Abstract
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 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.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Fungal Diversity |
| Vol/bind | 105 |
| Udgave nummer | 1 |
| Sider (fra-til) | 1-16 |
| Antal sider | 16 |
| ISSN | 1560-2745 |
| DOI | |
| Status | Udgivet - 2020 |
Bibliografisk note
Correction to: Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity (2021) DOI: 10.1007/s13225-021-00470-0Citationsformater
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FungalTraits : a user-friendly traits database of fungi and fungus-like stramenopiles. / Põlme, Sergei; Abarenkov, Kessy; Nilsson, R. Henrik; Lindahl, Björn D.; Clemmensen, Karina Engelbrecht; Kauserud, Havard; Nguyen, Nhu; Kjøller, Rasmus; Bates, Scott T.; Baldrian, Petr; Frøslev, Tobias Guldberg; Adojaan, Kristjan; Vizzini, Alfredo; Suija, Ave; Pfister, Donald; Baral, Hans Otto; Järv, Helle; Madrid, Hugo; Nordén, Jenni; Liu, Jian-Kui; Pawlowska, Julia; Põldmaa, Kadri; Pärtel, 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; Reynolds, Nicole K.; Drenkhan, Rein; Maharachchikumbura, Sajeewa S. N.; Gibertoni, Tatiana B.; Læssøe, Thomas; Davis, William; Tokarev, Yuri; Corrales, Adriana; Soares, Adriene Mayra; Agan, Ahto; Machado, Alexandre Reis; Argüelles-Moyao, Andrés; Detheridge, Andrew; de Meiras-Ottoni, Angelina; Verbeken, Annemieke; Dutta, Arun Kumar; Cui, Bao-Kai; Pradeep, C. K.; Marín, César; 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, József; Alvarez-Manjarrez, Julieta; Ilves, Kai; Loit, Kaire; Adamson, Kalev; Nara, Kazuhide; Küngas, Kati; Rojas-Jimenez, Keilor; Bitenieks, Krišs; Irinyi, Laszlo; Nagy, László G.; Soonvald, Liina; Zhou, Li-Wei; Wagner, Lysett; Aime, M. Catherine; Öpik, Maarja; Mujica, María 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; Chikowski, Renata dos Santos; 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; Kõljalg, Urmas; Tedersoo, Leho.
I: Fungal Diversity, Bind 105, Nr. 1, 2020, s. 1-16.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
}
TY - JOUR
T1 - FungalTraits
T2 - a user-friendly traits database of fungi and fungus-like stramenopiles
AU - Põlme, Sergei
AU - Abarenkov, Kessy
AU - Nilsson, R. Henrik
AU - Lindahl, Björn D.
AU - Clemmensen, Karina Engelbrecht
AU - Kauserud, Havard
AU - Nguyen, Nhu
AU - Kjøller, Rasmus
AU - Bates, Scott T.
AU - Baldrian, Petr
AU - Frøslev, Tobias Guldberg
AU - Adojaan, Kristjan
AU - Vizzini, Alfredo
AU - Suija, Ave
AU - Pfister, Donald
AU - Baral, Hans Otto
AU - Järv, Helle
AU - Madrid, Hugo
AU - Nordén, Jenni
AU - Liu, Jian-Kui
AU - Pawlowska, Julia
AU - Põldmaa, Kadri
AU - Pärtel, Kadri
AU - Runnel, Kadri
AU - Hansen, Karen
AU - Larsson, Karl-Henrik
AU - Hyde, Kevin David
AU - Sandoval-Denis, Marcelo
AU - Smith, Matthew E.
AU - Toome-Heller, Merje
AU - Wijayawardene, Nalin N.
AU - Menolli, Nelson
AU - Reynolds, Nicole K.
AU - Drenkhan, Rein
AU - Maharachchikumbura, Sajeewa S. N.
AU - Gibertoni, Tatiana B.
