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3. Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence

Author

Crespo, Ana, Kauff, Frank, Divakar, Pradeep K., del Prado, Ruth, Pérez-Ortega, Sergio, de Paz, Guillermo Amo, Ferencova, Zuzana, Blanco, Oscar, Roca-Valiente, Beatriz, Núñez-Zapata, Jano, Cubas, Paloma, Argüello, Arturo, Elix, John A., Esslinger, Theodore L., Hawksworth, David L., Millanes, Ana, Molina, M. Carmen, Wedin, Mats, Ahti, Teuvo, Aptroot, Andre, Barreno, Eva, Bungartz, Frank, Calvelo, Susana, Candan, Mehmet, Cole, Mariette, Ertz, Damien, Goffinet, Bernard, Lindblom, Louise, Lücking, Robert, Lutzoni, Francois, Mattsson, Jan-Eric, Messuti, María Inès, Miadlikowska, Jolanta, Piercey-Normore, Michele, Rico, Víctor J., Sipman, Harrie J.M., Schmitt, Imke, Spribille, Toby, Thell, Arne, Thor, Göran, Upreti, Dalip K., and Lumbsch, H. Thorsten

Published
2010

7. 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, P. Brandon, 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, de Hoog, G. Sybren, 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, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O'Donnell, 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

9. 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

10. 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

14. Reconstructing the early evolution of Fungi using a six-gene phylogeny

Author

James, Timothy Y., Kauff, Frank, Schoch, Conrad L., Matheny, P. Brandon, Hofstetter, Valerie, Cox, Cymon J., Celio, Gail, Gueidan, Cecile, Fraker, Emily, Miadlikowska, Jolanta, Lumbsch, H. Thorsten, Rauhut, Alexandra, Reeb, Valerie, 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., Schußler, 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., Lucking, Robert, Budel, Burkhard, Geiser, David M., Aptroot, Andre, Diederich, Paul, Schmitt, Imke, Schultz, Matthias, Yahr, Rebecca, Hibbett, David S., Lutzoni, Francois, McLaughlin, David J., Spatafora, Joseph W., and Vilgalys, Rytas

Abstract

Author(s): Timothy Y. James (corresponding author) [1]; Frank Kauff [1]; Conrad L. Schoch [2, 36]; P. Brandon Matheny [3, 36]; Valérie Hofstetter [1, 36]; Cymon J. Cox [1, 37]; Gail [...]

Published
2006
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15. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Author

Lutzoni, Francois, Kauff, Frank, Cox, Cymon J., McLaughlin, David, Celio, Gail, Dentinger, Bryn, Padamsee, Mahajabeen, Hibbett, David, James, Timothy Y., Baloch, Elisabeth, Grube, Martin, Reeb, Valerie, Hofstetter, Valerie, Schoch, Conrad, Arnold, A. Elizabeth, Miadlikowska, Jolanta, Spatafora, Joseph, Johnson, Desiree, Hambleton, Sarah, Crockett, Michael, Shoemaker, Robert, Sung, Gi-Ho, Lucking, Robert, Lumbsch, Thorsten, O'Donnell, Kerry, Binder, Manfred, Diederich, Paul, Ertz, Damien, Gueidan, Cecile, Hansen, Karen, Harris, Richard C., Hosaka, Kentaro, Lim, Young-Woon, Matheny, Brandon, Nishida, Hiromi, Pfister, Don, Rogers, Jack, Rossman, Amy, Schmitt, Imke, Sipman, Harrie, Stone, Jeffrey, Sugiyama, Junta, Yahr, Rebecca, and Vilgalys, Rytas

Subjects
Plants -- Evolution, Fungi, Phylogeny (Botany), Biological sciences
Abstract

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project 'Assembling the Fungal Tree of Life' (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi. Key words: fungal classification; fungal morphology and ultrastructure' fungal phylogenetics; fungal systematics; mitochondrial small subunit ribosomal DNA (mitSSU rDNA); nuclear small and large subunit ribosomal DNA (nucSSU and nucLSU rDNA); RNA polymerase subunit (RPB2).

