FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
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...
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| Veröffentlicht in: | Fungal diversity 2020, Vol.105 (1), p.1-16 |
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| creator | Põlme, Sergei Clemmensen, Karina Engelbrecht 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 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 Agan, Ahto Machado, Alexandre Reis Detheridge, Andrew de Meiras-Ottoni, Angelina Verbeken, Annemieke Dutta, Arun Kumar Cui, Bao-Kai Pradeep, C. K. Stanton, Daniel Gohar, Daniyal Wanasinghe, Dhanushka N. Lumbsch, Thorsten H. Grossart, Hans-Peter Masigol, Hossein Timling, Ina Hiiesalu, Inga Oja, Jane Kupagme, John Y. Ilves, Kai Loit, Kaire Adamson, Kalev Nara, Kazuhide Küngas, Kati Rojas-Jimenez, Keilor Bitenieks, Krišs Irinyi, Laszlo Soonvald, Liina Wagner, Lysett Öpik, Maarja Mujica, María Isabel Metsoja, Martin Ryberg, Martin Vasar, Martti Murata, Masao Nelsen, Matthew P. Samarakoon, Milan C. Doilom, Mingkwan Bahram, Mohammad Hagh-Doust, Niloufar Dulya, Olesya Johnston, Peter Kohout, Petr Chen, Qian Tian, Qing Nandi, Rajasree Amiri, Rasekh Gielen, Robin Phookamsak, Rungtiwa Jayawardena, Ruvishika S. Rahimlou, Saleh Karunarathna, Samantha C. Tibpromma, Saowaluck Brown, Shawn P. Sepp, Siim-Kaarel Mundra, Sunil Vahter, Tanel Netherway, Tarquin Yang, Teng May, Tom Coimbra, Victor Rafael Matos de Oliveira, Virton Rodrigo Targino Lu, Yongzhong Matsuda, Yosuke Miyamoto, Yumiko Kõljalg, Urmas Tedersoo, Leho |
| description | 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. |
| doi_str_mv | 10.1007/s13225-020-00466-2 |
| format | Article |
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N. ; Gibertoni, Tatiana B. ; Læssøe, Thomas ; Davis, William ; Tokarev, Yuri ; Corrales, Adriana ; Agan, Ahto ; Machado, Alexandre Reis ; Detheridge, Andrew ; de Meiras-Ottoni, Angelina ; Verbeken, Annemieke ; Dutta, Arun Kumar ; Cui, Bao-Kai ; Pradeep, C. K. ; Stanton, Daniel ; Gohar, Daniyal ; Wanasinghe, Dhanushka N. ; Lumbsch, Thorsten H. ; Grossart, Hans-Peter ; Masigol, Hossein ; Timling, Ina ; Hiiesalu, Inga ; Oja, Jane ; Kupagme, John Y. ; Ilves, Kai ; Loit, Kaire ; Adamson, Kalev ; Nara, Kazuhide ; Küngas, Kati ; Rojas-Jimenez, Keilor ; Bitenieks, Krišs ; Irinyi, Laszlo ; Soonvald, Liina ; Wagner, Lysett ; Öpik, Maarja ; Mujica, María Isabel ; Metsoja, Martin ; Ryberg, Martin ; Vasar, Martti ; Murata, Masao ; Nelsen, Matthew P. ; Samarakoon, Milan C. ; Doilom, Mingkwan ; Bahram, Mohammad ; Hagh-Doust, Niloufar ; Dulya, Olesya ; Johnston, Peter ; Kohout, Petr ; Chen, Qian ; Tian, Qing ; Nandi, Rajasree ; Amiri, Rasekh ; Gielen, Robin ; Phookamsak, Rungtiwa ; Jayawardena, Ruvishika S. ; Rahimlou, Saleh ; Karunarathna, Samantha C. ; Tibpromma, Saowaluck ; Brown, Shawn P. ; Sepp, Siim-Kaarel ; Mundra, Sunil ; Vahter, Tanel ; Netherway, Tarquin ; Yang, Teng ; May, Tom ; Coimbra, Victor Rafael Matos ; de Oliveira, Virton Rodrigo Targino ; Lu, Yongzhong ; Matsuda, Yosuke ; Miyamoto, Yumiko ; Kõljalg, Urmas ; Tedersoo, Leho</creator><creatorcontrib>Põlme, Sergei ; Clemmensen, Karina Engelbrecht ; 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 ; 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 ; Agan, Ahto ; Machado, Alexandre Reis ; Detheridge, Andrew ; de Meiras-Ottoni, Angelina ; Verbeken, Annemieke ; Dutta, Arun Kumar ; Cui, Bao-Kai ; Pradeep, C. K. ; Stanton, Daniel ; Gohar, Daniyal ; Wanasinghe, Dhanushka N. ; Lumbsch, Thorsten H. ; Grossart, Hans-Peter ; Masigol, Hossein ; Timling, Ina ; Hiiesalu, Inga ; Oja, Jane ; Kupagme, John Y. ; Ilves, Kai ; Loit, Kaire ; Adamson, Kalev ; Nara, Kazuhide ; Küngas, Kati ; Rojas-Jimenez, Keilor ; Bitenieks, Krišs ; Irinyi, Laszlo ; Soonvald, Liina ; Wagner, Lysett ; Öpik, Maarja ; Mujica, María Isabel ; Metsoja, Martin ; Ryberg, Martin ; Vasar, Martti ; Murata, Masao ; Nelsen, Matthew P. ; Samarakoon, Milan C. ; Doilom, Mingkwan ; Bahram, Mohammad ; Hagh-Doust, Niloufar ; Dulya, Olesya ; Johnston, Peter ; Kohout, Petr ; Chen, Qian ; Tian, Qing ; Nandi, Rajasree ; Amiri, Rasekh ; Gielen, Robin ; Phookamsak, Rungtiwa ; Jayawardena, Ruvishika S. ; Rahimlou, Saleh ; Karunarathna, Samantha C. ; Tibpromma, Saowaluck ; Brown, Shawn P. ; Sepp, Siim-Kaarel ; Mundra, Sunil ; Vahter, Tanel ; Netherway, Tarquin ; Yang, Teng ; May, Tom ; Coimbra, Victor Rafael Matos ; de Oliveira, Virton Rodrigo Targino ; Lu, Yongzhong ; Matsuda, Yosuke ; Miyamoto, Yumiko ; Kõljalg, Urmas ; Tedersoo, Leho ; Sveriges lantbruksuniversitet</creatorcontrib><description>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.</description><identifier>ISSN: 1560-2745</identifier><identifier>ISSN: 1878-9129</identifier><identifier>EISSN: 1878-9129</identifier><identifier>DOI: 10.1007/s13225-020-00466-2</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Biodiversity ; Bioinformatics ; Biomedical and Life Sciences ; Community ecology ; Ecology ; Ekologi ; Environmental studies ; Function ; Fungal traits ; Fungi ; Guild ; High-throughput sequencing ; Hypotheses ; Life Sciences ; Medical Microbiology ; Microbial Ecology ; Microbiology ; Mikrobiologi ; Mycology ; Plant Physiology ; Species ; Spreadsheets ; Trophic modes</subject><ispartof>Fungal diversity, 2020, Vol.105 (1), p.1-16</ispartof><rights>MUSHROOM RESEARCH FOUNDATION 2021. corrected publication 2021</rights><rights>MUSHROOM RESEARCH FOUNDATION 2021. corrected publication 2021.</rights><rights>info:eu-repo/semantics/openAccess</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0002-9658-1166</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s13225-020-00466-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s13225-020-00466-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,4010,26544,27900,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-435155$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://gup.ub.gu.se/publication/301583$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/110417$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Põlme, Sergei</creatorcontrib><creatorcontrib>Clemmensen, Karina Engelbrecht</creatorcontrib><creatorcontrib>Kjøller, Rasmus</creatorcontrib><creatorcontrib>Bates, Scott T.