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1. Megaphylogeny resolves global patterns of mushroom evolution

Author

Varga, Torda, Krizsán, Krisztina, Földi, Csenge, Dima, Bálint, Sánchez-García, Marisol, Sánchez-Ramírez, Santiago, Szöllősi, Gergely J, Szarkándi, János G, Papp, Viktor, Albert, László, Andreopoulos, William, Angelini, Claudio, Antonín, Vladimír, Barry, Kerrie W, Bougher, Neale L, Buchanan, Peter, Buyck, Bart, Bense, Viktória, Catcheside, Pam, Chovatia, Mansi, Cooper, Jerry, Dämon, Wolfgang, Desjardin, Dennis, Finy, Péter, Geml, József, Haridas, Sajeet, Hughes, Karen, Justo, Alfredo, Karasiński, Dariusz, Kautmanova, Ivona, Kiss, Brigitta, Kocsubé, Sándor, Kotiranta, Heikki, LaButti, Kurt M, Lechner, Bernardo E, Liimatainen, Kare, Lipzen, Anna, Lukács, Zoltán, Mihaltcheva, Sirma, Morgado, Louis N, Niskanen, Tuula, Noordeloos, Machiel E, Ohm, Robin A, Ortiz-Santana, Beatriz, Ovrebo, Clark, Rácz, Nikolett, Riley, Robert, Savchenko, Anton, Shiryaev, Anton, Soop, Karl, Spirin, Viacheslav, Szebenyi, Csilla, Tomšovský, Michal, Tulloss, Rodham E, Uehling, Jessie, Grigoriev, Igor V, Vágvölgyi, Csaba, Papp, Tamás, Martin, Francis M, Miettinen, Otto, Hibbett, David S, and Nagy, László G

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Agaricales, Genetic Variation, Genome, Fungal, Phylogeny, Evolutionary biology, Environmental management
Abstract

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.

Published
2019

2. Author Correction: Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György, Prasanna, Arun N, Walter, Mathias C, O’Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, Münsterkötter, Martin, and Nagy, László G

Subjects
Biological Sciences, Genetics, Ecology, Evolutionary biology, Environmental management
Abstract

In the version of this Article originally published, it was incorrectly stated that "16,687 protein-coding genes were inferred for the most recent common ancestor (MRCA) of Armillaria"; the value was incorrect and it should have read "15,787". This has now been corrected.

Published
2018

4. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György, Prasanna, Arun N, Walter, Mathias C, O’Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, Münsterkötter, Martin, and Nagy, László G

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Armillaria, Fungal Proteins, Genome, Fungal, Proteomics, Sequence Analysis, RNA, Species Specificity, Transcriptome, Ecology, Evolutionary biology, Environmental management
Abstract

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

Published
2017

6. Radiation of mushroom-forming fungi correlates with novel modes of protecting sexual fruiting bodies

Author

Varga, Torda, Földi, Csenge, Bense, Viktória, and Nagy, László G.

Subjects
Infectious Diseases, Ascomycota, Basidiomycota, Genetics, Fruiting Bodies, Fungal, Agaricales, Ecology, Evolution, Behavior and Systematics
Abstract

The protection of vulnerable developing structures evolved repeatedly in terrestrial organisms and includes, among others, viviparity in animals and the seed in land plants. In mushroom-forming fungi (Agaricomycetes), sexual spores are born on fruiting bodies, the growth of which is a complex developmental process that is exposed to environmental factors (e.g., desiccation, fungivorous animals). Mushroom-forming fungi evolved a series of innovations in fruiting body protection, however, how these emerged is obscure, leaving the evolutionary principles of fruiting body development poorly known. Here, we show that developmental innovations that lead to the spore-producing surface (hymenophore) being enclosed in a protected environment display asymmetry in their evolution and are associated with increased diversification rates. 'Enclosed' development evolved convergently and became a dominant developmental type in several clades of mushrooms. This probably mirrors spore production benefits for species with protected fruiting body initials, by better coping with environmental factors. Our observations highlight new morphological traits associated with mushroom diversification that parallel the evolution of protection strategies in other organisms, such as viviparity or the seed in animals or plants, respectively, but in the context of spore development, highlighting the general importance of protecting vulnerable progeny across the tree of life.

