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4. First draft of an annotated genome for a lichenised strain of the green alga Diplosphaera chodatii (Prasiolales, Trebouxiophyceae).

Author

Gueidan, Cécile, Mead, Oliver L., Nazem-Bokaee, Hadi, and Mathews, Sarah

Subjects
*CRUST vegetation, *GREEN algae, *NUCLEOTIDE sequencing, *GENOMES, *CELL division
Abstract

Although genome sequences of lichenized fungi are increasingly becoming available, genome sequences of microalgae involved in the lichen symbiosis are still scarce. For lichenized eukaryotic algae, genome sequencing has focused mostly on Trebouxia and Asterochloris, with little genomic data available for Stichococcus-like algae, such as Diplosphaera. The genus Diplosphaera is a common component of biological soil crusts, and often occurs associated with lichens of the family Verrucariaceae. It is characterized by cylindrical to spherical cells containing a plate-like chloroplast, and more specifically by a vegetative cell division that leads to the formation of typical two- to four-celled clusters. Here, we present a draft genome sequence for the algal partner of an Australian lichen specimen of Endocarpon pusillum. The genome was sequenced with Pac Bio long read and Illumina short read technologies, and transcriptome data were generated to inform the structural annotations. This algal strain is here identified as Diplosphaera chodatii based on nuSSU and ITS data. Compared with closely related lichenized and non-lichenized algae, the genome of D. chodatii stands out for its large size (85.6 Mb) and gene content (21,261 protein-encoding regions), as well as its high rate of duplicated genes (60% of the BUSCO genes are duplicated). These results suggest that whole genome duplication or large-scale segmental duplications may have occurred in the evolutionary history of this algal species. Little genome data are available for lichenized algae. We generated the first genome for a lichenized Diplosphaera chodatii. Results suggest a possible whole genome duplication in this species. [ABSTRACT FROM AUTHOR]

Published
2023
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5. 4 Pezizomycotina: Lecanoromycetes

Author

Gueidan, Cécile, Hill, David J., Miadlikowska, Jolanta, Lutzoni, Francois, Esser, Karl, Series editor, McLaughlin, David J., editor, and Spatafora, Joseph W., editor

Published
2015
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7. 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, Jr., 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 Gerlach, Alice Cruz Lima, Ghobad-Nejhad, Masoomeh, Gibertoni, Tatiana B., Grebenc, Tine, Greilhuber, Irmgard, Grishkan, Bella, Groenewald, Johannes Z., Grube, Martin, Gruhn, Gérald, Gueidan, Cécile, Gulden, Gro, Gusmão, Luis F. P., 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, Jansen, AnnaElise, Jayawardena, Ruvishika S., Jeppesen, Thomas Stjernegaard, Jeppson, Mikael, Johnston, Peter, 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, Kumar, T. K. Arun, 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, 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, Pereira, Olinto Liparini, Daniëls, Pablo Pérez, Capella, Miquel À. Pérez-De-Gregorio, 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, Raspé, Olivier, Raymundo, Tania, Réblová, Martina, Rebriev, Yury A., García, Juan de Dios Reyes, 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-Palacios, Aida M., Vauras, Jukka, Santos, Juan Manuel Velasco, 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

Published
2018
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20. Naming and outline of Dothideomycetes–2014 including proposals for the protection or suppression of generic names

Author

Wijayawardene, Nalin N., Crous, Pedro W., Kirk, Paul M., Hawksworth, David L., Boonmee, Saranyaphat, Braun, Uwe, Dai, Dong-Qin, D’souza, Melvina J., Diederich, Paul, Dissanayake, Asha, Doilom, Mingkhuan, Hongsanan, Singang, Jones, E. B. Gareth, Groenewald, Johannes Z., Jayawardena, Ruvishika, Lawrey, James D., Liu, Jian-Kui, Lücking, Robert, Madrid, Hugo, Manamgoda, Dimuthu S., Muggia, Lucia, Nelsen, Matthew P., Phookamsak, Rungtiwa, Suetrong, Satinee, Tanaka, Kazuaki, Thambugala, Kasun M., Wanasinghe, Dhanushka N., Wikee, Saowanee, Zhang, Ying, Aptroot, André, Ariyawansa, H. A., Bahkali, Ali H., Bhat, D. Jayarama, Gueidan, Cécile, Chomnunti, Putarak, De Hoog, G. Sybren, Knudsen, Kerry, Li, Wen-Jing, McKenzie, Eric H. C., Miller, Andrew N., Phillips, Alan J. L., Piątek, Marcin, Raja, Huzefa A., Shivas, Roger S., Slippers, Bernad, Taylor, Joanne E., Tian, Qing, Wang, Yong, Woudenberg, Joyce H. C., Cai, Lei, Jaklitsch, Walter M., and Hyde, Kevin D.

