virton Rodrigo Targino de Lima, Vitor Xavier Mikryukov, Vladimir S. Lu, Yongzhong Matsuda, Yosuke Miyamoto, Yumiko Koljalg, Urmas Tedersoo, Leho

第一作者:Polme, Sergei

通信作者:Polme, S[1];Polme, S[2]

机构:[1]Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia;[2]Univ Tartu, Nat Hist Museum, 46 Vanemuise Str, EE-51003 Tartu, Estonia;[3]Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden;[4]Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden;[5]Swedish Univ Agr Sci, Dept Soil & Environm, Box 7014, S-75007 Uppsala, Sweden;[6]Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Box 7026, S-75007 Uppsala, Sweden;[7]Univ Oslo, Sect Genet & Evolutionary Biol EvoGene, Dept Biosci, POB 1066, NO-0316 Oslo, Norway;[8]Univ Hawaii Manoa, 3190 Maile Way,St John 102, Honolulu, HI 96822 USA;[9]Univ Copenhagen, Dept Biol, Univ Parken 15, DK-2100 Copenhagen O, Denmark;[10]Purdue Univ Northwest, Westville, IN 46391 USA;[11]Czech Acad Sci, Inst Microbiol, Videnska 1083, Prague 14220 4, Czech Republic;[12]Univ Copenhagen, GLOBE Inst, Oster Farimagsgade 5,KH7-2-32, DK-1353 Copenhagen, Denmark;[13]Univ Torino, Dipartimento Sci Vita & Biol Sistemi, Viale Mattioli 25, I-10125 Turin, Italy;[14]Harvard Univ, Dept Organism & Evolutionary Biol, 22 Divin Ave, Cambridge, MA 02138 USA;[15]Harvard Univ, Farlow Lib & Herbarium, 22 Divin Ave, Cambridge, MA 02138 USA;[16]Blaihofstr 42, D-72074 Tubingen, Germany;[17]SYNLAB Estonia, Veerenni 53a, EE-11313 Tallinn, Estonia;[18]Univ Santo Tomas, Escuela Tecnol Med, Los Carreras 753, Osorno, Chile;[19]Univ Mayor, Ctr Genom & Bioinformat, Camino La Piramide 5750, Santiago, Chile;[20]Norwegian Inst Nat Res NINA, Sognsveien 68, N-0855 Oslo, Norway;[21]Univ Elect Sci & Technol China, Sch Life Sci & Technol, Chengdu 611731, Peoples R China;[22]Univ Warsaw, Biol & Chem Res Ctr, Evolutionary Biol, Fac Biol, Ul Zwirki & Wigury 101, PL-02089 Warsaw, Poland;[23]Swedish Museum Nat Hist, Dept Bot, POB 50007, S-10405 Stockholm, Sweden;[24]Gothenburg Global Biodivers Ctr, POB 461, S-40530 Gothenburg, Sweden;[25]Mae Fah Luang Univ, Ctr Excellence Fungal Res, Chiang Rai 57100, Thailand;[26]Westerdijk Fungal Biodivers Inst, Utrecht, Netherlands;[27]Univ Florida, Dept Plant Pathol, Gainesville, FL 32611 USA;[28]Minist Primary Ind, Plant Hlth & Environm Lab, Auckland 1140, New Zealand;[29]Qujing Normal Univ, Ctr Yunnan Plateau Biol Resources Protect & Utili, Qujing 655011, Yunnan, Peoples R China;[30]Inst Fed Educ Ciencia & Tecnol Sao Paulo IFSP, Campus Sao Paulo,Rua Pedro Vicente 625, BR-01109010 Sao Paulo, SP, Brazil;[31]Inst Bot, Nucl Pesquisa Micol, Av Miguel Stefano 3687, BR-04301012 Sao Paulo, SP, Brazil;[32]Estonian Univ Life Sci, Inst Agr & Environm Sci, Fr R Kreutzwaldi 5, EE-51006 Tartu, Estonia;[33]Univ Fed Pernambuco, Dept Micol, Ave Engn,S-N Cidade Univ, BR-50740600 Recife, PE, Brazil;[34]Univ Copenhagen, Globe Inst, Univ Parken 15, DK-2100 Copenhagen O, Denmark;[35]Oak Ridge Inst Sci & Educ, ARS Res Participat Program, Oak Ridge, TN 37830 USA;[36]All Russian Inst Plant Protect, Podbelskogo 3 Pushkin, St Petersburg 196608, Russia;[37]Univ Rosario, Dept Biol, Carrera 24 63C-69, Bogota 111221, DC, Colombia;[38]Univ Fed Rural Amazonia, Ciencias Biol, Rodovia PA-451,Km 03, BR-68680000 Bairro Acaizal, Brazil;[39]Univ Nacl Autonoma Mexico, Inst Biol, Mexico City, DF, Mexico;[40]Aberystwyth Univ, Inst Biol Environm & Rural Sci, Aberystwyth, Dyfed, Wales;[41]Univ Ghent, Dept Biol, Res Grp Mycol, Ledeganckstr 35, B-9000 Ghent, Belgium;[42]West Bengal State Univ, Dept Bot, North-24-Parganas, Barasat 700126, W Bengal, India;[43]Beijing Forestry Univ, Inst Microbiol, Sch Ecol & Nat Conservat, Beijing 100083, Peoples R China;[44]Jawaharlal Nehru Trop Bot Garden Res & Inst JNTBG, Thiruvananthapuram 695562, Kerala, India;[45]Univ Higgins, Inst Agrifood Anim & Environm Sci ICA3, San Fernando 3070000, Chile;[46]Pontificia Univ Catolica Chile, Ctr Appl Ecol & Sustainabil CAPES, Santiago 8320000, Chile;[47]Univ Minnesota Twin Cities, Dept Ecol Evolut & Behav, St Paul, MN 55108 USA;[48]Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China;[49]Field Museum, Sci & Educ, 1400 S Lake Shore Dr, Chicago, IL 60605 USA;[50]Field Museum, Grainger Bioinformat Ctr, 1400 S Lake Shore Dr, Chicago, IL 60605 USA;[51]Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Alte Fischerhuette 2, D-16775 Stechlin, Germany;[52]Univ Potsdam, Inst Biochem & Biol, Maulbeerallee 2, D-14469 Potsdam, Germany;[53]Univ Guilan, Dept Plant Protect, Rasht, Iran;[54]Univ Alaska, Inst Arctic Biol, 311 Irving Bldg,2140 Koyukuk Dr,POX 757000, Fairbanks, AK 99775 USA;[55]Eszterhazy Karoly Univ, MTA EKE Lendulet Environm Microbiome Res Grp, Eger, Hungary;[56]Estonian Univ Life Sci, Inst Agr & Environm Sci, Tartu, Estonia;[57]Univ Tokyo, Dept Nat Environm Studies, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2770882, Japan;[58]Univ Costa Rica, Escuela Biol, San Jose 11501, Costa Rica;[59]Latvian State Forest Res Inst Silava, Genet Resource Ctr, 111 Rigas Str, LV-2169 Salaspils, Latvia;[60]Univ Sydney, Sydney Med Sch, Sydney, NSW, Australia;[61]Univ Sydney, Westmead Clin Sch, Sydney, NSW, Australia;[62]Univ Sydney, Westmead Inst Med Res, Sydney, NSW, Australia;[63]Westmead Hosp, Sydney, NSW, Australia;[64]Biol Res Ctr Szeged, H-6726 Szeged, Hungary;[65]Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing 100101, Peoples R China;[66]Hans Knoll Inst HKI, Leibniz Inst Nat Prod Res & Infect Biol, Natl Reference Ctr Invas Fungal Infect NRZMyk, Jena, Germany;[67]Purdue Univ, Dept Bot & Plant Pathol, W Lafayette, IN 47907 USA;[68]Pontificia Univ Catolica Chile, Dept Ecol, Alameda 340, CA, Chile;[69]Uppsala Univ, Dept Organismal Biol, Uppsala, Sweden;[70]Swedish Univ Agr Sci SLU, Southern Swedish Forest Res Ctr, Alnarp, Sweden;[71]Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden;[72]Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, 8th MarchSt 202-3, Ekaterinburg 620144, Russia;[73]Manaaki Whenua Landcare Res, Private Bag 92170, Auckland 1142, New Zealand;[74]Univ Chittagong, Inst Forestry & Environm Sci, Chittagong, Bangladesh;[75]Univ Memphis, Dept Biol Sci, Memphis, TN 38152 USA;[76]United Arab Emirates Univ, Dept Biol, Coll Sci, Abu Dhabi, U Arab Emirates;[77]Minist Nat Resources, Inst Oceanog 3, Key Lab Marine Biogenet Resources, 184 Daxue Rd, Xiamen 361005, Peoples R China;[78]Univ Pretoria, Forestry Agr Biotechnol Inst FABI, Dept Biochem Genet & Microbiol, Pretoria, South Africa;[79]Chinese Acad Sci, Inst Soil Sci, State Key Lab Soil & Sustainable Agr, East Beijing Rd 71, Nanjing 210008, Peoples R China;[80]Royal Bot Gardens Victoria, Melbourne, Vic 3004, Australia;[81]Ocean Univ China, Coll Marine Life Sci, Qingdao 266003, Peoples R China;[82]Guizhou Inst Technol, Sch Food & Pharmaceut Engn, Guiyang 550003, Peoples R China;[83]Mie Univ, Grad Sch Bioresources, Tsu, Mie, Japan;[84]Hokkaido Univ, Arctic Res Ctr, Sapporo, Hokkaido, Japan

第一机构:Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia

通信机构:corresponding author), Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia;corresponding author), Univ Tartu, Nat Hist Museum, 46 Vanemuise Str, EE-51003 Tartu, Estonia.

年份:2020

卷号:105

期号:1

起止页码:1-16

外文期刊名:FUNGAL DIVERSITY

收录:;Scopus(收录号:2-s2.0-85099911596);WOS:【SCI-EXPANDED(收录号:WOS:000608948200001)】;

语种:英文

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

摘要: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 Fun(Fun) 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 studies. 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.

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