</creatorcontrib><creatorcontrib>Baldrian, Petr</creatorcontrib><creatorcontrib>Frøslev, Tobias Guldberg</creatorcontrib><creatorcontrib>Adojaan, Kristjan</creatorcontrib><creatorcontrib>Vizzini, Alfredo</creatorcontrib><creatorcontrib>Suija, Ave</creatorcontrib><creatorcontrib>Pfister, Donald</creatorcontrib><creatorcontrib>Baral, Hans-Otto</creatorcontrib><creatorcontrib>Järv, Helle</creatorcontrib><creatorcontrib>Madrid, Hugo</creatorcontrib><creatorcontrib>Nordén, Jenni</creatorcontrib><creatorcontrib>Liu, Jian-Kui</creatorcontrib><creatorcontrib>Pawlowska, Julia</creatorcontrib><creatorcontrib>Põldmaa, Kadri</creatorcontrib><creatorcontrib>Pärtel, Kadri</creatorcontrib><creatorcontrib>Runnel, Kadri</creatorcontrib><creatorcontrib>Hansen, Karen</creatorcontrib><creatorcontrib>Larsson, Karl-Henrik</creatorcontrib><creatorcontrib>Hyde, Kevin David</creatorcontrib><creatorcontrib>Smith, Matthew E.</creatorcontrib><creatorcontrib>Toome-Heller, Merje</creatorcontrib><creatorcontrib>Wijayawardene, Nalin N.</creatorcontrib><creatorcontrib>Menolli, Nelson</creatorcontrib><creatorcontrib>Reynolds, Nicole K.</creatorcontrib><creatorcontrib>Drenkhan, Rein</creatorcontrib><creatorcontrib>Maharachchikumbura, Sajeewa S. 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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.</description><subject>Biodiversity</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Community ecology</subject><subject>Ecology</subject><subject>Ekologi</subject><subject>Environmental studies</subject><subject>Function</subject><subject>Fungal traits</subject><subject>Fungi</subject><subject>Guild</subject><subject>High-throughput sequencing</subject><subject>Hypotheses</subject><subject>Life Sciences</subject><subject>Medical Microbiology</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Mikrobiologi</subject><subject>Mycology</subject><subject>Plant Physiology</subject><subject>Species</subject><subject>Spreadsheets</subject><subject>Trophic modes</subject><issn>1560-2745</issn><issn>1878-9129</issn><issn>1878-9129</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>3HK</sourceid><recordid>eNp1kU9P3jAMxivEJBDjC-xCpV0Js_OnTXZDMGAS0i7vdrXSt0kVKG1JGiG-_cL7InHCF1vW77EtP1X1DeECAdofCQXnigEHBiCbhvGD6hh1q5lBbg5LrRpgvJXqqDpN6QFKCJSNhONqc5OnwY6baMOafta2zslF5mNwUz--1uuuX_d2tZ1Nrp597Ysg1Hbqd1VObAyPrk6FfHLTvITRpa_VF2_H5E7f80n19-bX5uqO3f-5_X11ec-23KiVefQcvcQetUYFTc-940KDLqd1nemc5arc2W611AaM8hYabjveeQHSNF6cVBf7uenFLbmjJYYnG19ptoHSmDsb3xIlR4ggsS0C9qlgyAuV1rDjBaDSovDnn_LX4d8lzXGgnEkKhUoV_GyPb2NIa5homqMlBK04aQFgCvF9Tyxxfs4urfQw5ziVJxGXGkALI3ihxPvasnAaXPygEOjNc9p7TsVz2nlOXPwHmMud3g</recordid><startdate>2020</startdate><enddate>2020</enddate><creator>Põlme, Sergei</creator><creator>Clemmensen, Karina Engelbrecht</creator><creator>Kjøller, Rasmus</creator><creator>Bates, Scott T.</creator><creator>Baldrian, Petr</creator><creator>Frøslev, Tobias Guldberg</creator><creator>Adojaan, Kristjan</creator><creator>Vizzini, Alfredo</creator><creator>Suija, Ave</creator><creator>Pfister, Donald</creator><creator>Baral, Hans-Otto</creator><creator>Järv, Helle</creator><creator>Madrid, Hugo</creator><creator>Nordén, Jenni</creator><creator>Liu, Jian-Kui</creator><creator>Pawlowska, Julia</creator><creator>Põldmaa, Kadri</creator><creator>Pärtel, Kadri</creator><creator>Runnel, Kadri</creator><creator>Hansen, Karen</creator><creator>Larsson, Karl-Henrik</creator><creator>Hyde, Kevin David</creator><creator>Smith, Matthew E.</creator><creator>Toome-Heller, Merje</creator><creator>Wijayawardene, Nalin N.