Published
2014
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24. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Author

Geiser, David M., Gueidan, Cécile, Miadlikowska, Jolanta, Lutzoni, François, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Schoch, Conrad L., Tibell, Leif, Untereiner, Wendy A., and Aptroot, André

Published
2006

25. New Insights into Classification and Evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from Phylogenetic Analyses of Three Ribosomal RNA- and Two Protein-Coding Genes

Author

Miadlikowska, Jolanta, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Grube, Martin, Hafellner, Josef, Reeb, Valérie, Hodkinson, Brendan P., Kukwa, Martin, Lücking, Robert, Hestmark, Geir, Otalora, Monica Garcia, Rauhut, Alexandra, Büdel, Burkhard, Scheidegger, Christoph, Timdal, Einar, Stenroos, Soili, Brodo, Irwin, Perlmutter, Gary B., Ertz, Damien, Diederich, Paul, Lendemer, James C., May, Philip, Schoch, Conrad L., Arnold, A. Elizabeth, Gueidan, Cécile, Tripp, Erin, Yahr, Rebecca, Robertson, Connie, and Lutzoni, François

Published
2006

26. A Five-Gene Phylogeny of Pezizomycotina

Author

Spatafora, Joseph W., Sung, Gi-Ho, Johnson, Desiree, Hesse, Cedar, O'Rourke, Benjamin, Serdani, Maryna, Spotts, Robert, Lutzoni, François, Hofstetter, Valérie, Miadlikowska, Jolanta, Reeb, Valérie, Gueidan, Cécile, Fraker, Emily, Lumbsch, Thorsten, Lücking, Robert, Schmitt, Imke, Hosaka, Kentaro, Aptroot, André, Roux, Claude, Miller, Andrew N., Geiser, David M., Hafellner, Josef, Hestmark, Geir, Arnold, A. Elizabeth, Büdel, Burkhard, Rauhut, Alexandra, Hewitt, David, Untereiner, Wendy A., Cole, Mariette S., Scheidegger, Christoph, Schultz, Matthias, Sipman, Harrie, and Schoch, Conrad L.

Published
2006

27. Families of Dothideomycetes: In loving memory of Majorie Phyllis Hyde (affectionately known as Mum or Marj), 29 August 1921–18 January 2013—without mum’s determination, a character passed on to children, this treatise would never have been completed—K.D. Hyde

Author

Hyde, Kevin D., Jones, E. B. Gareth, Liu, Jian-Kui, Ariyawansa, Hiran, Boehm, Eric, Boonmee, Saranyaphat, Braun, Uwe, Chomnunti, Putarak, Crous, Pedro W., Dai, Dong-Qin, Diederich, Paul, Dissanayake, Asha, Doilom, Mingkhuan, Doveri, Francesco, Hongsanan, Singang, Jayawardena, Ruvishika, Lawrey, James D., Li, Yan-Mei, Liu, Yong-Xiang, Lücking, Robert, Monkai, Jutamart, Muggia, Lucia, Nelsen, Matthew P., Pang, Ka-Lai, Phookamsak, Rungtiwa, Senanayake, Indunil C., Shearer, Carol A., Suetrong, Satinee, Tanaka, Kazuaki, Thambugala, Kasun M., Wijayawardene, Nalin N., Wikee, Saowanee, Wu, Hai-Xia, Zhang, Ying, Aguirre-Hudson, Begoña, Alias, S. Aisyah, Aptroot, André, Bahkali, Ali H., Bezerra, Jose L., Bhat, D. Jayarama, Camporesi, Erio, Chukeatirote, Ekachai, Gueidan, Cécile, Hawksworth, David L., Hirayama, Kazuyuki, De Hoog, Sybren, Kang, Ji-Chuan, Knudsen, Kerry, Li, Wen-Jing, Li, Xing-Hong, Liu, Zou-Yi, Mapook, Ausana, McKenzie, Eric H. C., Miller, Andrew N., Mortimer, Peter E., Phillips, Alan J. L., Raja, Huzefa A., Scheuer, Christian, Schumm, Felix, Taylor, Joanne E., Tian, Qing, Tibpromma, Saowaluck, Wanasinghe, Dhanushka N., Wang, Yong, Xu, Jian-Chu, Yacharoen, Supalak, Yan, Ji-Ye, and Zhang, Min

Published
2013
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34. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hofstetter, Valérie, Robbertse, Barbara, Matheny, Brandon P., Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Sybren de Hoog, G., Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Gryzenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, Thorsten H., Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, OʼDonnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Lutzoni, François, and Spatafora, Joseph W.

