Author: "Nagy, László" / Publication Type: Electronic Resources - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Nagy, László"' showing total 40 results

Start Over Author "Nagy, László" Publication Type Electronic Resources

40 results on '"Nagy, László"'

1. Importance of aligning the implementation of new payment models for innovative pharmaceuticals in European countries

Author: Afd Pharmacoepi & Clinical Pharmacology, Pharmacoepidemiology and Clinical Pharmacology, PECP - Centre for Pharmaceutical Policy and Regulation, Kaló, Zoltán, Niewada, Maciej, Bereczky, Tamás, Goettsch, Wim, Vreman, Rick A, Xoxi, Entela, Trusheim, Mark, Callenbach, Marcelien H E, Nagy, László, Simoens, Steven, Afd Pharmacoepi & Clinical Pharmacology, Pharmacoepidemiology and Clinical Pharmacology, PECP - Centre for Pharmaceutical Policy and Regulation, Kaló, Zoltán, Niewada, Maciej, Bereczky, Tamás, Goettsch, Wim, Vreman, Rick A, Xoxi, Entela, Trusheim, Mark, Callenbach, Marcelien H E, Nagy, László, and Simoens, Steven
Published: 2024

2. Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits

Author: Merényi, Zsolt, Merényi, Zsolt, Krizsán, Krisztina, Sahu, Neha, Liu, Xiao-Bin, Bálint, Balázs, Stajich, Jason E, Spatafora, Joseph W, Nagy, László G, Merényi, Zsolt, Merényi, Zsolt, Krizsán, Krisztina, Sahu, Neha, Liu, Xiao-Bin, Bálint, Balázs, Stajich, Jason E, Spatafora, Joseph W, and Nagy, László G
Abstract: Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
Published: 2023

3. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.

Author: Bálint, Balázs, Bálint, Balázs, Henrissat, Bernard, Andreopoulos, Bill, Martin, Francis, Bugge Harder, Christoffer, Rigling, Daniel, Ford, Kathryn, Foster, Gary, Pangilinan, Jasmyn, Papanicolaou, Alexie, Barry, Kerrie, LaButti, Kurt, Virágh, Máté, Koriabine, Maxim, Yan, Mi, Sahu, Neha, Indic, Boris, Wong-Bajracharya, Johanna, Merényi, Zsolt, Ke, Huei-Mien, Ahrendt, Steven, Monk, Tori-Lee, Kocsubé, Sándor, Drula, Elodie, Champramary, Simang, Plett, Krista, Tsai, Isheng, Slot, Jason, Sipos, György, Plett, Jonathan, Nagy, László, Grigoriev, Igor, Lipzen, Anna, Riley, Robert, Bálint, Balázs, Bálint, Balázs, Henrissat, Bernard, Andreopoulos, Bill, Martin, Francis, Bugge Harder, Christoffer, Rigling, Daniel, Ford, Kathryn, Foster, Gary, Pangilinan, Jasmyn, Papanicolaou, Alexie, Barry, Kerrie, LaButti, Kurt, Virágh, Máté, Koriabine, Maxim, Yan, Mi, Sahu, Neha, Indic, Boris, Wong-Bajracharya, Johanna, Merényi, Zsolt, Ke, Huei-Mien, Ahrendt, Steven, Monk, Tori-Lee, Kocsubé, Sándor, Drula, Elodie, Champramary, Simang, Plett, Krista, Tsai, Isheng, Slot, Jason, Sipos, György, Plett, Jonathan, Nagy, László, Grigoriev, Igor, Lipzen, Anna, and Riley, Robert
Abstract: The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.
Published: 2023

4. Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria

Author: Sahu, Neha, Indic, Boris, Wong-Bajracharya, Johanna, Merényi, Zsolt, Ke, Huei Mien, Ahrendt, Steven, Monk, Tori Lee, Kocsubé, Sándor, Drula, Elodie, Lipzen, Anna, Bálint, Balázs, Henrissat, Bernard, Andreopoulos, Bill, Martin, Francis M., Bugge Harder, Christoffer, Rigling, Daniel, Ford, Kathryn L., Foster, Gary D., Pangilinan, Jasmyn, Papanicolaou, Alexie, Barry, Kerrie, LaButti, Kurt, Virágh, Máté, Koriabine, Maxim, Yan, Mi, Riley, Robert, Champramary, Simang, Plett, Krista L., Grigoriev, Igor V., Tsai, Isheng Jason, Slot, Jason, Sipos, György, Plett, Jonathan, Nagy, László G., Sahu, Neha, Indic, Boris, Wong-Bajracharya, Johanna, Merényi, Zsolt, Ke, Huei Mien, Ahrendt, Steven, Monk, Tori Lee, Kocsubé, Sándor, Drula, Elodie, Lipzen, Anna, Bálint, Balázs, Henrissat, Bernard, Andreopoulos, Bill, Martin, Francis M., Bugge Harder, Christoffer, Rigling, Daniel, Ford, Kathryn L., Foster, Gary D., Pangilinan, Jasmyn, Papanicolaou, Alexie, Barry, Kerrie, LaButti, Kurt, Virágh, Máté, Koriabine, Maxim, Yan, Mi, Riley, Robert, Champramary, Simang, Plett, Krista L., Grigoriev, Igor V., Tsai, Isheng Jason, Slot, Jason, Sipos, György, Plett, Jonathan, and Nagy, László G.
Abstract: The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens., The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.
Published: 2023

5. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.

Author: Hage, Hayat, Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Chaduli, Delphine, Navarro, David, Favel, Anne, Norest, Manon, Lesage-Meessen, Laurence, Bálint, Balázs, Merényi, Zsolt, de Eugenio, Laura, Morin, Emmanuelle, Martínez, Angel T, Baldrian, Petr, Štursová, Martina, Martínez, María Jesús, Novotny, Cenek, Magnuson, Jon K, Spatafora, Joey W, Maurice, Sundy, Pangilinan, Jasmyn, Andreopoulos, Willian, LaButti, Kurt, Hundley, Hope, Na, Hyunsoo, Kuo, Alan, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Riley, Robert, Ahrendt, Steven, Nagy, László G, Grigoriev, Igor V, Martin, Francis, Rosso, Marie-Noëlle, Hage, Hayat, Hage, Hayat, Miyauchi, Shingo, Virágh, Máté, Drula, Elodie, Min, Byoungnam, Chaduli, Delphine, Navarro, David, Favel, Anne, Norest, Manon, Lesage-Meessen, Laurence, Bálint, Balázs, Merényi, Zsolt, de Eugenio, Laura, Morin, Emmanuelle, Martínez, Angel T, Baldrian, Petr, Štursová, Martina, Martínez, María Jesús, Novotny, Cenek, Magnuson, Jon K, Spatafora, Joey W, Maurice, Sundy, Pangilinan, Jasmyn, Andreopoulos, Willian, LaButti, Kurt, Hundley, Hope, Na, Hyunsoo, Kuo, Alan, Barry, Kerrie, Lipzen, Anna, Henrissat, Bernard, Riley, Robert, Ahrendt, Steven, Nagy, László G, Grigoriev, Igor V, Martin, Francis, and Rosso, Marie-Noëlle
Abstract: Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
Published: 2021

6. 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, 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, and Tedersoo, Leho
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

7. Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species

Author: Sahu, Neha, Merényi, Zsolt, Bálint, Balázs, Kiss, Brigitta, Sipos, György, Owens, Rebecca A., Nagy, László G., Sahu, Neha, Merényi, Zsolt, Bálint, Balázs, Kiss, Brigitta, Sipos, György, Owens, Rebecca A., and Nagy, László G.
Abstract: Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.
Published: 2021

8. Use of carbon paste electrode and modified by gold nanoparticles for selected macrolide antibiotics determination as standard and in pharmaceutical preparations

Author: Vajdle, Olga, Šekuljica, Sanja, Guzsvány, Valéria, Nagy, László, Kónya, Zoltán, Avramov Ivić, Milka, Mijin, Dušan, Petrović, Slobodan D., Anojčić, Jasmina, Vajdle, Olga, Šekuljica, Sanja, Guzsvány, Valéria, Nagy, László, Kónya, Zoltán, Avramov Ivić, Milka, Mijin, Dušan, Petrović, Slobodan D., and Anojčić, Jasmina
Abstract: In this work, carbon paste electrode (CPE) and carbon paste electrode modified with gold nanoparticles (AuNPs/CPE) were employed with rapid direct anodic square wave voltammetry (SWV) for macrolide antibiotics erythromycin ethylsuccinate (EES), azithromycin (AZI), clarithromycin (CLA) and roxithromycin (ROX) determination. The surfaceof working electrodes was morphologically characterized by scanning electron microscopic (SEM) measurements whereby the presence of randomly distributed AuNPs of 10 nmdiameter size on CPE surface was confirmed by energy dispersive spectrometer (EDS). SWV determination of four macrolide antibiotics using CPE was performed in aqueous Britton-Robinson buffer solutions (pH 2.0 to 11.98) showing that oxidation signals strongly depend upon pH (at pH ≥ 6) and exhibited the most favorable characteristics at pH 8.0 in the case of EES and pH 11.98 in the case of AZI, CLA and ROX. Under optimized conditions, the SWV method using CPE enables determination of all investigated macrolide antibiotics in low μg mL−1 concentration ranges with relative standard deviations (RSDs) lower than 6%and achieved detection limits (LODs) as 0.18, 0.045, 1.43 and 0.30 μgmL−1 for EES, AZI, CLA and ROX, respectively. In the case of AZI and ROX, it was demonstrated that the use of AuNPs/CPE as working electrode could additionally improve the results obtained with the SWV method concerning exhibited sensitivity, reproducibility and linear concentrationrange, due to the electrocatalytic properties of synthesized AuNPs. The optimized experimental parameters with the use of SWV method and CPE or AuNPs/CPE were successfully applied for determination of ROX and AZI in their pharmaceutical preparations Runac® and Hemomycin®, respectively. The reliability of the elaborated procedures and thus the accuracy of the obtained results were validated by comparing them with those obtained by means of HPLC-DAD measurements.
Published: 2020

9. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.