Published
2004

18. Four versus Two Years of Rituximab Maintenance (R-Maintenance) Following Bendamustine Plus Rituximab (B-R): Results of a Prospective, Randomized Multicenter Phase 3 Study in First-Line Follicular Lymphoma (the StiL NHL7-2008 MAINTAIN Study)

Author

Balser, Christina, Lerchenmüller, Christian, Koenigsmann, Michael, Maschmeyer, Georg, Kaiser, Ulrich, Lange, Elisabeth, Behringer, Dirk, Kauff, Frank, Dürig, Jan, Greil, Richard, Barth, Juergen, Gaska, Tobias, Burchardt, Alexander C., Reeb, Manfred, Rummel, Mathias, Hertenstein, Bernd, Buske, Christian, Schliesser, Georg, and Hinke, Axel

Subjects
03 medical and health sciences, Cancer Research, 0302 clinical medicine, Oncology, 030220 oncology & carcinogenesis, Medizin, Hematology, 030215 immunology
Published
2018

19. Two Years Rituximab Maintenance Vs. Observation after First Line Treatment with Bendamustine Plus Rituximab (B-R) in Patients with Waldenström's Macroglobulinemia (MW) : Results of a Prospective, Randomized, Multicenter Phase 3 Study (the StiL NHL7-2008 MAINTAIN trial)

Author

Rummel, Mathias J, Lerchenmüller, Christian, Hensel, Manfred, Goerner, Martin, Buske, Christian, Schulz, Holger, Schmidt, Burkhard, Kojouharoff, Georgi, Lange, Elisabeth, Willenbacher, Wolfgang, Dürig, Jan, Engel, Erik, Kauff, Frank, Barth, Jürgen, Burchardt, Alexander Christoph, Hinke, Axel, Wupperfeld, Jasmin, and Greil, Richard

Subjects
Medizin
Published
2019

20. Two Years Rituximab Maintenance Vs. Observation after First Line Treatment with Bendamustine Plus Rituximab (B-R) in Patients with Waldenström's Macroglobulinemia (MW): Results of a Prospective, Randomized, Multicenter Phase 3 Study (the StiL NHL7-2008 MAINTAIN trial)

Author

Rummel, Mathias J, primary, Lerchenmüller, Christian, primary, Hensel, Manfred, primary, Goerner, Martin, primary, Buske, Christian, primary, Schulz, Holger, primary, Schmidt, Burkhard, primary, Kojouharoff, Georgi, primary, Lange, Elisabeth, primary, Willenbacher, Wolfgang, primary, Dürig, Jan, primary, Engel, Erik, primary, Kauff, Frank, primary, Barth, Jürgen, primary, Burchardt, Alexander Christoph, primary, Hinke, Axel, primary, Wupperfeld, Jasmin, primary, and Greil, Richard, primary

Published
2019
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21. Prognostic Value of Circulating Bcl-2/Igh Levels before and after Treatment in 415 Patients with Advanced Follicular Lymphoma Receiving First-Line Immuno-Chemotherapy in 2 Prospective StiL Trials - the Effect of Rituximab Maintenance

Author

Kobbe, Guido, primary, Pechtel, Sabrina, additional, Zohren, Fabian, additional, Barth, Jürgen, additional, Burchardt, Alexander Christoph, additional, Buske, Christian, additional, Dienst, Ariane, additional, Germing, Ulrich, additional, Greil, Richard, additional, Hertenstein, Bernd, additional, Kauff, Frank, additional, Koenigsmann, Michael, additional, Lerchenmüller, Christian, additional, Schroeder, Thomas Michael, additional, Haas, Rainer, additional, and Rummel, Mathias J, additional

Published
2018
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23. Four Versus Two Years of Rituximab Maintenance (R-maintenance) Following Bendamustine Plus Rituximab (B-R): Initial Results of a Prospective, Randomized Multicenter Phase 3 Study in First-Line Follicular Lymphoma (the StiL NHL7-2008 MAINTAIN study)

Author

Rummel, Mathias J, Buske, Christian, Hertenstein, Bernd, Lerchenmüller, Christian, Koenigsmann, Michael, Lange, Elisabeth, Reeb, Manfred, Kaiser, Ulrich, Balser, Christina, Behringer, Dirk, Dürig, Jan, Gaska, Tobias, Maschmeyer, Georg, Schliesser, Georg, Burchardt, Alexander Christoph, Barth, Juergen, Kauff, Frank, Hinke, Axel, and Greil, Richard

Published
2017
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24. Bendamustine Plus Rituximab Versus Fludarabine Plus Rituximab in Patients with Relapsed Follicular, Indolent, or Mantle Cell Lymphomas – 8-Year Follow-up Results of the Randomized Phase III Study NHL 2-2003 on Behalf of the StiL (Study Group Indolent Lymphomas, Germany)