Published
2009
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35. A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens.

Author

Gueidan, Cécile and Lan Li

Subjects
*BOTANICAL specimens, *GENETIC barcoding, *LICHENS, *IDENTIFICATION of fungi, *FUNGAL cultures, *BAR codes, *BIOLOGICAL specimens
Abstract

Reference sequence databases are critical to the accurate detection and identification of fungi in the environment. As repositories of large numbers of well-curated specimens, herbaria and fungal culture collections have the material resources to generate sequence data for large number of taxa, and could therefore allow filling taxonomic gaps often present in reference sequence databases. Financial resources to do that are however often lacking, so that recent efforts have focused on decreasing sequencing cost by increasing the number of multiplexed samples per sequencing run while maintaining high sequence quality. Following a previous study that aimed at decreasing sequencing cost for lichen specimens by generating fungal ITS barcodes for 96 specimens using PacBio amplicon sequencing, we present a method that further decreases lichen specimen metabarcoding costs. A total of 384 mixed DNA extracts obtained from lichen herbarium specimens, mostly from the four genera Buellia, Catillaria, Endocarpon and Parmotrema, were used to generate new fungal ITS sequences using a Sequel I sequencing platform and the PacBio M13 barcoded primers. The average success rate across all taxa was high (86.5%), with particularly high rates for the crustose saxicolous taxa (Buellia, Catillaria and others; 93.3%) and the terricolous squamulose taxa (Endocarpon and others; 96.5%). On the other hand, the success rate for the foliose genus Parmotrema was lower (60.4%). With this taxon sampling, greater specimen age did not appear to impact sequencing success. In fact, the 1966-1980 collection date category showed the highest success rate (97.3%). Compared to the previous study, the abundance-based sequence denoising method showed some limitations, but the cost of generating ITS barcodes was further decreased thanks to the higher multiplexing level. In addition to contributing new ITS barcodes for specimens of four interesting lichen genera, this study further highlights the potential and challenges of using new sequencing technologies on collection specimens to generate DNA sequences for reference databases. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Reconstructing the early evolution of Fungi using a six-gene phylogeny

Author

James, Timothy Y., Kauff, Frank, Schoch, Conrad L., Matheny, P. Brandon, Hofstetter, Valérie, Cox, Cymon J., Celio, Gail, Gueidan, Cécile, Fraker, Emily, Miadlikowska, Jolanta, Lumbsch, H. Thorsten, Rauhut, Alexandra, Reeb, Valérie, Arnold, A. Elizabeth, Amtoft, Anja, Stajich, Jason E., Hosaka, Kentaro, Sung, Gi-Ho, Johnson, Desiree, O'Rourke, Ben, Crockett, Michael, Binder, Manfred, Curtis, Judd M., Slot, Jason C., Wang, Zheng, Wilson, Andrew W., Schüler, Arthur, Longcore, Joyce E., O'Donnell, Kerry, Mozley-Standridge, Sharon, Porter, David, Letcher, Peter M., Powell, Martha J., Taylor, John W., White, Merlin M., Griffith, Gareth W., Davies, David R., Humber, Richard A., Morton, Joseph B., Sugiyama, Junta, Rossman, Amy Y., Rogers, Jack D., Pfister, Don H., Hewitt, David, Hansen, Karen, Hambleton, Sarah, Shoemaker, Robert A., Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Spotts, Robert A., Serdani, Maryna, Crous, Pedro W., Hughes, Karen W., Matsuura, Kenji, Langer, Ewald, Langer, Gitta, Untereiner, Wendy A., Lücking, Robert, Büdel, Burkhard, Geiser, David M., Aptroot, André, Diederich, Paul, Schmitt, Imke, Schultz, Matthias, Yahr, Rebecca, Hibbett, David S., Lutzoni, François, McLaughlin, David J., Spatafora, Joseph W., and Vilgalys, Rytas

Published
2006

38. PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens

Author

Gueidan, Cécile, Elix, John, McCarthy, Patrick M., Roux, Claude, Mallen-Cooper, Max, Kantvilas, Gintaras, Gueidan, Cécile, Elix, John, McCarthy, Patrick M., Roux, Claude, Mallen-Cooper, Max, and Kantvilas, Gintaras

Abstract

The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities.