Author: Miyauchi, Shingo, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W, Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W, Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D, Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A, Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W, Tedersoo, Leho, Vaario, Lu-Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V, Hibbett, David, Nagy, László G, Martin, Francis M, Miyauchi, Shingo, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W, Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W, Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D, Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A, Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W, Tedersoo, Leho, Vaario, Lu-Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V, Hibbett, David, Nagy, László G, and Martin, Francis M
Abstract: Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
Published: 2020

10. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Author: Molecular Microbiology, Sub Molecular Microbiology, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W., Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W., Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D., Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A., Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J. Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W., Tedersoo, Leho, Vaario, Lu Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V., Hibbett, David, Nagy, László G., Martin, Francis M., Molecular Microbiology, Sub Molecular Microbiology, Miyauchi, Shingo, Kiss, Enikő, Kuo, Alan, Drula, Elodie, Kohler, Annegret, Sánchez-García, Marisol, Morin, Emmanuelle, Andreopoulos, Bill, Barry, Kerrie W., Bonito, Gregory, Buée, Marc, Carver, Akiko, Chen, Cindy, Cichocki, Nicolas, Clum, Alicia, Culley, David, Crous, Pedro W., Fauchery, Laure, Girlanda, Mariangela, Hayes, Richard D., Kéri, Zsófia, LaButti, Kurt, Lipzen, Anna, Lombard, Vincent, Magnuson, Jon, Maillard, François, Murat, Claude, Nolan, Matt, Ohm, Robin A., Pangilinan, Jasmyn, Pereira, Maíra de Freitas, Perotto, Silvia, Peter, Martina, Pfister, Stephanie, Riley, Robert, Sitrit, Yaron, Stielow, J. Benjamin, Szöllősi, Gergely, Žifčáková, Lucia, Štursová, Martina, Spatafora, Joseph W., Tedersoo, Leho, Vaario, Lu Min, Yamada, Akiyoshi, Yan, Mi, Wang, Pengfei, Xu, Jianping, Bruns, Tom, Baldrian, Petr, Vilgalys, Rytas, Dunand, Christophe, Henrissat, Bernard, Grigoriev, Igor V., Hibbett, David, Nagy, László G., and Martin, Francis M.
Published: 2020

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. Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.

Author: Nagy, László G, Nagy, László G, Riley, Robert, Bergmann, Philip J, Krizsán, Krisztina, Martin, Francis M, Grigoriev, Igor V, Cullen, Dan, Hibbett, David S, Nagy, László G, Nagy, László G, Riley, Robert, Bergmann, Philip J, Krizsán, Krisztina, Martin, Francis M, Grigoriev, Igor V, Cullen, Dan, and Hibbett, David S
Abstract: Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.
Published: 2017

14. Megaphylogeny resolves global patterns of mushroom evolution.

Author: Varga, Torda, 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, Varga, Torda, 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
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

15. Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.

Author: Almási, Éva, Almási, Éva, Sahu, Neha, Krizsán, Krisztina, Bálint, Balázs, Kovács, Gábor M, Kiss, Brigitta, Cseklye, Judit, Drula, Elodie, Henrissat, Bernard, Nagy, István, Chovatia, Mansi, Adam, Catherine, LaButti, Kurt, Lipzen, Anna, Riley, Robert, Grigoriev, Igor V, Nagy, László G, Almási, Éva, Almási, Éva, Sahu, Neha, Krizsán, Krisztina, Bálint, Balázs, Kovács, Gábor M, Kiss, Brigitta, Cseklye, Judit, Drula, Elodie, Henrissat, Bernard, Nagy, István, Chovatia, Mansi, Adam, Catherine, LaButti, Kurt, Lipzen, Anna, Riley, Robert, Grigoriev, Igor V, and Nagy, László G
Abstract: Agaricomycetes are fruiting body-forming fungi that produce some of the most efficient enzyme systems to degrade wood. Despite decades-long interest in their biology, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known. We performed comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies, an enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall-degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes revealed a high rate of divergence in developmental gene expression, but also several genes with conserved expression patterns, including novel transcription factors and small-secreted proteins, some of the latter which might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in an important family of mushroom-forming fungi.
Published: 2019

16. Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.

Author: Krizsán, Krisztina, Krizsán, Krisztina, Almási, Éva, Merényi, Zsolt, Sahu, Neha, Virágh, Máté, Kószó, Tamás, Mondo, Stephen, Kiss, Brigitta, Bálint, Balázs, Kües, Ursula, Barry, Kerrie, Cseklye, Judit, Hegedüs, Botond, Henrissat, Bernard, Johnson, Jenifer, Lipzen, Anna, Ohm, Robin A, Nagy, István, Pangilinan, Jasmyn, Yan, Juying, Xiong, Yi, Grigoriev, Igor V, Hibbett, David S, Nagy, László G, Krizsán, Krisztina, Krizsán, Krisztina, Almási, Éva, Merényi, Zsolt, Sahu, Neha, Virágh, Máté, Kószó, Tamás, Mondo, Stephen, Kiss, Brigitta, Bálint, Balázs, Kües, Ursula, Barry, Kerrie, Cseklye, Judit, Hegedüs, Botond, Henrissat, Bernard, Johnson, Jenifer, Lipzen, Anna, Ohm, Robin A, Nagy, István, Pangilinan, Jasmyn, Yan, Juying, Xiong, Yi, Grigoriev, Igor V, Hibbett, David S, and Nagy, László G
Abstract: The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
Published: 2019

17. Notes, outline and divergence times of Basidiomycota

Author: UCL - SST/ELI/ELIM - Applied Microbiology, He, Mao-Qiang, Zhao, Rui-Lin, Hyde, Kevin D., Begerow, Dominik, Kemler, Martin, Yurkov, Andrey, McKenzie, Eric H. C., Raspé, Olivier, Kakishima, Makoto, Sánchez-Ramírez, Santiago, Vellinga, Else C., Halling, Roy, Papp, Viktor, Zmitrovich, Ivan V., Buyck, Bart, Ertz, Damien, Wijayawardene, Nalin N., Cui, Bao-Kai, Schoutteten, Nathan, Liu, Xin-Zhan, Li, Tai-Hui, Yao, Yi-Jian, Zhu, Xin-Yu, Liu, An-Qi, Li, Guo-Jie, Zhang, Ming-Zhe, Ling, Zhi-Lin, Cao, Bin, Antonín, Vladimír, Boekhout, Teun, da Silva, Bianca Denise Barbosa, De Crop, Eske, Decock, Cony, Dima, Bálint, Dutta, Arun Kumar, Fell, Jack W., Geml, József, Ghobad-Nejhad, Masoomeh, Giachini, Admir J., Gibertoni, Tatiana B., Gorjón, Sergio P., Haelewaters, Danny, He, Shuang-Hui, Hodkinson, Brendan P., Horak, Egon, Hoshino, Tamotsu, Justo, Alfredo, Lim, Young Woon, Menolli, Nelson, Mešić, Armin, Moncalvo, Jean-Marc, Mueller, Gregory M., Nagy, László G., Nilsson, R. Henrik, Noordeloos, Machiel, Nuytinck, Jorinde, Orihara, Takamichi, Ratchadawan, Cheewangkoon, Rajchenberg, Mario, Silva-Filho, Alexandre G. S., Sulzbacher, Marcelo Aloisio, Tkalčec, Zdenko, Valenzuela, Ricardo, Verbeken, Annemieke, Vizzini, Alfredo, Wartchow, Felipe, Wei, Tie-Zheng, Weiß, Michael, Zhao, Chang-Lin, Kirk, Paul M., UCL - SST/ELI/ELIM - Applied Microbiology, He, Mao-Qiang, Zhao, Rui-Lin, Hyde, Kevin D., Begerow, Dominik, Kemler, Martin, Yurkov, Andrey, McKenzie, Eric H. C., Raspé, Olivier, Kakishima, Makoto, Sánchez-Ramírez, Santiago, Vellinga, Else C., Halling, Roy, Papp, Viktor, Zmitrovich, Ivan V., Buyck, Bart, Ertz, Damien, Wijayawardene, Nalin N., Cui, Bao-Kai, Schoutteten, Nathan, Liu, Xin-Zhan, Li, Tai-Hui, Yao, Yi-Jian, Zhu, Xin-Yu, Liu, An-Qi, Li, Guo-Jie, Zhang, Ming-Zhe, Ling, Zhi-Lin, Cao, Bin, Antonín, Vladimír, Boekhout, Teun, da Silva, Bianca Denise Barbosa, De Crop, Eske, Decock, Cony, Dima, Bálint, Dutta, Arun Kumar, Fell, Jack W., Geml, József, Ghobad-Nejhad, Masoomeh, Giachini, Admir J., Gibertoni, Tatiana B., Gorjón, Sergio P., Haelewaters, Danny, He, Shuang-Hui, Hodkinson, Brendan P., Horak, Egon, Hoshino, Tamotsu, Justo, Alfredo, Lim, Young Woon, Menolli, Nelson, Mešić, Armin, Moncalvo, Jean-Marc, Mueller, Gregory M., Nagy, László G., Nilsson, R. Henrik, Noordeloos, Machiel, Nuytinck, Jorinde, Orihara, Takamichi, Ratchadawan, Cheewangkoon, Rajchenberg, Mario, Silva-Filho, Alexandre G. S., Sulzbacher, Marcelo Aloisio, Tkalčec, Zdenko, Valenzuela, Ricardo, Verbeken, Annemieke, Vizzini, Alfredo, Wartchow, Felipe, Wei, Tie-Zheng, Weiß, Michael, Zhao, Chang-Lin, and Kirk, Paul M.
Abstract: The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
Published: 2019