Author

Rummel, Mathias J., primary, Balser, Christina, additional, Kaiser, Ulrich, additional, Böck, Hans Peter, additional, Stauch, Martina Beate, additional, Heider, Andrea, additional, Welslau, Manfred, additional, Losem, Christoph, additional, Weidmann, Eckhart, additional, Blau, Wolfgang, additional, Burchardt, Alexander, additional, Barth, Jürgen, additional, Kauff, Frank, additional, Hinke, Axel, additional, and Brugger, Wolfram, additional

Published
2014
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25. Bendamustine Plus Rituximab (B-R) Versus CHOP Plus Rituximab (CHOP-R) As First-Line Treatment in Patients with Indolent and Mantle Cell Lymphomas (MCL) – 7 Year Updated Results from the StiL NHL1 Study

Author

Rummel, Mathias J., primary, Maschmeyer, Georg, additional, Ganser, Arnold, additional, Heider, Andrea, additional, von Grünhagen, Ulrich, additional, Losem, Christoph, additional, Heil, Gerhard, additional, Welslau, Manfred, additional, Balser, Christina, additional, Kaiser, Ulrich, additional, Weidmann, Eckhart, additional, Dürk, Heinz, additional, Böck, Hans Peter, additional, Stauch, Martina Beate, additional, Barth, Jürgen, additional, Blau, Wolfgang, additional, Burchardt, Alexander, additional, Kauff, Frank, additional, Hinke, Axel, additional, and Brugger, Wolfram, additional

Published
2014
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26. Bendamustine Plus Rituximab Followed By Rituximab Maintenance for Patients with Untreated Advanced Follicular Lymphomas. Results from the StiL NHL 7-2008 Trial (MAINTAIN trial) (ClinicalTrials.gov Identifier: NCT00877214)

Author

Rummel, Mathias J., primary, Viardot, Andreas, additional, Greil, Richard, additional, Hertenstein, Bernd, additional, Lerchenmüller, Christian, additional, Ganser, Arnold, additional, Reeb, Manfred, additional, Kaiser, Ulrich, additional, Balser, Christina, additional, Maschmeyer, Georg, additional, Dürk, Heinz, additional, Schliesser, Georg, additional, Gaska, Tobias, additional, Dürig, Jan, additional, Matzdorff, Axel C., additional, Weide, Rudolf, additional, Hinke, Axel, additional, Blau, Wolfgang, additional, Burchardt, Alexander, additional, Kauff, Frank, additional, Barth, Jürgen, additional, and Brugger, Wolfram, additional

Published
2014
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27. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

Author

Carbone, Ignazio, White, James B., Miadlikowska, Jolanta, Arnold, A. Elizabeth, Miller, Mark A., Kauff, Frank, U'Ren, Jana M., May, Georgiana, and Lutzoni, François

Subjects
PHYLOGENY, NUCLEOTIDE sequencing, FUNGAL cultures, CULTURES (Biology), METADATA
Abstract

Motivation: High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single-and multi-locus alignments for specific clades. Results: In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi--Pezizomycotina (Ascomycota)--based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogenybased approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. [ABSTRACT FROM AUTHOR]

Published
2017
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28. Biopython: freely available Python tools for computational molecular biology and bioinformatics

Author

Cock, Peter J A, Antao, Tiago, Chang, Jeffrey T, Chapman, Brad A, Cox, Cymon J, Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, de Hoon, Michiel J L, Cock, Peter J A, Antao, Tiago, Chang, Jeffrey T, Chapman, Brad A, Cox, Cymon J, Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, and de Hoon, Michiel J L

Abstract

Udgivelsesdato: 2009-Jun-1, SUMMARY: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. AVAILABILITY: Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

Published
2009

29. The ascomycota tree of life:a phylum-wide phylogeny clarifies the origin and evolutionof fundamental reproductive and ecological traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O’Donnell, 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, Francois Lutzoni, Spatafora, Joseph W., Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O’Donnell, 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, Francois Lutzoni, and Spatafora, Joseph W.