Published
2019

40. Supplementary material 1 from: Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G (2019) PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 53: 73-91. https://doi.org/10.3897/mycokeys.53.34761

Author

Gueidan, Cécile, primary, Elix, John A., additional, McCarthy, Patrick M., additional, Roux, Claude, additional, Mallen-Cooper, Max, additional, and Kantvilas, Gintaras, additional

Published
2019
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41. Figure S1 from A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

Author

Vasse, Marie, Voglmayr, Hermann, Mayer, Veronika, Gueidan, Cécile, Nepel, Maximilian, Moreno, Leandro, Hoog, Sybren De, Marc-André Selosse, McKey, Doyle, and Rumsaïs Blatrix

Abstract

Distribution of pairwise similarity at ITS for 38 strains of ant-associated Cyphellophoraceae, showing a drop of values at 0.99 but not at 0.97.

Published
2017
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46. A pot-pourri of new species of Trypetheliaceae resulting from molecular phylogenetic studies

Author

LÜCKING, Robert, primary, NELSEN, Matthew P., additional, APTROOT, André, additional, BENATTI, Michel N., additional, BINH, Nguyen Quoc, additional, GUEIDAN, Cécile, additional, GUTIÉRREZ, Martha Cecilia, additional, JUNGBLUTH, Patricia, additional, LUMBSCH, H. Thorsten, additional, MARCELLI, Marcelo P., additional, MONCADA, Bibiana, additional, NAKSUWANKUL, Khwanruan, additional, OROZCO, Thelma, additional, SALAZAR-ALLEN, Noris, additional, and UPRETI, Dalip K., additional

Published
2016
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47. A phylogenetic framework for reassessing generic concepts and species delimitation in the lichenized family Trypetheliaceae (Ascomycota: Dothideomycetes)

Author

LÜCKING, Robert, primary, NELSEN, Matthew P., additional, APTROOT, André, additional, BARILLAS DE KLEE, Roselvira, additional, BAWINGAN, Paulina A., additional, BENATTI, Michel N., additional, BINH, Nguyen Quoc, additional, BUNGARTZ, Frank, additional, CÁCERES, Marcela E. S., additional, CANÊZ, Luciana da Silva, additional, CHAVES, José-Luis, additional, ERTZ, Damien, additional, ESQUIVEL, Rhina Esmeralda, additional, FERRARO, Lidia Itati, additional, GRIJALVA, Alfredo, additional, GUEIDAN, Cécile, additional, HERNÁNDEZ M., Jesús E., additional, KNIGHT, Allison, additional, LUMBSCH, H. Thorsten, additional, MARCELLI, Marcelo P., additional, MERCADO-DÍAZ, Joel A., additional, MONCADA, Bibiana, additional, MORALES, Eduardo A., additional, NAKSUWANKUL, Khwanruan, additional, OROZCO, Thelma, additional, PARNMEN, Sittiporn, additional, RIVAS PLATA, Eimy, additional, SALAZAR-ALLEN, Noris, additional, SPIELMANN, Adriano A., additional, and VENTURA, Nohemy, additional

Published
2016
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48. Phylogeny and taxonomy of Staurothele (Verrucariaceae, lichenized ascomycetes) from the karst of northern Vietnam

Author

Gueidan, Cécile, Van Do, Truong, and Lu, Ngan Thi

Subjects
ddc:580, Klassifizierung, Endocarpon, generische Abgrenzung, Flechten, Verrucariales, Willeya, classification, Endocarpon, generic delimitation, lichens, Verrucariales, Willeya
Abstract

The crustose genus Staurothele (Verrucariaceae, Ascomycota) is a common component of the lichen flora from subneutral to alkaline silicate rocks in temperate to cold-temperate climates. Our field study in the karst system of northern Vietnam showed that it is also common on dry to humid limestone in the wet tropics. Molecular data revealed that species of Staurothele from Vietnam belong to an unnamed clade sister to the genus Endocarpon, together with the tropical Australian species Staurothele pallidopora and Staurothele diffractella, a North American species recently transferred to Endocarpon based on molecular data. The genus Willeya is here resurrected for this clade of crustose epilithic Staurothele with pale ascospores. Eight new combinations are proposed and three new species of Willeya are described from Vietnam. Sampling tropical members of a lichen family previously mostly known from temperate areas contributed significantly to improving its generic classification.

Published
2014

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