18. 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

19. Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi

Author: Sub Molecular Microbiology, Molecular Microbiology, Krizsán, Krisztina, Almási, Éva, Merényi, Zsolt, Sahu, Neha, Virágh, Máté, Kószó, Tamás, Mondo, Stephen, Kiss, Brigitta, Bálint, Balázs, Kües, Ursula, Barry, Kerrie, Cseklye, Judit, Hegedüs, Botond, Henrissat, Bernard, Johnson, Jenifer, Lipzen, Anna, Ohm, Robin A., Nagy, István, Pangilinan, Jasmyn, Yan, Juying, Xiong, Yi, Grigoriev, Igor V., Hibbett, David S., Nagy, László G., Sub Molecular Microbiology, Molecular Microbiology, Krizsán, Krisztina, Almási, Éva, Merényi, Zsolt, Sahu, Neha, Virágh, Máté, Kószó, Tamás, Mondo, Stephen, Kiss, Brigitta, Bálint, Balázs, Kües, Ursula, Barry, Kerrie, Cseklye, Judit, Hegedüs, Botond, Henrissat, Bernard, Johnson, Jenifer, Lipzen, Anna, Ohm, Robin A., Nagy, István, Pangilinan, Jasmyn, Yan, Juying, Xiong, Yi, Grigoriev, Igor V., Hibbett, David S., and Nagy, László G.
Published: 2019

20. Common garden comparisons confirm inherited differences in sensitivity to climate change between forest tree species

Author: Sáenz-Romero, Cuauhtémoc, Kremer, Antoine, Nagy, László, Újvári-Jármay, Éva, Ducousso, Alexis, Kóczán-Horváth, Anikó, Hansen, Jon Kehlet, Mátyás, Csaba, Sáenz-Romero, Cuauhtémoc, Kremer, Antoine, Nagy, László, Újvári-Jármay, Éva, Ducousso, Alexis, Kóczán-Horváth, Anikó, Hansen, Jon Kehlet, and Mátyás, Csaba
Published: 2019

21. Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.

Author: Nagy, László G, Nagy, László G, Riley, Robert, Tritt, Andrew, Adam, Catherine, Daum, Chris, Floudas, Dimitrios, Sun, Hui, Yadav, Jagjit S, Pangilinan, Jasmyn, Larsson, Karl-Henrik, Matsuura, Kenji, Barry, Kerrie, Labutti, Kurt, Kuo, Rita, Ohm, Robin A, Bhattacharya, Sukanta S, Shirouzu, Takashi, Yoshinaga, Yuko, Martin, Francis M, Grigoriev, Igor V, Hibbett, David S, Nagy, László G, Nagy, László G, Riley, Robert, Tritt, Andrew, Adam, Catherine, Daum, Chris, Floudas, Dimitrios, Sun, Hui, Yadav, Jagjit S, Pangilinan, Jasmyn, Larsson, Karl-Henrik, Matsuura, Kenji, Barry, Kerrie, Labutti, Kurt, Kuo, Rita, Ohm, Robin A, Bhattacharya, Sukanta S, Shirouzu, Takashi, Yoshinaga, Yuko, Martin, Francis M, Grigoriev, Igor V, and Hibbett, David S
Abstract: Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
Published: 2016

22. Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies.

Author: Wu, Baojun, Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A, Grigoriev, Igor V, Nagy, László G, Gibbons, John, Hibbett, David, Wu, Baojun, Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A, Grigoriev, Igor V, Nagy, László G, Gibbons, John, and Hibbett, David
Abstract: Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.
Published: 2018

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

Author: Sipos, György, 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, Nagy, László G, Sipos, György, 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
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

24. Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

Author: Knapp, Dániel G, Knapp, Dániel G, Németh, Julianna B, Barry, Kerrie, Hainaut, Matthieu, Henrissat, Bernard, Johnson, Jenifer, Kuo, Alan, Lim, Joanne Hui Ping, Lipzen, Anna, Nolan, Matt, Ohm, Robin A, Tamás, László, Grigoriev, Igor V, Spatafora, Joseph W, Nagy, László G, Kovács, Gábor M, Knapp, Dániel G, Knapp, Dániel G, Németh, Julianna B, Barry, Kerrie, Hainaut, Matthieu, Henrissat, Bernard, Johnson, Jenifer, Kuo, Alan, Lim, Joanne Hui Ping, Lipzen, Anna, Nolan, Matt, Ohm, Robin A, Tamás, László, Grigoriev, Igor V, Spatafora, Joseph W, Nagy, László G, and Kovács, Gábor M
Abstract: Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.
Published: 2018

25. Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Author: Molecular Microbiology, Sub Molecular Microbiology, Knapp, Dániel G, Németh, Julianna B, Barry, Kerrie, Hainaut, Matthieu, Henrissat, Bernard, Johnson, Jenifer, Kuo, Alan, Lim, Joanne Hui Ping, Lipzen, Anna, Nolan, Matt, Ohm, Robin A, Tamás, László, Grigoriev, Igor V, Spatafora, Joseph W, Nagy, László G, Kovács, Gábor M., Molecular Microbiology, Sub Molecular Microbiology, Knapp, Dániel G, Németh, Julianna B, Barry, Kerrie, Hainaut, Matthieu, Henrissat, Bernard, Johnson, Jenifer, Kuo, Alan, Lim, Joanne Hui Ping, Lipzen, Anna, Nolan, Matt, Ohm, Robin A, Tamás, László, Grigoriev, Igor V, Spatafora, Joseph W, Nagy, László G, and Kovács, Gábor M.
Published: 2018

26. Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies

Author: Sub Molecular Microbiology, Molecular Microbiology, Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A, Grigoriev, Igor V, Nagy, László G, Gibbons, John, Hibbett, David, Sub Molecular Microbiology, Molecular Microbiology, Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A, Grigoriev, Igor V, Nagy, László G, Gibbons, John, and Hibbett, David
Published: 2018

27. Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Author: Zamora, Juan Carlos, Svensson, Måns, Kirschner, Roland, Olariaga, Ibai, Ryman, Svengunnar, Parra, Luis Alberto, Geml, József, Rosling, Anna, Adamčík, Slavomír, Ahti, Teuvo, Aime, M. Catherine, Ainsworth, A. Martyn, Albert, László, Albertó, Edgardo, García, Alberto Altés, Ageev, Dmitry, Agerer, Reinhard, Aguirre-Hudson, Begoña, Ammirati, Joe, Andersson, Harry, Angelini, Claudio, Antonín, Vladimír, Aoki, Takayuki, Aptroot, André, Argaud, Didier, Sosa, Blanca Imelda Arguello, Aronsen, Arne, Arup, Ulf, Asgari, Bita, Assyov, Boris, Atienza, Violeta, Bandini, Ditte, Baptista-Ferreira, João Luís, Baral, Hans-Otto, Baroni, Tim, Barreto, Robert Weingart, Beker, Henry, Bell, Ann, Bellanger, Jean-Michel, Bellù, Francesco, Bemmann, Martin, Bendiksby, Mika, Bendiksen, Egil, Bendiksen, Katriina, Benedek, Lajos, Bérešová-Guttová, Anna, Berger, Franz, Berndt, Reinhard, Bernicchia, Annarosa, Biketova, Alona Yu, Bizio, Enrico, Bjork, Curtis, Boekhout, Teun, Boertmann, David, Böhning, Tanja, Boittin, Florent, Boluda, Carlos G, Boomsluiter, Menno W, Borovička, Jan, Brandrud, Tor Erik, Braun, Uwe, Brodo, Irwin, Bulyonkova, Tatiana, Burdsall, Harold H, Buyck, Bart, Burgaz, Ana Rosa, Calatayud, Vicent, Callac, Philippe, Campo, Emanuele, Candusso, Massimo, Capoen, Brigitte, Carbó, Joaquim, Carbone, Matteo, Castañeda-Ruiz, Rafael F., Castellano, Michael A, Chen, Jie, Clerc, Philippe, Consiglio, Giovanni, Corriol, Gilles, Courtecuisse, Régis, Crespo, Ana, Cripps, Cathy, Crous, Pedro W, da Silva, Gladstone Alves, da Silva, Meiriele, Dam, Marjo, Dam, Nico, Dämmrich, Frank, Das, Kanad, Davies, Linda, De Crop, Eske, De Kesel, Andre, De Lange, Ruben, De Madrignac Bonzi, Bárbara, Dela Cruz, Thomas Edison E, Delgat, Lynn, Demoulin, Vincent, Desjardin, Dennis E., Diederich, Paul, Dima, Bálint, Dios, Maria Martha, Divakar, Pradeep Kumar, Douanla-Meli, Clovis, Douglas, Brian, Drechsler-Santos, Elisandro Ricardo, Dyer, Paul S, Eberhardt, Ursula, Ertz, Damien, Esteve-Raventós, Fernando, Salazar, Javier Angel Etayo, Evenson, Vera, Eyssartier, Guillaume, Farkas, Edit, Favre, Alain, Fedosova, Anna G, Filippa, Mario, Finy, Péter, Flakus, Adam, Fos, Simón, Fournier, Jacques, Fraiture, André, Franchi, Paolo, Molano, Ana Esperanza Franco, Friebes, Gernot, Frisch, Andreas, Fryday, Alan, Furci, Giuliana, Márquez, Ricardo Galán, Garbelotto, Matteo, García-Martín, Joaquina María, Otálora, Mónica A García, Sánchez, Dania García, Gardiennet, Alain, Garnica, Sigisfredo, Benavent, Isaac Garrido, Gates, Genevieve, da Cruz Lima Gerlach, Alice, Ghobad-Nejhad, Masoomeh, Gibertoni, Tatiana B, Grebenc, Tine, Krisai-Greilhuber, Irmgard, Grishkan, Bella, Groenewald, Johannes Z, Grube, Martin, Gruhn, Gérald, Gueidan, Cécile, Gulden, Gro, Gusmão, Luis Fp, Hafellner, Josef, Hairaud, Michel, Halama, Marek, Hallenberg, Nils, Halling, Roy E, Hansen, Karen, Harder, Christoffer Bugge, Heilmann-Clausen, Jacob, Helleman, Stip, Henriot, Alain, Hernandez-Restrepo, Margarita, Herve, Raphaël, Hobart, Caroline, Hoffmeister, Mascha, Høiland, Klaus, Holec, Jan, Holien, Håkon, Hughes, Karen, Hubka, Vit, Huhtinen, Seppo, Ivančević, Boris, Jagers, Marian, Jaklitsch, Walter M., Jansen, AnnaElise, Jayawardena, Ruvishika S., Jeppesen, Thomas Stjernegaard, Jeppson, Mikael, Johnston, Peter R., Jørgensen, Per Magnus, Kärnefelt, Ingvar, Kalinina, Liudmila B, Kantvilas, Gintaras, Karadelev, Mitko, Kasuya, Taiga, Kautmanová, Ivona, Kerrigan, Richard W, Kirchmair, Martin, Kiyashko, Anna, Knapp, Dániel G, Knudsen, Henning, Knudsen, Kerry, Knutsson, Tommy, Kolařík, Miroslav, Kõljalg, Urmas, Košuthová, Alica, Koszka, Attila, Kotiranta, Heikki, Kotkova, Vera, Koukol, Ondřej, Kout, Jiří, Kovács, Gábor M, Kříž, Martin, Kruys, Åsa, Kučera, Viktor, Kudzma, Linas, Kuhar, Francisco, Kukwa, Martin, Arun Kumar, T K, Kunca, Vladimír, Kušan, Ivana, Kuyper, Thomas W., Lado, Carlos, Læssøe, Thomas, Lainé, Patrice, Langer, Ewald, Larsson, Ellen, Larsson, Karl-Henrik, Laursen, Gary, Lechat, Christian, Lee, Serena, Lendemer, James C, Levin, Laura, Lindemann, Uwe, Lindström, Håkan, Liu, Xingzhong, Hernandez, Regulo Carlos Llarena, Llop, Esteve, Locsmándi, Csaba, Lodge, Deborah Jean, Loizides, Michael, Lőkös, László, Luangsa-ard, Jennifer, Lüderitz, Matthias, Lumbsch, H. Thorsten, Lutz, Matthias, Mahoney, Dan, Malysheva, Ekaterina, Malysheva, Vera, Manimohan, Patinjareveettil, Marin-Felix, Yasmina, Marques, Guilhermina, Martínez-Gil, Rubén, Marson, Guy, Mata, Gerardo, Matheny, P Brandon, Mathiassen, Geir Harald, Matočec, Neven, Mayrhofer, Helmut, Mehrabi, Mehdi, Melo, Ireneia, Mešić, Armin, Methven, Andrew S, Miettinen, Otto, Romero, Ana M Millanes, Miller, Andrew N., Mitchell, James K, Moberg, Roland, Moreau, Pierre-Arthur, Moreno, Gabriel, Morozova, Olga, Morte, Asunción, Muggia, Lucia, González, Guillermo Muñoz, Myllys, Leena, Nagy, István, Nagy, László G, Neves, Maria Alice, Niemelä, Tuomo, Nimis, Pier Luigi, Niveiro, Nicolas, Noordeloos, Machiel E, Nordin, Anders, Noumeur, Sara Raouia, Novozhilov, Yuri, Nuytinck, Jorinde, Ohenoja, Esteri, Fiuza, Patricia Oliveira, Orange, Alan, Ordynets, Alexander, Ortiz-Santana, Beatriz, Pacheco, Leticia, Pál-Fám, Ferenc, Palacio, Melissa, Palice, Zdeněk, Papp, Viktor, Pärtel, Kadri, Pawlowska, Julia, Paz, Aurelia, Peintner, Ursula, Pennycook, Shaun R., Pereira, Olinto Liparini, Daniëls, Pablo Pérez, Pérez-De-Gregorio Capella, Miquel À, Del Amo, Carlos Manuel Pérez, Gorjón, Sergio Pérez, Pérez-Ortega, Sergio, Pérez-Vargas, Israel, Perry, Brian A, Petersen, Jens H, Petersen, Ronald H, Pfister, Donald H., Phukhamsakda, Chayanard, Piątek, Marcin, Piepenbring, Meike, Pino-Bodas, Raquel, Esquivel, Juan Pablo Pinzón, Pirot, Paul, Popov, Eugene S, Popoff, Orlando, Álvaro, María Prieto, Printzen, Christian, Psurtseva, Nadezhda, Purahong, Witoon, Quijada, Luis, Rambold, Gerhard, Ramírez, Natalia A, Raja, Huzefa A., Raspé, Olivier, Raymundo, Tania, Réblová, Martina, Rebriev, Yury A, de Dios Reyes García, Juan, Ripoll, Miguel Ángel Ribes, Richard, Franck, Richardson, Mike J, Rico, Víctor J, Robledo, Gerardo Lucio, Barbosa, Flavia Rodrigues, Rodriguez-Caycedo, Cristina, Rodriguez-Flakus, Pamela, Ronikier, Anna, Casas, Luis Rubio, Rusevska, Katerina, Saar, Günter, Saar, Irja, Salcedo, Isabel, Martínez, Sergio M Salcedo, Montoya, Carlos A Salvador, Sánchez-Ramírez, Santiago, Sandoval-Sierra, J Vladimir, Santamaria, Sergi, Monteiro, Josiane Santana, Schroers, Hans Josef, Schulz, Barbara, Schmidt-Stohn, Geert, Schumacher, Trond, Senn-Irlet, Beatrice, Ševčíková, Hana, Shchepin, Oleg, Shirouzu, Takashi, Shiryaev, Anton, Siepe, Klaus, Sir, Esteban B, Sohrabi, Mohammad, Soop, Karl, Spirin, Viacheslav, Spribille, Toby, Stadler, Marc, Stalpers, Joost, Stenroos, Soili, Suija, Ave, Sunhede, Stellan, Svantesson, Sten, Svensson, Sigvard, Svetasheva, Tatyana Yu, Świerkosz, Krzysztof, Tamm, Heidi, Taskin, Hatira, Taudière, Adrien, Tedebrand, Jan-Olof, Lahoz, Raúl Tena, Temina, Marina, Thell, Arne, Thines, Marco, Thor, Göran, Thüs, Holger, Tibell, Leif, Tibell, Sanja, Timdal, Einar, Tkalčec, Zdenko, Tønsberg, Tor, Trichies, Gérard, Triebel, Dagmar, Tsurykau, Andrei, Tulloss, Rodham E, Tuovinen, Veera, Sosa, Miguel Ulloa, Urcelay, Carlos, Valade, François, Garza, Ricardo Valenzuela, van den Boom, Pieter, Van Vooren, Nicolas, Vasco, Aida, Vauras, Jukka, Velasco Santos, Juan Manuel, Vellinga, Else, Verbeken, Annemieke, Vetlesen, Per, Vizzini, Alfredo, Voglmayr, Hermann, Volobuev, Sergey, von Brackel, Wolfgang, Voronina, Elena, Walther, Grit, Watling, Roy, Weber, Evi, Wedin, Mats, Weholt, Øyvind, Westberg, Martin, Yurchenko, Eugene, Zehnálek, Petr, Zhang, Huang, Zhurbenko, Mikhail P, Ekman, Stefan, Zamora, Juan Carlos, Svensson, Måns, Kirschner, Roland, Olariaga, Ibai, Ryman, Svengunnar, Parra, Luis Alberto, Geml, József, Rosling, Anna, Adamčík, Slavomír, Ahti, Teuvo, Aime, M. Catherine, Ainsworth, A. Martyn, Albert, László, Albertó, Edgardo, García, Alberto Altés, Ageev, Dmitry, Agerer, Reinhard, Aguirre-Hudson, Begoña, Ammirati, Joe, Andersson, Harry, Angelini, Claudio, Antonín, Vladimír, Aoki, Takayuki, Aptroot, André, Argaud, Didier, Sosa, Blanca Imelda Arguello, Aronsen, Arne, Arup, Ulf, Asgari, Bita, Assyov, Boris, Atienza, Violeta, Bandini, Ditte, Baptista-Ferreira, João Luís, Baral, Hans-Otto, Baroni, Tim, Barreto, Robert Weingart, Beker, Henry, Bell, Ann, Bellanger, Jean-Michel, Bellù, Francesco, Bemmann, Martin, Bendiksby, Mika, Bendiksen, Egil, Bendiksen, Katriina, Benedek, Lajos, Bérešová-Guttová, Anna, Berger, Franz, Berndt, Reinhard, Bernicchia, Annarosa, Biketova, Alona Yu, Bizio, Enrico, Bjork, Curtis, Boekhout, Teun, Boertmann, David, Böhning, Tanja, Boittin, Florent, Boluda, Carlos G, Boomsluiter, Menno W, Borovička, Jan, Brandrud, Tor Erik, Braun, Uwe, Brodo, Irwin, Bulyonkova, Tatiana, Burdsall, Harold H, Buyck, Bart, Burgaz, Ana Rosa, Calatayud, Vicent, Callac, Philippe, Campo, Emanuele, Candusso, Massimo, Capoen, Brigitte, Carbó, Joaquim, Carbone, Matteo, Castañeda-Ruiz, Rafael F., Castellano, Michael A, Chen, Jie, Clerc, Philippe, Consiglio, Giovanni, Corriol, Gilles, Courtecuisse, Régis, Crespo, Ana, Cripps, Cathy, Crous, Pedro W, da Silva, Gladstone Alves, da Silva, Meiriele, Dam, Marjo, Dam, Nico, Dämmrich, Frank, Das, Kanad, Davies, Linda, De Crop, Eske, De Kesel, Andre, De Lange, Ruben, De Madrignac Bonzi, Bárbara, Dela Cruz, Thomas Edison E, Delgat, Lynn, Demoulin, Vincent, Desjardin, Dennis E., Diederich, Paul, Dima, Bálint, Dios, Maria Martha, Divakar, Pradeep Kumar, Douanla-Meli, Clovis, Douglas, Brian, Drechsler-Santos, Elisandro Ricardo, Dyer, Paul S, Eberhardt, Ursula, Ertz, Damien, Esteve-Raventós, Fernando, Salazar, Javier Angel Etayo, Evenson, Vera, Eyssartier, Guillaume, Farkas, Edit, Favre, Alain, Fedosova, Anna G, Filippa, Mario, Finy, Péter, Flakus, Adam, Fos, Simón, Fournier, Jacques, Fraiture, André, Franchi, Paolo, Molano, Ana Esperanza Franco, Friebes, Gernot, Frisch, Andreas, Fryday, Alan, Furci, Giuliana, Márquez, Ricardo Galán, Garbelotto, Matteo, García-Martín, Joaquina María, Otálora, Mónica A García, Sánchez, Dania García, Gardiennet, Alain, Garnica, Sigisfredo, Benavent, Isaac Garrido, Gates, Genevieve, da Cruz Lima Gerlach, Alice, Ghobad-Nejhad, Masoomeh, Gibertoni, Tatiana B, Grebenc, Tine, Krisai-Greilhuber, Irmgard, Grishkan, Bella, Groenewald, Johannes Z, Grube, Martin, Gruhn, Gérald, Gueidan, Cécile, Gulden, Gro, Gusmão, Luis Fp, Hafellner, Josef, Hairaud, Michel, Halama, Marek, Hallenberg, Nils, Halling, Roy E, Hansen, Karen, Harder, Christoffer Bugge, Heilmann-Clausen, Jacob, Helleman, Stip, Henriot, Alain, Hernandez-Restrepo, Margarita, Herve, Raphaël, Hobart, Caroline, Hoffmeister, Mascha, Høiland, Klaus, Holec, Jan, Holien, Håkon, Hughes, Karen, Hubka, Vit, Huhtinen, Seppo, Ivančević, Boris, Jagers, Marian, Jaklitsch, Walter M., Jansen, AnnaElise, Jayawardena, Ruvishika S., Jeppesen, Thomas Stjernegaard, Jeppson, Mikael, Johnston, Peter R., Jørgensen, Per Magnus, Kärnefelt, Ingvar, Kalinina, Liudmila B, Kantvilas, Gintaras, Karadelev, Mitko, Kasuya, Taiga, Kautmanová, Ivona, Kerrigan, Richard W, Kirchmair, Martin, Kiyashko, Anna, Knapp, Dániel G, Knudsen, Henning, Knudsen, Kerry, Knutsson, Tommy, Kolařík, Miroslav, Kõljalg, Urmas, Košuthová, Alica, Koszka, Attila, Kotiranta, Heikki, Kotkova, Vera, Koukol, Ondřej, Kout, Jiří, Kovács, Gábor M, Kříž, Martin, Kruys, Åsa, Kučera, Viktor, Kudzma, Linas, Kuhar, Francisco, Kukwa, Martin, Arun Kumar, T K, Kunca, Vladimír, Kušan, Ivana, Kuyper, Thomas W., Lado, Carlos, Læssøe, Thomas, Lainé, Patrice, Langer, Ewald, Larsson, Ellen, Larsson, Karl-Henrik, Laursen, Gary, Lechat, Christian, Lee, Serena, Lendemer, James C, Levin, Laura, Lindemann, Uwe, Lindström, Håkan, Liu, Xingzhong, Hernandez, Regulo Carlos Llarena, Llop, Esteve, Locsmándi, Csaba, Lodge, Deborah Jean, Loizides, Michael, Lőkös, László, Luangsa-ard, Jennifer, Lüderitz, Matthias, Lumbsch, H. Thorsten, Lutz, Matthias, Mahoney, Dan, Malysheva, Ekaterina, Malysheva, Vera, Manimohan, Patinjareveettil, Marin-Felix, Yasmina, Marques, Guilhermina, Martínez-Gil, Rubén, Marson, Guy, Mata, Gerardo, Matheny, P Brandon, Mathiassen, Geir Harald, Matočec, Neven, Mayrhofer, Helmut, Mehrabi, Mehdi, Melo, Ireneia, Mešić, Armin, Methven, Andrew S, Miettinen, Otto, Romero, Ana M Millanes, Miller, Andrew N., Mitchell, James K, Moberg, Roland, Moreau, Pierre-Arthur, Moreno, Gabriel, Morozova, Olga, Morte, Asunción, Muggia, Lucia, González, Guillermo Muñoz, Myllys, Leena, Nagy, István, Nagy, László G, Neves, Maria Alice, Niemelä, Tuomo, Nimis, Pier Luigi, Niveiro, Nicolas, Noordeloos, Machiel E, Nordin, Anders, Noumeur, Sara Raouia, Novozhilov, Yuri, Nuytinck, Jorinde, Ohenoja, Esteri, Fiuza, Patricia Oliveira, Orange, Alan, Ordynets, Alexander, Ortiz-Santana, Beatriz, Pacheco, Leticia, Pál-Fám, Ferenc, Palacio, Melissa, Palice, Zdeněk, Papp, Viktor, Pärtel, Kadri, Pawlowska, Julia, Paz, Aurelia, Peintner, Ursula, Pennycook, Shaun R., Pereira, Olinto Liparini, Daniëls, Pablo Pérez, Pérez-De-Gregorio Capella, Miquel À, Del Amo, Carlos Manuel Pérez, Gorjón, Sergio Pérez, Pérez-Ortega, Sergio, Pérez-Vargas, Israel, Perry, Brian A, Petersen, Jens H, Petersen, Ronald H, Pfister, Donald H., Phukhamsakda, Chayanard, Piątek, Marcin, Piepenbring, Meike, Pino-Bodas, Raquel, Esquivel, Juan Pablo Pinzón, Pirot, Paul, Popov, Eugene S, Popoff, Orlando, Álvaro, María Prieto, Printzen, Christian, Psurtseva, Nadezhda, Purahong, Witoon, Quijada, Luis, Rambold, Gerhard, Ramírez, Natalia A, Raja, Huzefa A., Raspé, Olivier, Raymundo, Tania, Réblová, Martina, Rebriev, Yury A, de Dios Reyes García, Juan, Ripoll, Miguel Ángel Ribes, Richard, Franck, Richardson, Mike J, Rico, Víctor J, Robledo, Gerardo Lucio, Barbosa, Flavia Rodrigues, Rodriguez-Caycedo, Cristina, Rodriguez-Flakus, Pamela, Ronikier, Anna, Casas, Luis Rubio, Rusevska, Katerina, Saar, Günter, Saar, Irja, Salcedo, Isabel, Martínez, Sergio M Salcedo, Montoya, Carlos A Salvador, Sánchez-Ramírez, Santiago, Sandoval-Sierra, J Vladimir, Santamaria, Sergi, Monteiro, Josiane Santana, Schroers, Hans Josef, Schulz, Barbara, Schmidt-Stohn, Geert, Schumacher, Trond, Senn-Irlet, Beatrice, Ševčíková, Hana, Shchepin, Oleg, Shirouzu, Takashi, Shiryaev, Anton, Siepe, Klaus, Sir, Esteban B, Sohrabi, Mohammad, Soop, Karl, Spirin, Viacheslav, Spribille, Toby, Stadler, Marc, Stalpers, Joost, Stenroos, Soili, Suija, Ave, Sunhede, Stellan, Svantesson, Sten, Svensson, Sigvard, Svetasheva, Tatyana Yu, Świerkosz, Krzysztof, Tamm, Heidi, Taskin, Hatira, Taudière, Adrien, Tedebrand, Jan-Olof, Lahoz, Raúl Tena, Temina, Marina, Thell, Arne, Thines, Marco, Thor, Göran, Thüs, Holger, Tibell, Leif, Tibell, Sanja, Timdal, Einar, Tkalčec, Zdenko, Tønsberg, Tor, Trichies, Gérard, Triebel, Dagmar, Tsurykau, Andrei, Tulloss, Rodham E, Tuovinen, Veera, Sosa, Miguel Ulloa, Urcelay, Carlos, Valade, François, Garza, Ricardo Valenzuela, van den Boom, Pieter, Van Vooren, Nicolas, Vasco, Aida, Vauras, Jukka, Velasco Santos, Juan Manuel, Vellinga, Else, Verbeken, Annemieke, Vetlesen, Per, Vizzini, Alfredo, Voglmayr, Hermann, Volobuev, Sergey, von Brackel, Wolfgang, Voronina, Elena, Walther, Grit, Watling, Roy, Weber, Evi, Wedin, Mats, Weholt, Øyvind, Westberg, Martin, Yurchenko, Eugene, Zehnálek, Petr, Zhang, Huang, Zhurbenko, Mikhail P, and Ekman, Stefan
Abstract: Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
Published: 2018

28. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Author: Murat, Claude, Payen, Thibaut, Noel, Benjamin, Kuo, Alan, Morin, Emmanuelle, Chen, Juan, Kohler, Annegret, Krizsán, Krisztina, Balestrini, Raffaella, Da Silva, Corinne, Montanini, Barbara, Hainaut, Mathieu, Levati, Elisabetta, Barry, Kerrie W., Belfiori, Beatrice, Cichocki, Nicolas, Clum, Alicia, Dockter, Rhyan B., Fauchery, Laure, Guy, Julie, Iotti, Mirco, Le Tacon, François, Lindquist, Erika A., Lipzen, Anna, Malagnac, Fabienne, Mello, Antonietta, Molinier, Virginie, Miyauchi, Shingo, Poulain, Julie, Riccioni, Claudia, Rubini, Andrea, Sitrit, Yaron, Splivallo, Richard, Traeger, Stefanie, Wang, Mei, Žifčáková, Lucia, Wipf, Daniel, Zambonelli, Alessandra, Paolocci, Francesco, Nowrousian, Minou, Ottonello, Simone, Baldrian, Petr, Spatafora, Joseph W., Henrissat, Bernard, Nagy, László, Aury, Jean-Marc, Wincker, Patrick, Grigoriev, Igor V., Bonfante, Paola, Martin, Francis, Murat, Claude, Payen, Thibaut, Noel, Benjamin, Kuo, Alan, Morin, Emmanuelle, Chen, Juan, Kohler, Annegret, Krizsán, Krisztina, Balestrini, Raffaella, Da Silva, Corinne, Montanini, Barbara, Hainaut, Mathieu, Levati, Elisabetta, Barry, Kerrie W., Belfiori, Beatrice, Cichocki, Nicolas, Clum, Alicia, Dockter, Rhyan B., Fauchery, Laure, Guy, Julie, Iotti, Mirco, Le Tacon, François, Lindquist, Erika A., Lipzen, Anna, Malagnac, Fabienne, Mello, Antonietta, Molinier, Virginie, Miyauchi, Shingo, Poulain, Julie, Riccioni, Claudia, Rubini, Andrea, Sitrit, Yaron, Splivallo, Richard, Traeger, Stefanie, Wang, Mei, Žifčáková, Lucia, Wipf, Daniel, Zambonelli, Alessandra, Paolocci, Francesco, Nowrousian, Minou, Ottonello, Simone, Baldrian, Petr, Spatafora, Joseph W., Henrissat, Bernard, Nagy, László, Aury, Jean-Marc, Wincker, Patrick, Grigoriev, Igor V., Bonfante, Paola, and Martin, Francis
Abstract: Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
Published: 2018

