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

Sergei Põlme; Kessy Abarenkov; R. Henrik 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; 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

doi:10.1007/s13225-020-00466-2

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

, Sergei Põlme, Kessy Abarenkov, R. Henrik 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 NordénJian 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, 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

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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 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.

Translated title of the contribution	FungalTraits: una base de datos de rasgos fácil de usar de hongos y stramenopiles similares a hongos
Original language	English (US)
Pages (from-to)	1-16
Number of pages	16
Journal	Fungal Diversity
Volume	105
Issue number	1
DOIs	https://doi.org/10.1007/s13225-020-00466-2
State	Published - Nov 2020

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Ecology

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10.1007/s13225-020-00466-2

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, Põlme, S., Abarenkov, K., Henrik Nilsson, R., Lindahl, B. D., Clemmensen, K. E., Kauserud, H., Nguyen, N., Kjøller, R., Bates, S. T., Baldrian, P., Frøslev, T. G., Adojaan, K., Vizzini, A., Suija, A., Pfister, D., Baral, H. O., Järv, H., Madrid, H., ... Pradeep, C. K. (2020). FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity, 105(1), 1-16. https://doi.org/10.1007/s13225-020-00466-2

@article{9267826021fe40b8b35ec13c20cb69e6,

title = "FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles",

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.",

author = "Sergei P{\~o}lme and Kessy Abarenkov and {Henrik Nilsson}, R. and Lindahl, {Bj{\"o}rn D.} and Clemmensen, {Karina Engelbrecht} and Havard Kauserud and Nhu Nguyen and Rasmus Kj{\o}ller and Bates, {Scott T.} and Petr Baldrian and Fr{\o}slev, {Tobias Guldberg} and Kristjan Adojaan and Alfredo Vizzini and Ave Suija and Donald Pfister and Baral, {Hans Otto} and Helle J{\"a}rv and Hugo Madrid and Jenni Nord{\'e}n and Liu, {Jian Kui} and Julia Pawlowska and Kadri P{\~o}ldmaa and Kadri P{\"a}rtel and Kadri Runnel and Karen Hansen and Larsson, {Karl Henrik} and Hyde, {Kevin David} and Marcelo Sandoval-Denis and Smith, {Matthew E.} and Merje Toome-Heller and Wijayawardene, {Nalin N.} and Nelson Menolli and Reynolds, {Nicole K.} and Rein Drenkhan and Maharachchikumbura, {Sajeewa S.N.} and Gibertoni, {Tatiana B.} and Thomas L{\ae}ss{\o}e and William Davis and Yuri Tokarev and Adriana Corrales and Soares, {Adriene Mayra} and Ahto Agan and Machado, {Alexandre Reis} and Andr{\'e}s Arg{\"u}elles-Moyao and Andrew Detheridge and {de Meiras-Ottoni}, Angelina and Annemieke Verbeken and Dutta, {Arun Kumar} and Cui, {Bao Kai} and Pradeep, {C. K.}",

note = "Funding Information: We thank Dr. Mario Saare for help with the R software. Publisher Copyright: {\textcopyright} 2021, MUSHROOM RESEARCH FOUNDATION. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2020",

month = nov,

doi = "10.1007/s13225-020-00466-2",

language = "English (US)",

volume = "105",

pages = "1--16",

journal = "Fungal Diversity",

issn = "1560-2745",

publisher = "Springer Netherlands",

number = "1",

}

Põlme, S, Abarenkov, K, Henrik Nilsson, R, Lindahl, BD, Clemmensen, KE, Kauserud, H, Nguyen, N, Kjøller, R, Bates, ST, Baldrian, P, Frøslev, TG, Adojaan, K, Vizzini, A, Suija, A, Pfister, D, Baral, HO, Järv, H, Madrid, H, Nordén, J, Liu, JK, Pawlowska, J, Põldmaa, K, Pärtel, K, Runnel, K, Hansen, K, Larsson, KH, Hyde, KD, Sandoval-Denis, M, Smith, ME, Toome-Heller, M, Wijayawardene, NN, Menolli, N, Reynolds, NK, Drenkhan, R, Maharachchikumbura, SSN, Gibertoni, TB, Læssøe, T, Davis, W, Tokarev, Y, Corrales, A, Soares, AM, Agan, A, Machado, AR, Argüelles-Moyao, A, Detheridge, A, de Meiras-Ottoni, A, Verbeken, A, Dutta, AK & Cui, BK & Pradeep, CK 2020, 'FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles', Fungal Diversity, vol. 105, no. 1, pp. 1-16. https://doi.org/10.1007/s13225-020-00466-2

TY - JOUR

T1 - FungalTraits

T2 - a user-friendly traits database of fungi and fungus-like stramenopiles

AU - Põlme, Sergei

AU - Abarenkov, Kessy

AU - Henrik Nilsson, R.

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.

N1 - Funding Information: We thank Dr. Mario Saare for help with the R software. Publisher Copyright: © 2021, MUSHROOM RESEARCH FOUNDATION. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/11

Y1 - 2020/11

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.

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DO - 10.1007/s13225-020-00466-2

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JO - Fungal Diversity

JF - Fungal Diversity

IS - 1

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

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