</creator><creator>Menolli, Nelson</creator><creator>Reynolds, Nicole K.</creator><creator>Drenkhan, Rein</creator><creator>Maharachchikumbura, Sajeewa S. N.</creator><creator>Gibertoni, Tatiana B.</creator><creator>Læssøe, Thomas</creator><creator>Davis, William</creator><creator>Tokarev, Yuri</creator><creator>Corrales, Adriana</creator><creator>Agan, Ahto</creator><creator>Machado, Alexandre Reis</creator><creator>Detheridge, Andrew</creator><creator>de Meiras-Ottoni, Angelina</creator><creator>Verbeken, Annemieke</creator><creator>Dutta, Arun Kumar</creator><creator>Cui, Bao-Kai</creator><creator>Pradeep, C. K.</creator><creator>Stanton, Daniel</creator><creator>Gohar, Daniyal</creator><creator>Wanasinghe, Dhanushka N.</creator><creator>Lumbsch, Thorsten H.</creator><creator>Grossart, Hans-Peter</creator><creator>Masigol, Hossein</creator><creator>Timling, Ina</creator><creator>Hiiesalu, Inga</creator><creator>Oja, Jane</creator><creator>Kupagme, John Y.</creator><creator>Ilves, Kai</creator><creator>Loit, Kaire</creator><creator>Adamson, Kalev</creator><creator>Nara, Kazuhide</creator><creator>Küngas, Kati</creator><creator>Rojas-Jimenez, Keilor</creator><creator>Bitenieks, Krišs</creator><creator>Irinyi, Laszlo</creator><creator>Soonvald, Liina</creator><creator>Wagner, Lysett</creator><creator>Öpik, Maarja</creator><creator>Mujica, María Isabel</creator><creator>Metsoja, Martin</creator><creator>Ryberg, Martin</creator><creator>Vasar, Martti</creator><creator>Murata, Masao</creator><creator>Nelsen, Matthew P.</creator><creator>Samarakoon, Milan C.</creator><creator>Doilom, Mingkwan</creator><creator>Bahram, Mohammad</creator><creator>Hagh-Doust, Niloufar</creator><creator>Dulya, Olesya</creator><creator>Johnston, Peter</creator><creator>Kohout, Petr</creator><creator>Chen, Qian</creator><creator>Tian, Qing</creator><creator>Nandi, Rajasree</creator><creator>Amiri, Rasekh</creator><creator>Gielen, Robin</creator><creator>Phookamsak, Rungtiwa</creator><creator>Jayawardena, Ruvishika S.</creator><creator>Rahimlou, Saleh</creator><creator>Karunarathna, Samantha C.</creator><creator>Tibpromma, Saowaluck</creator><creator>Brown, Shawn P.</creator><creator>Sepp, Siim-Kaarel</creator><creator>Mundra, Sunil</creator><creator>Vahter, Tanel</creator><creator>Netherway, Tarquin</creator><creator>Yang, Teng</creator><creator>May, Tom</creator><creator>Coimbra, Victor Rafael Matos</creator><creator>de Oliveira, Virton Rodrigo Targino</creator><creator>Lu, Yongzhong</creator><creator>Matsuda, Yosuke</creator><creator>Miyamoto, Yumiko</creator><creator>Kõljalg, Urmas</creator><creator>Tedersoo, Leho</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>7SN</scope><scope>7TM</scope><scope>C1K</scope><scope>M7N</scope><scope>3HK</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DF2</scope><scope>F1U</scope><orcidid>https://orcid.org/0000-0002-9658-1166</orcidid></search><sort><creationdate>2020</creationdate><title>FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles</title><author>Põlme, Sergei ; Clemmensen, Karina Engelbrecht ; 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 ; 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 ; Agan, Ahto ; Machado, Alexandre Reis ; Detheridge, Andrew ; de Meiras-Ottoni, Angelina ; Verbeken, Annemieke ; Dutta, Arun Kumar ; Cui, Bao-Kai ; Pradeep, C. K. ; Stanton, Daniel ; Gohar, Daniyal ; Wanasinghe, Dhanushka N. ; Lumbsch, Thorsten H. ; Grossart, Hans-Peter ; Masigol, Hossein ; Timling, Ina ; Hiiesalu, Inga ; Oja, Jane ; Kupagme, John Y. ; Ilves, Kai ; Loit, Kaire ; Adamson, Kalev ; Nara, Kazuhide ; Küngas, Kati ; Rojas-Jimenez, Keilor ; Bitenieks, Krišs ; Irinyi, Laszlo ; Soonvald, Liina ; Wagner, Lysett ; Öpik, Maarja ; Mujica, María Isabel ; Metsoja, Martin ; Ryberg, Martin ; Vasar, Martti ; Murata, Masao ; Nelsen, Matthew P. ; Samarakoon, Milan C. ; Doilom, Mingkwan ; Bahram, Mohammad ; Hagh-Doust, Niloufar ; Dulya, Olesya ; Johnston, Peter ; Kohout, Petr ; Chen, Qian ; Tian, Qing ; Nandi, Rajasree ; Amiri, Rasekh ; Gielen, Robin ; Phookamsak, Rungtiwa ; Jayawardena, Ruvishika S. ; Rahimlou, Saleh ; Karunarathna, Samantha C. ; Tibpromma, Saowaluck ; Brown, Shawn P. ; Sepp, Siim-Kaarel ; Mundra, Sunil ; Vahter, Tanel ; Netherway, Tarquin ; Yang, Teng ; May, Tom ; Coimbra, Victor Rafael Matos ; de Oliveira, Virton Rodrigo Targino ; Lu, Yongzhong ; Matsuda, Yosuke ; Miyamoto, Yumiko ; Kõljalg, Urmas ; Tedersoo, Leho</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c295t-f1f21f41d1881506d2fe23808464bb9bea253147c8489095fa062ab2bf30496f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Biodiversity</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Community ecology</topic><topic>Ecology</topic><topic>Ekologi</topic><topic>Environmental studies</topic><topic>Function</topic><topic>Fungal traits</topic><topic>Fungi</topic><topic>Guild</topic><topic>High-throughput sequencing</topic><topic>Hypotheses</topic><topic>Life Sciences</topic><topic>Medical Microbiology</topic><topic>Microbial Ecology</topic><topic>Microbiology</topic><topic>Mikrobiologi</topic><topic>Mycology</topic><topic>Plant Physiology</topic><topic>Species</topic><topic>Spreadsheets</topic><topic>Trophic modes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Põlme, Sergei</creatorcontrib><creatorcontrib>Clemmensen, Karina Engelbrecht</creatorcontrib><creatorcontrib>Kjøller, Rasmus</creatorcontrib><creatorcontrib>Bates, Scott T.</creatorcontrib><creatorcontrib>Baldrian, Petr</creatorcontrib><creatorcontrib>Frøslev, Tobias Guldberg</creatorcontrib><creatorcontrib>Adojaan, Kristjan</creatorcontrib><creatorcontrib>Vizzini, Alfredo</creatorcontrib><creatorcontrib>Suija, Ave</creatorcontrib><creatorcontrib>Pfister, Donald</creatorcontrib><creatorcontrib>Baral, Hans-Otto</creatorcontrib><creatorcontrib>Järv, Helle</creatorcontrib><creatorcontrib>Madrid, Hugo</creatorcontrib><creatorcontrib>Nordén, Jenni</creatorcontrib><creatorcontrib>Liu, Jian-Kui</creatorcontrib><creatorcontrib>Pawlowska, Julia</creatorcontrib><creatorcontrib>Põldmaa, Kadri</creatorcontrib><creatorcontrib>Pärtel, Kadri</creatorcontrib><creatorcontrib>Runnel, Kadri</creatorcontrib><creatorcontrib>Hansen, Karen</creatorcontrib><creatorcontrib>Larsson, Karl-Henrik</creatorcontrib><creatorcontrib>Hyde, Kevin David</creatorcontrib><creatorcontrib>Smith, Matthew E.</creatorcontrib><creatorcontrib>Toome-Heller, Merje</creatorcontrib><creatorcontrib>Wijayawardene, Nalin N.</creatorcontrib><creatorcontrib>Menolli, Nelson</creatorcontrib><creatorcontrib>Reynolds, Nicole K.</creatorcontrib><creatorcontrib>Drenkhan, Rein</creatorcontrib><creatorcontrib>Maharachchikumbura, Sajeewa S. 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N.</au><au>Gibertoni, Tatiana B.</au><au>Læssøe, Thomas</au><au>Davis, William</au><au>Tokarev, Yuri</au><au>Corrales, Adriana</au><au>Agan, Ahto</au><au>Machado, Alexandre Reis</au><au>Detheridge, Andrew</au><au>de Meiras-Ottoni, Angelina</au><au>Verbeken, Annemieke</au><au>Dutta, Arun Kumar</au><au>Cui, Bao-Kai</au><au>Pradeep, C. K.</au><au>Stanton, Daniel</au><au>Gohar, Daniyal</au><au>Wanasinghe, Dhanushka N.</au><au>Lumbsch, Thorsten H.</au><au>Grossart, Hans-Peter</au><au>Masigol, Hossein</au><au>Timling, Ina</au><au>Hiiesalu, Inga</au><au>Oja, Jane</au><au>Kupagme, John Y.</au><au>Ilves, Kai</au><au>Loit, Kaire</au><au>Adamson, Kalev</au><au>Nara, Kazuhide</au><au>Küngas, Kati</au><au>Rojas-Jimenez, Keilor</au><au>Bitenieks, Krišs</au><au>Irinyi, Laszlo</au><au>Soonvald, Liina</au><au>Wagner, Lysett</au><au>Öpik, Maarja</au><au>Mujica, María Isabel</au><au>Metsoja, Martin</au><au>Ryberg, Martin</au><au>Vasar, Martti</au><au>Murata, Masao</au><au>Nelsen, Matthew P.</au><au>Samarakoon, Milan C.</au><au>Doilom, Mingkwan</au><au>Bahram, Mohammad</au><au>Hagh-Doust, Niloufar</au><au>Dulya, Olesya</au><au>Johnston, Peter</au><au>Kohout, Petr</au><au>Chen, Qian</au><au>Tian, Qing</au><au>Nandi, Rajasree</au><au>Amiri, Rasekh</au><au>Gielen, Robin</au><au>Phookamsak, Rungtiwa</au><au>Jayawardena, Ruvishika S.</au><au>Rahimlou, Saleh</au><au>Karunarathna, Samantha C.</au><au>Tibpromma, Saowaluck</au><au>Brown, Shawn P.</au><au>Sepp, Siim-Kaarel</au><au>Mundra, Sunil</au><au>Vahter, Tanel</au><au>Netherway, Tarquin</au><au>Yang, Teng</au><au>May, Tom</au><au>Coimbra, Victor Rafael Matos</au><au>de Oliveira, Virton Rodrigo Targino</au><au>Lu, Yongzhong</au><au>Matsuda, Yosuke</au><au>Miyamoto, Yumiko</au><au>Kõljalg, Urmas</au><au>Tedersoo, Leho</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles</atitle><jtitle>Fungal diversity</jtitle><stitle>Fungal Diversity</stitle><date>2020</date><risdate>2020</risdate><volume>105</volume><issue>1</issue><spage>1</spage><epage>16</epage><pages>1-16</pages><issn>1560-2745</issn><issn>1878-9129</issn><eissn>1878-9129</eissn><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.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s13225-020-00466-2</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-9658-1166</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1560-2745 |
| ispartof | Fungal diversity, 2020, Vol.105 (1), p.1-16 |
| issn | 1560-2745 1878-9129 1878-9129 |
| language | eng |
| recordid | cdi_swepub_primary_oai_slubar_slu_se_110417 |
| source | NORA - Norwegian Open Research Archives; Springer Online Journals |
| subjects | Biodiversity Bioinformatics Biomedical and Life Sciences Community ecology Ecology Ekologi Environmental studies Function Fungal traits Fungi Guild High-throughput sequencing Hypotheses Life Sciences Medical Microbiology Microbial Ecology Microbiology Mikrobiologi Mycology Plant Physiology Species Spreadsheets Trophic modes |
| title | FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles |
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