Published
2009

30. 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. Protein import and oxidative folding in the mitochondrial intermembrane space of intact mammalian cells

Author

Fischer, Manuel, primary, Horn, Sebastian, additional, Belkacemi, Anouar, additional, Kojer, Kerstin, additional, Petrungaro, Carmelina, additional, Habich, Markus, additional, Ali, Muna, additional, Küttner, Victoria, additional, Bien, Melanie, additional, Kauff, Frank, additional, Dengjel, Jörn, additional, Herrmann, Johannes M., additional, and Riemer, Jan, additional

Published
2013
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35. Partial suppression of Oxa1 mutants by mitochondria-targeted signal recognition particle provides insights into the evolution of the cotranslational insertion systems

Author

Funes, Soledad, primary, Westerburg, Heike, additional, Jaimes-Miranda, Fabiola, additional, Woellhaf, Michael W., additional, Aguilar-Lopez, Jose L., additional, Janßen, Linda, additional, Bonnefoy, Nathalie, additional, Kauff, Frank, additional, and Herrmann, Johannes M., additional

Published
2012
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36. 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, Schüssler, 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, Vilgalys, Rytas, 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, Schüssler, 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

Abstract

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

Published
2006

37. Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genusLecideasensu Zahlbruckner (Lecanoromycetes, Ascomycota)

Author

Schmull, Michaela, primary, Miadlikowska, Jolanta, additional, Pelzer, Monika, additional, Stocker-Wörgötter, Elfie, additional, Hofstetter, Valerie, additional, Fraker, Emily, additional, Hodkinson, Brendan P., additional, Reeb, Valerie, additional, Kukwa, Martin, additional, Lumbsch, H. Thorsten, additional, Kauff, Frank, additional, and Lutzoni, François, additional

Published
2011
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39. ASSEMBLING THE FUNGAL TREE OF LIFE: PROGRESS, CLASSIFICATION, AND EVOLUTION OF SUB CELLULAR TRAITS.

Author

Lutzoni, François, Kauff, Frank, Cox, Cymon J., McLaughlin, David, Cello, Gail, Dentinger, Bryn, Padamsee, Mahajabeen, Hibbett, David, James, Timothy Y., Baloch, Elisabeth, Grube, Martin, Reeb, Valerie, Hofstetter, Valerie, Schoch, Conrad, Arnold, A. Elizabeth, Miadlikowska, Jolanta, Spatafora, Joseph, Johnson, Desiree, Hambleton, Sarah, and Crockett, Michael

Subjects
*FUNGI, *PLANT phylogeny, *PLANT classification, *PLANT morphology, *FUNGAL ultrastructure, *DNA
Abstract

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi. [ABSTRACT FROM AUTHOR]

Published
2004
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40. Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecideasensu Zahlbruckner (Lecanoromycetes, Ascomycota)

Author

Schmull, Michaela, Miadlikowska, Jolanta, Pelzer, Monika, Stocker-Wörgötter, Elfie, Hofstetter, Valerie, Fraker, Emily, Hodkinson, Brendan P., Reeb, Valerie, Kukwa, Martin, Lumbsch, H. Thorsten, Kauff, Frank, and Lutzoni, François

Abstract

The genus LecideaAch. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecideasensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecideasensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecideasensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereriaand Strangosporaare outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecideasensu stricto based on morphology (including the type species, Lecidea fuscoatra[L.] Ach.) form, with Porpidiaspecies, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecideamust be redefined to apply only to Lecideasensu stricto and to include at least some members of the genus Porpidia.Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullatasister to Frutidella caesioatra, the new combination Frutidella pullatais proposed here.

Published
2011
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41. The Ascomycota Tree of Life: A Phylum Wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Author

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

Subjects
lichenization, ancestral character reconstruction, large data sets, phylogeny, Fungi
Abstract

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species., Organismic and Evolutionary Biology

Published
2009
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42. Preserving accuracy in GenBank

Author

Bidartondo, M. I., Bruns, Thomas D., Blackwell, Meredith, Edwards, Ivan, Taylor, Andy F. S., Horton, Thomas, Zhang, Ning, Koljalg, 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, Kjoller, 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, Lumbsch, H. Thorsten, 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, Aime, M. Catherine, Kauff, Frank, Porras-Alfaro, Andrea, Gueidan, Cecile, Beck, Andreas, Andersen, Birgitte, Marek, Stephen, Crouch, Jo A., Kerrigan, Julia, Ristaino, Jean Beagle, Hodge, Kathie T., Kuldau, Gretchen, Samuels, Gary J., Raja, Huzefa A., Hermann Voglmayr, Gardes, Monique, Janos, David P., Rogers, Jack D., Cannon, Paul, Woolfolk, Sandra W., Kistler, H. C., Castellano, Michael A., Maldonado-Ramirez, 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., 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, Laszlo, Roy, Barbara A., Laessoe, Thomas, Hallenberg, Nils, Tichy, Hans-Volker, Stalpers, Joost, Langer, Ewald, Scholler, Markus, Krueger, Dirk, Pacioni, Giovanni, Poeder, 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, Jozsef, 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, Ngala, George Ndzi, 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., Dianese, Jose Carmine, 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, Galan Marquez, R., Horak, Egon, Fitzsimons, Michael, Doering, Heidi, Yao, Su, Hynson, Nicole, Ryberg, Martin, Arnold, A. E., Hughes, Karen, and Universidade do Minho

Subjects
0106 biological sciences, 0303 health sciences, Science & Technology, Multidisciplinary, Otras Ciencias Biológicas, BIOINFORMATICS, Value (computer science), Computational biology, TAXONOMY, Biology, ECOLOGY, Bioinformatics, 01 natural sciences, Public repository, Ciencias Biológicas, 03 medical and health sciences, Annotation, GenBank, ITS, Biological sciences, CIENCIAS NATURALES Y EXACTAS, 030304 developmental biology, 010606 plant biology & botany, Sequence (medicine)
Abstract

GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors (1), common annotation errors also reduce the value of this database. In fact, for organisms such as fungi, which are notoriously difficult to identify, up to 20% of DNA sequence records may have erroneous lineage designations in GenBank (2). Gene function annotation in protein sequence databases is similarly error-prone (3, 4). Because identity and function of new sequences are often determined by bioinformatic analyses, both types of errors are propagated into new accessions, leading to long-term degradation of the quality of the database. Currently, primary sequence data are annotated by the authors of those data, and can only be reannotated by the same authors. This is inefficient and unsustainable over the long term as authors eventually leave the field. Although it is possible to link third-party databases to GenBank records, this is a short-term solution that has little guarantee of permanence. Similarly, the current third-party annotation option in GenBank (TPA) complicates rather than solves the problem by creating an identical record with a new annotation, while leaving the original record unflagged and unlinked to the new record. Since the origin of public zoological and botanical specimen collections, an open system of cumulative annotation has evolved, whereby the original name is retained, but additional opinion is directly appended and used for filing and retrieval. This was needed as new specimens and analyses allowed for reevaluation of older specimens and the original depositors became unavailable. The time has come for the public sequence database to incorporate a community-curated, cumulative annotation process that allows third parties to improve the annotations of sequences when warranted by published peer-reviewed analyses (5)., (undefined)

43. Gray Mold Populations in German Strawberry Fields Are Resistant to Multiple Fungicides and Dominated by a Novel Glade Glosely Related to Botrytis cinerea.

Author

Leroch, Michaela, Plesken, Cecilia, Weber, Roland W. S., Kauff, Frank, Scalliet, Gabriel, and Hahna, Matthias

Subjects
*STRAWBERRY gray mold, *FUNGICIDE resistance, *BOTRYTIS cinerea, *MOLDS (Fungi), *PHYSIOLOGICAL effects of fungicides, *MULTIDRUG resistance, *GENETIC transcription, *FUNGI
Abstract

The gray mold fungus Botrytis cinerea is a major threat to fruit and vegetable production. Strawberry fields usually receive several fungicide treatments against Botrytis per season. Gray mold isolates from several German strawberry-growing regions were analyzed to determine their sensitivity against botryticides. Fungicide resistance was commonly observed, with many isolates possessing resistance to multiple (up to six) fungicides. A stronger variant of the previously described multidrug resistance (MDR) phenotype MDR1, called MDR1h, was found to be widely distributed, conferring increased partial resistance to two important botryticides, cyprodinil and fludioxonil. A 3-bp deletion mutation in a transcription factor-encoding gene, mrrl, was found to be correlated with MDR1h. All MDR1h isolates and the majority of isolates with resistance to multiple fungicides were found to be genetically distinct. Multiple-gene sequencing confirmed that they belong to a novel dade, called Botrytis group S, which is closely related to B. cinerea and the host-specific species B. fabae. Isolates of Botrytis group S genotypes were found to be widespread in all German strawberry-growing regions but almost absent from vineyards. Our data indicate a clear subdivision of gray mold populations, which are differentially distributed according to their host preference and adaptation to chemical treatments. [ABSTRACT FROM AUTHOR]

Published
2013
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