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

Author: Sipos, György, 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, Nagy, László G, Sipos, György, 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
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

30. Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities

Author: Sub Molecular Microbiology, Molecular Microbiology, Nagy, László G, Riley, Robert, Tritt, Andrew, Adam, Catherine, Daum, Chris, Floudas, Dimitrios, Sun, Hui, Yadav, Jagjit S, Pangilinan, Jasmyn, Larsson, Karl-Henrik, Matsuura, Kenji, Barry, Kerrie, Labutti, Kurt, Kuo, Rita, Ohm, Robin A, Bhattacharya, Sukanta S, Shirouzu, Takashi, Yoshinaga, Yuko, Martin, Francis M, Grigoriev, Igor V, Hibbett, David S, Sub Molecular Microbiology, Molecular Microbiology, Nagy, László G, Riley, Robert, Tritt, Andrew, Adam, Catherine, Daum, Chris, Floudas, Dimitrios, Sun, Hui, Yadav, Jagjit S, Pangilinan, Jasmyn, Larsson, Karl-Henrik, Matsuura, Kenji, Barry, Kerrie, Labutti, Kurt, Kuo, Rita, Ohm, Robin A, Bhattacharya, Sukanta S, Shirouzu, Takashi, Yoshinaga, Yuko, Martin, Francis M, Grigoriev, Igor V, and Hibbett, David S
Published: 2016

31. Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

Author: Nagy, László G, Ohm, Robin A, Kovács, Gábor M, Floudas, Dimitrios, Riley, Robert, Gácser, Attila, Sipiczki, Mátyás, Davis, John M, Doty, Sharon L, de Hoog, G Sybren, Lang, B Franz, Spatafora, Joseph W, Martin, Francis M, Grigoriev, Igor V, Hibbett, David S, Nagy, László G, Ohm, Robin A, Kovács, Gábor M, Floudas, Dimitrios, Riley, Robert, Gácser, Attila, Sipiczki, Mátyás, Davis, John M, Doty, Sharon L, de Hoog, G Sybren, Lang, B Franz, Spatafora, Joseph W, Martin, Francis M, Grigoriev, Igor V, and Hibbett, David S
Abstract: Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast-filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.
Published: 2014