Published
2022

7. Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

Author

Merényi, Zsolt, Virágh, Máté, Gluck-Thaler, Emile, Slot, Jason C, Kiss, Brigitta, Varga, Torda, Geösel, András, Hegedüs, Botond, Bálint, Balázs, and Nagy, László G

Subjects
Fungal Proteins, Ascomycota, General Immunology and Microbiology, Basidiomycota, Gene Expression Regulation, Fungal, General Neuroscience, Fruiting Bodies, Fungal, General Medicine, Agaricales, General Biochemistry, Genetics and Molecular Biology
Abstract

Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans, a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.

Published
2022
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8. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

Author

Wu, Gang, primary, Miyauchi, Shingo, additional, Morin, Emmanuelle, additional, Kuo, Alan, additional, Drula, Elodie, additional, Varga, Torda, additional, Kohler, Annegret, additional, Feng, Bang, additional, Cao, Yang, additional, Lipzen, Anna, additional, Daum, Christopher, additional, Hundley, Hope, additional, Pangilinan, Jasmyn, additional, Johnson, Jenifer, additional, Barry, Kerrie, additional, LaButti, Kurt, additional, Ng, Vivian, additional, Ahrendt, Steven, additional, Min, Byoungnam, additional, Choi, In‐Geol, additional, Park, Hongjae, additional, Plett, Jonathan M., additional, Magnuson, Jon, additional, Spatafora, Joseph W., additional, Nagy, László G., additional, Henrissat, Bernard, additional, Grigoriev, Igor V., additional, Yang, Zhu‐Liang, additional, Xu, Jianping, additional, and Martin, Francis M., additional

Published
2021
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9. Correction to: FungalTraits: a user friendly traits database of fungi and fungus-like stramenopiles (Fungal Diversity, (2020), 105, 1, (1-16), 10.1007/s13225-020-00466-2)

Author

Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., 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, László, 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, 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, Kõljalg, Urmas, Tedersoo, Leho, Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology

Abstract

There were errors in the name of author László G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.

Published
2021

10. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.

Author

Wu, Gang, Miyauchi, Shingo, Morin, Emmanuelle, Kuo, Alan, Drula, Elodie, Varga, Torda, Kohler, Annegret, Feng, Bang, Cao, Yang, Lipzen, Anna, Daum, Christopher, Hundley, Hope, Pangilinan, Jasmyn, Johnson, Jenifer, Barry, Kerrie, LaButti, Kurt, Ng, Vivian, Ahrendt, Steven, Min, Byoungnam, and Choi, In‐Geol

Subjects
PLANT enzymes, GENES, GENE families, OXIDOREDUCTASES, LIGNOCELLULOSE, LACCASE, LIPASES
Abstract

Summary: We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown‐rot relatives.Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae.Ectomycorrhizal Boletales have a reduced set of plant cell‐wall‐degrading enzymes (PCWDEs) compared with their brown‐rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown‐rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector‐like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay.This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes. [ABSTRACT FROM AUTHOR]

Published
2022
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11. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Author

Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., 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 Laszlo, 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, 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, Kõljalg, Urmas, Tedersoo, Leho, Põlme, Sergei, Abarenkov, Kessy, Henrik Nilsson, R., 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 Laszlo, 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, 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, Kõljalg, Urmas, and Tedersoo, Leho

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.

Published
2020

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

Author

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, 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, and Tedersoo, Leho

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.