AU - Læssøe, Thomas
AU - Davis, William
AU - Tokarev, Yuri
AU - Corrales, Adriana
AU - Soares, Adriene Mayra
AU - Agan, Ahto
AU - Machado, Alexandre Reis
AU - Argüelles-Moyao, Andrés
AU - Detheridge, Andrew
AU - de Meiras-Ottoni, Angelina
AU - Verbeken, Annemieke
AU - Dutta, Arun Kumar
AU - Cui, Bao-Kai
AU - Pradeep, C. K.
AU - Marín, César
AU - Stanton, Daniel
AU - Gohar, Daniyal
AU - Wanasinghe, Dhanushka N.
AU - Otsing, Eveli
AU - Aslani, Farzad
AU - Griffith, Gareth W.
AU - Lumbsch, Thorsten H.
AU - Grossart, Hans-Peter
AU - Masigol, Hossein
AU - Timling, Ina
AU - Hiiesalu, Inga
AU - Oja, Jane
AU - Kupagme, John Y.
AU - Geml, József
AU - Alvarez-Manjarrez, Julieta
AU - Ilves, Kai
AU - Loit, Kaire
AU - Adamson, Kalev
AU - Nara, Kazuhide
AU - Küngas, Kati
AU - Rojas-Jimenez, Keilor
AU - Bitenieks, Krišs
AU - Irinyi, Laszlo
AU - Nagy, László G.
AU - Soonvald, Liina
AU - Zhou, Li-Wei
AU - Wagner, Lysett
AU - Aime, M. Catherine
AU - Öpik, Maarja
AU - Mujica, María Isabel
AU - Metsoja, Martin
AU - Ryberg, Martin
AU - Vasar, Martti
AU - Murata, Masao
AU - Nelsen, Matthew P.
AU - Cleary, Michelle
AU - Samarakoon, Milan C.
AU - Doilom, Mingkwan
AU - Bahram, Mohammad
AU - Hagh-Doust, Niloufar
AU - Dulya, Olesya
AU - Johnston, Peter
AU - Kohout, Petr
AU - Chen, Qian
AU - Tian, Qing
AU - Nandi, Rajasree
AU - Amiri, Rasekh
AU - Perera, Rekhani Hansika
AU - Chikowski, Renata dos Santos
AU - Mendes-Alvarenga, Renato L.
AU - Garibay-Orijel, Roberto
AU - Gielen, Robin
AU - Phookamsak, Rungtiwa
AU - Jayawardena, Ruvishika S.
AU - Rahimlou, Saleh
AU - Karunarathna, Samantha C.
AU - Tibpromma, Saowaluck
AU - Brown, Shawn P.
AU - Sepp, Siim-Kaarel
AU - Mundra, Sunil
AU - Luo, Zhu-Hua
AU - Bose, Tanay
AU - Vahter, Tanel
AU - Netherway, Tarquin
AU - Yang, Teng
AU - May, Tom
AU - Varga, Torda
AU - Li, Wei
AU - Coimbra, Victor Rafael Matos
AU - de Oliveira, Virton Rodrigo Targino
AU - de Lima, Vitor Xavier
AU - Mikryukov, Vladimir S.
AU - Lu, Yongzhong
AU - Matsuda, Yosuke
AU - Miyamoto, Yumiko
AU - Kõljalg, Urmas
AU - Tedersoo, Leho
N1 - Correction to: Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity (2021) DOI: 10.1007/s13225-021-00470-0
PY - 2020
Y1 - 2020
N2 - 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 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.
AB - 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 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.
KW - Bioinformatics
KW - Community ecology
KW - Function
KW - Fungal traits
KW - Guild
KW - High-throughput sequencing
KW - Trophic modes
U2 - 10.1007/s13225-020-00466-2
DO - 10.1007/s13225-020-00466-2
M3 - Journal article
AN - SCOPUS:85099911596
VL - 105
SP - 1
EP - 16
JO - Fungal Diversity
JF - Fungal Diversity
SN - 1560-2745
IS - 1
ER -