32. Preserving Accuracy in GenBank

Author: Bruns, Thomas D., Blackwell, Meredith, Edwards, Ivan, Taylor, Andy F. S., Horton, Thomas, Zhang, Ning, Kõljalg, Urmas, May, Georgiana, Kuyper, Thomas W., Bever, James D., Gilbert, Gregory, Taylor, John W., DeSantis, Todd Z., Pringle, Anne, Borneman, James, Thorn, Greg, Berbee, Mary, Mueller, Gregory M., Andersen, Gary L., Vellinga, Else C., Branco, Sara, Anderson, Ian, Dickie, Ian A., Avis, Peter, Timonen, Sari, Kjøller, Rasmus, Lodge, D. J., Bateman, Richard M., Purvis, Andy, Crous, Pedro W., Hawkes, Christine, Barraclough, Tim, Burt, Austin, Nilsson, R. H., Larsson, Karl-Henrik, Alexander, Ian, Moncalvo, Jean-Marc, Berube, Jean, Spatafora, Joseph, Thorsten Lumbsch, H., Blair, Jaime E., Suh, Sung-Oui, Pfister, Donald H., Binder, Manfred, Boehm, Eric W., Kohn, Linda, Mata, Juan L., Dyer, Paul, Sung, Gi-Ho, Dentinger, Bryn, Simmons, Emory G., Baird, Richard E., Volk, Thomas J., Perry, Brian A., Kerrigan, Richard W., Campbell, Jinx, Rajesh, Jeewon, Reynolds, Don R., Geiser, David, Humber, Richard A., Hausmann, Natasha, Szaro, Tim, Stajich, Jason, Gathman, Allen, Peay, Kabir G., Henkel, Terry, Robinson, Clare H., Pukkila, Patricia J., Nguyen, Nhu H., Villalta, Christopher, Kennedy, Peter, Bergemann, Sarah, Catherine Aime, M., Kauff, Frank, Porras-Alfaro, Andrea, Gueidan, Cecile, Beck, Andreas, Andersen, Birgitte, Marek, Stephen, Crouch, Jo A., Kerrigan, Julia, Beagle Ristaino, Jean, Hodge, Kathie T., Kuldau, Gretchen, Samuels, Gary J., Raja, Huzefa A., Voglmayr, Hermann, Gardes, Monique, Janos, David P., Rogers, Jack D., Cannon, Paul, Woolfolk, Sandra W., Kistler, H. C., Castellano, Michael A., Maldonado-Ramírez, Sandra L., Kirk, Paul M., Farrar, James J., Osmundson, Todd, Currah, Randolph S., Vujanovic, Vladimir, Chen, Weidong, Korf, Richard P., Atallah, Zahi K., Harrison, Ken J., Guarro, Josep, Bates, Scott T., Enrico Bonello, Pierluigi, Bridge, Paul, Schell, Wiley, Rossi, Walter, Stenlid, Jan, Frisvad, Jens C., Miller, R. M., Baker, Scott E., Hallen, Heather E., Janso, Jeffrey E., Wilson, Andrew W., Conway, Kenneth E., Egerton-Warburton, Louise, Wang, Zheng, Eastburn, Darin, Ho, Wellcome W. Hong, Kroken, Scott, Stadler, Marc, Turgeon, Gillian, Lichtwardt, Robert W., Stewart, Elwin L., Wedin, Mats, Li, De-Wei, Uchida, Janice Y., Jumpponen, Ari, Deckert, Ron J., Beker, Henry J., Rogers, Scott O., Xu, Jianping, Johnston, Peter, Shoemaker, R. A., Liu, Miao, Marques, G., Summerell, Brett, Sokolski, Serge, Thrane, Ulf, Widden, Paul, Bruhn, Johann N., Bianchinotti, Virginia, Tuthill, Dorothy, Baroni, Timothy J., Barron, George, Hosaka, Kentaro, Jewell, Kelsea, Piepenbring, Meike, Sullivan, Raymond, Griffith, Gareth W., Bradley, S. G., Aoki, Takayuki, Yoder, Wendy T., Ju, Yu-Ming, Berch, Shannon M., Trappe, Matt, Duan, Weijun, Bonito, Gregory, Taber, Ruth A., Coelho, Gilberto, Bills, Gerald, Ganley, Austen, Agerer, Reinhard, Nagy, László, Roy, Barbara A., Læssøe, Thomas, Hallenberg, Nils, Tichy, Hans-Volker, Stalpers, Joost, Langer, Ewald, Scholler, Markus, Krueger, Dirk, Pacioni, Giovanni, Pöder, Reinhold, Pennanen, Taina, Capelari, Marina, Nakasone, Karen, Tewari, J. P., Miller, Andrew N., Decock, Cony, Huhndorf, Sabine, Wach, Mark, Vishniac, Helen S., Yohalem, David S., Smith, Matthew E., Glenn, Anthony E., Spiering, Martin, Lindner, Daniel L., Schoch, Conrad, Redhead, Scott A., Ivors, Kelly, Jeffers, Steven N., Geml, József, Okafor, Florence, Spiegel, Frederick W., Dewsbury, Damon, Carroll, Juliet, Porter, Terri M., Pashley, Catherine, Carpenter, Steven E., Abad, Gloria, Voigt, Kerstin, Arenz, Brett, Methven, Andrew S., Schechter, Shannon, Vance, Paula, Mahoney, Dan, Kang, Seogchan, Rheeder, John P., Mehl, James, Greif, Matthew, Ndzi Ngala, George, Ammirati, Joe, Kawasaki, Masako, Gwo-Fang, Yuan, Matsumoto, Tadahiko, Smith, David, Koenig, Gina, Luoma, Daniel, May, Tom, Leonardi, Marco, Sigler, Lynne, Taylor, D. L., Gibson, Cara, Sharpton, Thomas, Hawksworth, David L., Carmine Dianese, Jose, Trudell, Steven A., Paulus, Barbara, Padamsee, Mahajabeen, Callac, Philippe, Lima, Nelson, White, Merlin, Barreau, C., Juncai, M. A., Buyck, Bart, Rabeler, Richard K., Liles, Mark R., Estes, Dwayne, Carter, Richard, Herr, J. M., Chandler, Gregory, Kerekes, Jennifer, Cruse-Sanders, Jennifer, Galán Márquez, R., Horak, Egon, Fitzsimons, Michael, Döring, Heidi, Yao, Su, Hynson, Nicole, Ryberg, Martin, Arnold, A. E., Hughes, Karen, Bruns, Thomas D., Blackwell, Meredith, Edwards, Ivan, Taylor, Andy F. S., Horton, Thomas, Zhang, Ning, Kõljalg, Urmas, May, Georgiana, Kuyper, Thomas W., Bever, James D., Gilbert, Gregory, Taylor, John W., DeSantis, Todd Z., Pringle, Anne, Borneman, James, Thorn, Greg, Berbee, Mary, Mueller, Gregory M., Andersen, Gary L., Vellinga, Else C., Branco, Sara, Anderson, Ian, Dickie, Ian A., Avis, Peter, Timonen, Sari, Kjøller, Rasmus, Lodge, D. J., Bateman, Richard M., Purvis, Andy, Crous, Pedro W., Hawkes, Christine, Barraclough, Tim, Burt, Austin, Nilsson, R. H., Larsson, Karl-Henrik, Alexander, Ian, Moncalvo, Jean-Marc, Berube, Jean, Spatafora, Joseph, Thorsten Lumbsch, H., Blair, Jaime E., Suh, Sung-Oui, Pfister, Donald H., Binder, Manfred, Boehm, Eric W., Kohn, Linda, Mata, Juan L., Dyer, Paul, Sung, Gi-Ho, Dentinger, Bryn, Simmons, Emory G., Baird, Richard E., Volk, Thomas J., Perry, Brian A., Kerrigan, Richard W., Campbell, Jinx, Rajesh, Jeewon, Reynolds, Don R., Geiser, David, Humber, Richard A., Hausmann, Natasha, Szaro, Tim, Stajich, Jason, Gathman, Allen, Peay, Kabir G., Henkel, Terry, Robinson, Clare H., Pukkila, Patricia J., Nguyen, Nhu H., Villalta, Christopher, Kennedy, Peter, Bergemann, Sarah, Catherine Aime, M., Kauff, Frank, Porras-Alfaro, Andrea, Gueidan, Cecile, Beck, Andreas, Andersen, Birgitte, Marek, Stephen, Crouch, Jo A., Kerrigan, Julia, Beagle Ristaino, Jean, Hodge, Kathie T., Kuldau, Gretchen, Samuels, Gary J., Raja, Huzefa A., Voglmayr, Hermann, Gardes, Monique, Janos, David P., Rogers, Jack D., Cannon, Paul, Woolfolk, Sandra W., Kistler, H. C., Castellano, Michael A., Maldonado-Ramírez, Sandra L., Kirk, Paul M., Farrar, James J., Osmundson, Todd, Currah, Randolph S., Vujanovic, Vladimir, Chen, Weidong, Korf, Richard P., Atallah, Zahi K., Harrison, Ken J., Guarro, Josep, Bates, Scott T., Enrico Bonello, Pierluigi, Bridge, Paul, Schell, Wiley, Rossi, Walter, Stenlid, Jan, Frisvad, Jens C., Miller, R. M., Baker, Scott E., Hallen, Heather E., Janso, Jeffrey E., Wilson, Andrew W., Conway, Kenneth E., Egerton-Warburton, Louise, Wang, Zheng, Eastburn, Darin, Ho, Wellcome W. Hong, Kroken, Scott, Stadler, Marc, Turgeon, Gillian, Lichtwardt, Robert W., Stewart, Elwin L., Wedin, Mats, Li, De-Wei, Uchida, Janice Y., Jumpponen, Ari, Deckert, Ron J., Beker, Henry J., Rogers, Scott O., Xu, Jianping, Johnston, Peter, Shoemaker, R. A., Liu, Miao, Marques, G., Summerell, Brett, Sokolski, Serge, Thrane, Ulf, Widden, Paul, Bruhn, Johann N., Bianchinotti, Virginia, Tuthill, Dorothy, Baroni, Timothy J., Barron, George, Hosaka, Kentaro, Jewell, Kelsea, Piepenbring, Meike, Sullivan, Raymond, Griffith, Gareth W., Bradley, S. G., Aoki, Takayuki, Yoder, Wendy T., Ju, Yu-Ming, Berch, Shannon M., Trappe, Matt, Duan, Weijun, Bonito, Gregory, Taber, Ruth A., Coelho, Gilberto, Bills, Gerald, Ganley, Austen, Agerer, Reinhard, Nagy, László, Roy, Barbara A., Læssøe, Thomas, Hallenberg, Nils, Tichy, Hans-Volker, Stalpers, Joost, Langer, Ewald, Scholler, Markus, Krueger, Dirk, Pacioni, Giovanni, Pöder, Reinhold, Pennanen, Taina, Capelari, Marina, Nakasone, Karen, Tewari, J. P., Miller, Andrew N., Decock, Cony, Huhndorf, Sabine, Wach, Mark, Vishniac, Helen S., Yohalem, David S., Smith, Matthew E., Glenn, Anthony E., Spiering, Martin, Lindner, Daniel L., Schoch, Conrad, Redhead, Scott A., Ivors, Kelly, Jeffers, Steven N., Geml, József, Okafor, Florence, Spiegel, Frederick W., Dewsbury, Damon, Carroll, Juliet, Porter, Terri M., Pashley, Catherine, Carpenter, Steven E., Abad, Gloria, Voigt, Kerstin, Arenz, Brett, Methven, Andrew S., Schechter, Shannon, Vance, Paula, Mahoney, Dan, Kang, Seogchan, Rheeder, John P., Mehl, James, Greif, Matthew, Ndzi Ngala, George, Ammirati, Joe, Kawasaki, Masako, Gwo-Fang, Yuan, Matsumoto, Tadahiko, Smith, David, Koenig, Gina, Luoma, Daniel, May, Tom, Leonardi, Marco, Sigler, Lynne, Taylor, D. L., Gibson, Cara, Sharpton, Thomas, Hawksworth, David L., Carmine Dianese, Jose, Trudell, Steven A., Paulus, Barbara, Padamsee, Mahajabeen, Callac, Philippe, Lima, Nelson, White, Merlin, Barreau, C., Juncai, M. A., Buyck, Bart, Rabeler, Richard K., Liles, Mark R., Estes, Dwayne, Carter, Richard, Herr, J. M., Chandler, Gregory, Kerekes, Jennifer, Cruse-Sanders, Jennifer, Galán Márquez, R., Horak, Egon, Fitzsimons, Michael, Döring, Heidi, Yao, Su, Hynson, Nicole, Ryberg, Martin, Arnold, A. E., and Hughes, Karen
Published: 2008