Published
2020

13. Megaphylogeny resolves global patterns of mushroom evolution

Author

Sub Molecular Microbiology, Molecular Microbiology, Varga, Torda, Krizsán, Krisztina, Földi, Csenge, Dima, Bálint, Sánchez-García, Marisol, Sánchez-Ramírez, Santiago, Szöllősi, Gergely J., Szarkándi, János G., Papp, Viktor, Albert, László, Andreopoulos, William, Angelini, Claudio, Antonín, Vladimír, Barry, Kerrie W., Bougher, Neale L., Buchanan, Peter, Buyck, Bart, Bense, Viktória, Catcheside, Pam, Chovatia, Mansi, Cooper, Jerry, Dämon, Wolfgang, Desjardin, Dennis, Finy, Péter, Geml, József, Haridas, Sajeet, Hughes, Karen, Justo, Alfredo, Karasiński, Dariusz, Kautmanova, Ivona, Kiss, Brigitta, Kocsubé, Sándor, Kotiranta, Heikki, LaButti, Kurt M., Lechner, Bernardo E., Liimatainen, Kare, Lipzen, Anna, Lukács, Zoltán, Mihaltcheva, Sirma, Morgado, Louis N., Niskanen, Tuula, Noordeloos, Machiel E., Ohm, Robin A., Ortiz-Santana, Beatriz, Ovrebo, Clark, Rácz, Nikolett, Riley, Robert, Savchenko, Anton, Shiryaev, Anton, Soop, Karl, Spirin, Viacheslav, Szebenyi, Csilla, Tomšovský, Michal, Tulloss, Rodham E., Uehling, Jessie, Grigoriev, Igor V., Vágvölgyi, Csaba, Papp, Tamás, Martin, Francis M., Miettinen, Otto, Hibbett, David S., Nagy, László G., Sub Molecular Microbiology, Molecular Microbiology, Varga, Torda, Krizsán, Krisztina, Földi, Csenge, Dima, Bálint, Sánchez-García, Marisol, Sánchez-Ramírez, Santiago, Szöllősi, Gergely J., Szarkándi, János G., Papp, Viktor, Albert, László, Andreopoulos, William, Angelini, Claudio, Antonín, Vladimír, Barry, Kerrie W., Bougher, Neale L., Buchanan, Peter, Buyck, Bart, Bense, Viktória, Catcheside, Pam, Chovatia, Mansi, Cooper, Jerry, Dämon, Wolfgang, Desjardin, Dennis, Finy, Péter, Geml, József, Haridas, Sajeet, Hughes, Karen, Justo, Alfredo, Karasiński, Dariusz, Kautmanova, Ivona, Kiss, Brigitta, Kocsubé, Sándor, Kotiranta, Heikki, LaButti, Kurt M., Lechner, Bernardo E., Liimatainen, Kare, Lipzen, Anna, Lukács, Zoltán, Mihaltcheva, Sirma, Morgado, Louis N., Niskanen, Tuula, Noordeloos, Machiel E., Ohm, Robin A., Ortiz-Santana, Beatriz, Ovrebo, Clark, Rácz, Nikolett, Riley, Robert, Savchenko, Anton, Shiryaev, Anton, Soop, Karl, Spirin, Viacheslav, Szebenyi, Csilla, Tomšovský, Michal, Tulloss, Rodham E., Uehling, Jessie, Grigoriev, Igor V., Vágvölgyi, Csaba, Papp, Tamás, Martin, Francis M., Miettinen, Otto, Hibbett, David S., and Nagy, László G.

Published
2019

14. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György; https://orcid.org/0000-0002-6666-1384, Prasanna, Arun N; https://orcid.org/0000-0001-6995-9293, Walter, Mathias C; https://orcid.org/0000-0003-3012-2626, O'Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba; https://orcid.org/0000-0003-0009-7773, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, et al, Sipos, György; https://orcid.org/0000-0002-6666-1384, Prasanna, Arun N; https://orcid.org/0000-0001-6995-9293, Walter, Mathias C; https://orcid.org/0000-0003-3012-2626, O'Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba; https://orcid.org/0000-0003-0009-7773, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, and et al

Abstract

Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.

Published
2017

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