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

doi:10.1007/s13225-020-00466-2

KIB OpenIR

	FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
	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
	2020
发表期刊	FUNGAL DIVERSITY
ISSN	1560-2745
卷号	105 期号:1 页码:1-16
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.
关键词	Fungal traits Trophic modes Function Guild Bioinformatics High-throughput sequencing Community ecology PLANT IDENTIFICATION ENDOPHYTES ECOLOGY BIODIVERSITY RECOGNITION EVOLUTION LINEAGES PARADIGM DECAY
DOI	10.1007/s13225-020-00466-2
WOS记录号	WOS:000608948200001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73373
专题	中国科学院昆明植物研究所
作者单位	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.Henrik Nilsson, R.] Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden 5.Lindahl, Bjorn D.] 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.Bates, Scott T.] 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.Liu, Jian-Kui; Maharachchikumbura, Sajeewa S. N.] 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.Hyde, Kevin David; Samarakoon, Milan C.; Tian, Qing; Perera, Rekhani Hansika; Jayawardena, Ruvishika S.] Mae Fah Luang Univ, Ctr Excellence Fungal Res, Chiang Rai 57100, Thailand 26.Westerdijk Fungal Biodivers Inst, Utrecht, Netherlands 27.Smith, Matthew E.; Reynolds, Nicole K.] Univ Florida, Dept Plant Pathol, Gainesville, FL 32611 USA 28.Minist Primary Ind, Plant Hlth & Environm Lab, Auckland 1140, New Zealand 29.Wijayawardene, Nalin N.] Qujing Normal Univ, Ctr Yunnan Plateau Biol Resources Protect & Utili, Qujing 655011, Yunnan, Peoples R China 30.Menolli, Nelson, Jr.] Inst Fed Educ Ciencia & Tecnol Sao Paulo IFSP, Campus Sao Paulo,Rua Pedro Vicente 625, BR-01109010 Sao Paulo, SP, Brazil 31.Menolli, Nelson, Jr.] 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.Detheridge, Andrew; Griffith, Gareth W.] 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.Pradeep, C. K.] 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.Lumbsch, Thorsten H.; Nelsen, Matthew P.] Field Museum, Sci & Educ, 1400 S Lake Shore Dr, Chicago, IL 60605 USA 50.Lumbsch, Thorsten H.; Nelsen, Matthew P.] 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.Brown, Shawn P.] 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
推荐引用方式 GB/T 7714	Polme,Sergei,Abarenkov,Kessy,Henrik Nilsson,R.,et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles[J]. FUNGAL DIVERSITY,2020,105(1):1-16.
APA	Polme,Sergei.,Abarenkov,Kessy.,Henrik Nilsson,R..,Lindahl,Bjorn D..,Clemmensen,Karina Engelbrecht.,...&Tedersoo,Leho.(2020).FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles.FUNGAL DIVERSITY,105(1),1-16.
MLA	Polme,Sergei,et al."FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles".FUNGAL DIVERSITY 105.1(2020):1-16.

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