33. Erkundungen der Moderne : László Moholy-Nagy: zwei Debatten mit Erwin Quedenfeldt und Hans Windisch

Author: Moholy-Nagy, László, Quedenfeldt, Erwin, Windisch, Hans, Stiegler, Bernd, Moholy-Nagy, László, Quedenfeldt, Erwin, Windisch, Hans, and Stiegler, Bernd
Abstract: Wir wollen nicht das objektiv der unzulänglichkeit unseres seh- und erkenntnisvermögens unterordnen, sondern es soll uns gerade helfen, unsere augen aufzuschließen. Lázló Moholy-Nagy Wenn László Moholy-Nagy in seiner Zusammenfassung einer Debatte mit Hans Windisch, die 1929 in der Avantgarde-Zeitschrift i10 erschien, in der Replik von Windisch in Klammern ein Fragezeichen ergänzt, so markiert er damit eine radikale Differenz, kennzeichnet eine Sollbruchstelle in den zeitgenössischen Debatten über die Aufgabe der Photographie, in denen es um nichts geringeres als eine Grundorientierung der Moderne insgesamt geht. Zur Diskussion steht eine grundlegende Frage der Moderne, ja die Klärung einer für "den heutigen stand der fotografie lebenswichtigen" Frage. Der Satz in der von Moholy-Nagy annotierten Fassung lautet: "die ergänzenden vorstellungen unserer einbildungskraft sind viel revolutionärer (? m-n), als es die exakteste abschrift unseres daseins ist." Es geht, mit anderen Worten, um die Klärung der Frage, ob und in welcher Weise Kunst beanspruchen könne, revolutionär zu sein und Entscheidendes zur Revolution der Wahrnehmung und auch der Denkungsart beizutragen.
Published: 2007

34. Bauhausbücher 5, Piet Mondrian: Neue Gestaltung

Author: Moholy-Nagy, László, Moholy-Nagy, László, Moholy-Nagy, László, and Moholy-Nagy, László
Abstract: Book jacket, http://name.umdl.umich.edu/IC-UMMU-X-05-09163%5D05_09163, https://quod.lib.umich.edu/cgi/i/image/api/thumb/ummu/05-09163/05_09163/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. These materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Library Information Technology.; Davis Digital Images, https://www.lib.umich.edu/about-us/policies/copyright-policy
Published: 1924

35. Nude

Author: Moholy-Nagy, László, Moholy-Nagy, László, Moholy-Nagy, László, and Moholy-Nagy, László
Abstract: http://name.umdl.umich.edu/IC-UMMU-X-02-07174%5D02_07174, https://quod.lib.umich.edu/cgi/i/image/api/thumb/ummu/02-07174/02_07174/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. These materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Library Information Technology.; Universal Color Slide, https://www.lib.umich.edu/about-us/policies/copyright-policy

36. Nude

Author: Moholy-Nagy, László, Moholy-Nagy, László, Moholy-Nagy, László, and Moholy-Nagy, László
Abstract: http://name.umdl.umich.edu/IC-UMMU-X-02-07174%5D02_07174, https://quod.lib.umich.edu/cgi/i/image/api/thumb/ummu/02-07174/02_07174/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. These materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Library Information Technology.; Universal Color Slide, https://www.lib.umich.edu/about-us/policies/copyright-policy

37. Brief von Walter Gropius, Paul Klee, Wassily Kandinsky, Lyonel Feininger, Oskar Schlemmer, Georg Muche und László Moholy-Nagy von Kreis der Freunde des Bauhauses <Dessau> an Gerhart Hauptmann

Author: Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, Moholy-Nagy, László, Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, and Moholy-Nagy, László
Published: 1926

38. Brief von Walter Gropius, Paul Klee, Wassily Kandinsky, Lyonel Feininger, Oskar Schlemmer, Georg Muche und László Moholy-Nagy von Kreis der Freunde des Bauhauses <Dessau> an Gerhart Hauptmann

Author: Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, Moholy-Nagy, László, Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, and Moholy-Nagy, László

39. Brief von Walter Gropius, Paul Klee, Wassily Kandinsky, Lyonel Feininger, Oskar Schlemmer, Georg Muche und László Moholy-Nagy von Kreis der Freunde des Bauhauses <Dessau> an Gerhart Hauptmann

Author: Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, Moholy-Nagy, László, Gropius, Walter, Klee, Paul, Kandinsky, Wassily, Feininger, Lyonel, Schlemmer, Oskar, Muche, Georg, and Moholy-Nagy, László

40. Languages and Cultures in Research and Education: Jubilee Volume Presented to Professor Ralf-Peter Ritter on his Seventieth Birthday

Author: Nagy, László Kálmán, editor, Németh, Michał, editor, and Tátrai, Szilárd, editor

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

40 results on '"Nagy, László"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources