28 results on '"Peter R. Johnston"'
Search Results
2. Author Correction
- Author
-
Maarja Öpik, Conrad L. Schoch, Ning Zhang, Kevin D. Hyde, Takayuki Aoki, Barbara Robbertse, Robert Lücking, Irina S. Druzhinina, Gianluigi Cardinali, Rajesh Jeewon, Tom W. May, Marc Stadler, David M. Geiser, Pedro W. Crous, Andrey Yurkov, Hiran A. Ariyawansa, Peter R. Johnston, David L. Hawksworth, Laszlo Irinyi, Wieland Meyer, Vincent Robert, Andrew N. Miller, Marco Thines, Henrik R. Nilsson, M. Catherine Aime, Paul M. Kirk, Elaine Malosso, Duong Vu, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute - Software and Databasing, and Westerdijk Fungal Biodiversity Institute - Collection
- Subjects
Microbiology (medical) ,Fungal biodiversity ,History ,Published Erratum ,Immunology ,Biodiversity ,Library science ,Cell Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Laboratorium voor Phytopathologie ,Research centre ,Taxonomy (general) ,Laboratory of Phytopathology ,Genetics ,Life Science ,Nomenclature - Abstract
In the version of this Perspective originally published, the author Vincent Robert’s affiliation with the Westerdijk Fungal Biodiversity Institute was mistakenly omitted. In addition, the author Marco Thines’s affiliation with the Senckenberg Biodiversity and Climate Research Centre was mistakenly omitted. Vincent Robert’s affiliation has now been corrected to: Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy; and Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. Marco Thines’s affiliation has now been corrected to: International Commission on the Taxonomy of Fungi (ICTF), https://www. fungaltaxonomy.org/; Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany; and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany.
- Published
- 2021
3. Fungal taxonomy and sequence-based nomenclature
- Author
-
Maarja Öpik, Marc Stadler, Paul M. Kirk, Elaine Malosso, Conrad L. Schoch, Robert Lücking, Vincent Robert, Tom W. May, Laszlo Irinyi, Gianluigi Cardinali, Pedro W. Crous, Wieland Meyer, David L. Hawksworth, Takayuki Aoki, Hiran A. Ariyawansa, Duong Vu, Barbara Robbertse, Peter R. Johnston, Irina S. Druzhinina, David M. Geiser, Ning Zhang, Andrey Yurkov, Andrew N. Miller, Rajesh Jeewon, M. Catherine Aime, Henrik R. Nilsson, Kevin D. Hyde, and Marco Thines
- Subjects
Microbiology (medical) ,Sequence analysis ,Immunology ,Biology ,Applied Microbiology and Biotechnology ,Microbiology ,Article ,03 medical and health sciences ,Terminology as Topic ,Environmental Microbiology ,Genetics ,Animals ,Humans ,Life Science ,DNA, Fungal ,Nomenclature ,Plant Diseases ,030304 developmental biology ,Sequence (medicine) ,0303 health sciences ,030306 microbiology ,Fungi ,Fungal genetics ,Bacterial taxonomy ,DNA ,Sequence Analysis, DNA ,Cell Biology ,Laboratorium voor Phytopathologie ,Fungal ,Taxon ,Mycoses ,Evolutionary biology ,Laboratory of Phytopathology ,Taxonomy (biology) ,Identification (biology) ,Sequence Analysis - Abstract
The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.
- Published
- 2021
4. Comparing diversity of fungi from living leaves using culturing and high-throughput environmental sequencing
- Author
-
Peter R. Johnston, Rob D. Smissen, and Duckchul Park
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,media_common.quotation_subject ,Computational biology ,Forests ,Biology ,01 natural sciences ,Trees ,03 medical and health sciences ,DNA, Ribosomal Spacer ,Endophytes ,Environmental Microbiology ,Genetics ,DNA, Fungal ,skin and connective tissue diseases ,Molecular Biology ,Throughput (business) ,Ecology, Evolution, Behavior and Systematics ,media_common ,Sampling bias ,Ecology ,Fungi ,Biodiversity ,Cell Biology ,General Medicine ,Amplicon ,Plant Leaves ,030104 developmental biology ,Multivariate Analysis ,Pyrosequencing ,sense organs ,Mycobiome ,New Zealand ,010606 plant biology & botany ,Diversity (politics) - Abstract
High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected. Here we use high-throughput amplicon sequencing from bulk DNA extracts to test the impact that biases associated with culture-based methods had on an earlier study that compared the influence of site and host on fungal diversity in Nothofagaceae forests in New Zealand. Both detection methods sampled tissue from the same set of symptomless, living leaves. We found that both the culturing and high-throughput approaches show that host is a stronger driver of fungal community structure than site, but that both methods have some taxonomic biases. We also found that the individual trees selected for high-throughput sampling can impact the alpha-diversity detected and through this could potentially affect subsequent analyses based on a comparison of this diversity.
- Published
- 2017
5. Genetic validation of historical plant pathology records - a case study based on the fungal genus Phoma from the ICMP culture collection
- Author
-
W. W. H. Ho, B. J. R. Alexander, Peter R. Johnston, and Duckchul Park
- Subjects
0301 basic medicine ,biology ,Biosecurity ,Zoology ,Plant Science ,030108 mycology & parasitology ,Horticulture ,biology.organism_classification ,DNA sequencing ,03 medical and health sciences ,Genus Phoma ,Species level ,Phylogenetics ,Genetics ,Phoma ,Taxonomy (biology) ,Agronomy and Crop Science ,Historical record - Abstract
Fungal taxonomy and classification, and fungal identification tools, are increasingly based on DNA sequencing technologies. In contrast, many historical records of fungi are based on morphologically identified specimens. Scientific collections of specimens or living cultures provide a resource to enable these early records to be genetically validated using modern techniques. This project uses a set of cultures deposited prior to 2008 in the International Collection of Microorganisms from Plants (ICMP) culture collection as Phoma, a genus of high biosecurity importance that is notoriously difficult to identify accurately using morphological characters. Of the 265 cultures sequenced, 23% had been misidentified. These misidentifications mean that six species previously thought to be present in New Zealand probably do not occur there. Fifty specimens had not previously been identified to species level; amongst these were eight species newly reported from New Zealand. Genetic validation projects such as this, using existing scientific collections, are essential for maintaining a robust global biosecurity system.
- Published
- 2017
6. Genetic diversity ofBotrytisin New Zealand vineyards and the significance of its seasonal and regional variation
- Author
-
Duckchul Park, K. Hoksbergen, Peter R. Johnston, and Ross E. Beever
- Subjects
Genetic diversity ,food.ingredient ,biology ,food and beverages ,Plant Science ,Fungus ,Horticulture ,biology.organism_classification ,Fungicide ,Phylogenetic diversity ,food ,Phylogenetics ,Botany ,Genetics ,Clade ,human activities ,Agronomy and Crop Science ,Botrytis cinerea ,Botrytis - Abstract
Species- and population-specific differences in fungicide resistance and aggressiveness within Botrytis makes basic data on genetic diversity important for understanding disease caused by this fungus. Genetic diversity of Botrytis was surveyed between 2008 and 2012 from grapes from five New Zealand wine-growing regions. A total of 1226 isolates were gathered from symptomless flower buds at the start of the growing season and 1331 isolates from diseased fruit at harvest. Two species were found, B. cinerea and B. pseudocinerea. Botrytis pseudocinerea was common in both Auckland vineyards sampled, and infrequent elsewhere. However, even in Auckland, it was rarely isolated from diseased fruit. The presence of the Boty and Flipper transposons was assessed. Isolates with all four transposon states (Boty only, Flipper only, both Boty and Flipper, no transposons) were found for both species. Both vineyards in the Auckland region had high numbers of Flipper-only isolates at flowering; both vineyards from the Waipara region had high numbers of Boty-only isolates at flowering. Most isolates from diseased fruit at harvest contained both transposons. These observations suggest that B. pseudocinerea, and isolates with one or both of the transposons missing, may be less aggressive than B. cinerea, or than isolates with both transposons present. Two clades were resolved within B. pseudocinerea, only one of which has been reported from European vineyards. Phylogenetic diversity within B. cinerea in New Zealand was similar to that known from Europe, including isolates that appear to match Botrytis ‘Group S’. The taxonomic implications of this genetic diversity are discussed.
- Published
- 2013
7. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
- Author
-
Martin Grube, Gi-Ho Sung, Tom W. May, Ursula Eberhardt, Franck O.P. Stefani, Filip Högnabba, Dirk Redecker, Peter M. Hollingsworth, Kwang Deuk An, M. Teresa Telleria, Yuuri Hirooka, Tamás Petkovits, Paul Harrold, Bevan S. Weir, E. B. Gareth Jones, Wen Chen, László Nagy, Kerstin Hoffmann, Imke Schmitt, Ferry Hagen, Robert W. Barreto, Agathe Vialle, Satinee Suetrong, Javier Diéguez-Uribeondo, Grit Walther, Steven D. Leavitt, Andrew N. Miller, Kazuyuki Hirayama, Andrey Yurkov, Michael J. Wingfield, Sara Landvik, Tuan A. Duong, Dániel G. Knapp, Merlin M. White, Ibai Olariaga, Ana Rosa Burgaz, Herbert Stockinger, Mesfin Bogale, Pedro W. Crous, M. Catherine Aime, Keith A. Seifert, Constantino Ruibal, Wen Ying Zhuang, Katerina Fliegerova, Paul M. Kirk, Zai-Wei Ge, Marizeth Groenewald, Laura J. Kelly, Peter R. Johnston, K. Griffiths, Urmas Kõljalg, Kozue Sotome, Jean-Marc Moncalvo, Gábor M. Kovács, Seung-Beom Hong, W. Quaedvlieg, Duckchul Park, Cesar S. Herrera, Richard C. Hamelin, Joan E. Edwards, Ning Zhang, Timothy Y. James, Raquel Pino-Bodas, John L. Spouge, Sabine M. Huhndorf, Arthur Schüßler, Conrad L. Schoch, Ruth Del-Prado, Sajeewa S. N. Maharachchikumbura, J. Jennifer Luangsa-ard, Hector Urbina, Michael Weiß, Dominik Begerow, Elena Bolchacova, Gen Okada, Andrew S. Methven, Joan E. Johnson, Qing Cai, Carol A. Shearer, Gianluigi Cardinali, Priscila Chaverri, Thuy Duong Vu, Tuula Niskanen, Rebecca Yahr, Z. Wilhelm de Beer, Kazuaki Tanaka, Leho Tedersoo, Csaba Vágvölgyi, María P. Martín, Gregory Heller, Hsiao Man Ho, Kentaro Hosaka, Eric D. Tretter, Wiel Meyer, Johannes Z. Groenewald, Harinad Maganti, C. André Lévesque, Yan Wang, Vincent Robert, Miguel A. García, H. Thorsten Lumbsch, Jürgen Otte, Manohar R. Furtado, Juan Carlos Zamora, Craig Cummings, Mostafa S. Elshahed, Feng-Yan Bai, Kevin D. Hyde, Tara L. Rintoul, Brian Douglas, Jos Houbraken, Karen W. Hughes, Qi Ming Wang, David Schindel, Motofumi Suzuki, Kerstin Voigt, Lei Cai, Suchada Mongkolsamrit, Zhu L. Yang, Sung-Oui Suh, Kare Liimatainen, Huzefa A. Raja, Seppo Huhtinen, B. Stielow, Audra S. Liggenstoffer, Wendy A. Untereiner, Jianping Xu, Ana Crespo, Brian J. Coppins, Cletus P. Kurtzman, R. Henrik Nilsson, Liang-Dong Guo, Paloma Cubas, Izumi Okane, Soili Stenroos, Jullie M. Sarmiento-Ramírez, Bart Buyck, Lorenzo Lombard, Alistair R. McTaggart, Gareth W. Griffith, Teun Boekhout, Marieka Gryzenhout, G. Sybren de Hoog, Karen Hansen, Nattawut Boonyuen, Margarita Dueñas, Eric M. Johnson, Valérie Hofstetter, Marie Josée Bergeron, Ulrike Damm, Tamás Papp, Pradeep K. Divakar, Meredith Blackwell, Sarah Hambleton, Bryn T. M. Dentinger, Ildikó Nyilasi, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food [Ottawa] (AAFC), Field Museum, Royal Netherlands Academy of Arts and Sciences (KNAW), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Ontario Genomics Institute
- Subjects
ectomycorrhizal fungi ,[SDV]Life Sciences [q-bio] ,arbuscular mycorrhizal fungi ,dna ,basidiomycetous yeasts ,Biology ,Polymerase Chain Reaction ,DNA barcoding ,18S ribosomal RNA ,03 medical and health sciences ,ribosomal ,Species Specificity ,species recognition ,Cistron ,sequence-analysis ,28S ribosomal RNA ,DNA, Ribosomal Spacer ,DNA barcode ,DNA Barcoding, Taxonomic ,Letters ,subunit ,Internal transcribed spacer ,DNA, Fungal ,phylogenetic-relationships ,Phylogeny ,030304 developmental biology ,Cell Nucleus ,2. Zero hunger ,Genetics ,0303 health sciences ,Multidisciplinary ,030306 microbiology ,EPS-4 ,Fungi ,Intron ,Fungal genetics ,Reproducibility of Results ,rdna ,Ribosomal RNA ,Laboratorium voor Phytopathologie ,nuclear ,rpb1 sequences ,[SDE]Environmental Sciences ,Laboratory of Phytopathology ,ta1181 ,intragenomic variation - Abstract
Se evaluaron seis regiones de ADN como posibles códigos de barras de ADN para Hongos, el segundo reino más grande de vida eucariota, por un consorcio multinacional y de laboratorios múltiples. La región de la mitocondria se utilizó la subunidad 1 de la citocromo c oxidasa como código de barras animal excluido como un marcador potencial, porque es difícil de amplificar en hongos, a menudo incluye intrones grandes y puede ser insuficientemente variable. Tres subunidades del cistrón de ARN ribosómico nuclear fueron en comparación con las regiones de tres genes de codificación proteica representativos (la subunidad más grande de la ARN polimerasa II, la segunda más grande subunidad de la ARN polimerasa II y mantenimiento de minicromosomas proteína). Aunque las regiones de genes que codifican proteínas a menudo tenían un porcentaje más alto de identificación correcta en comparación con ribosomal marcadores, baja amplificación por PCR y éxito de secuenciación eliminados ellos como candidatos para un código de barras universal para hongos. Entre la regiones del cistrón ribosómico, el espaciador transcrito interno (ITS) tiene la mayor probabilidad de identificación exitosa para la gama más amplia de hongos, con la brecha de código de barras más claramente definida entre la variación inter e intraespecífica. El nuclear subunidad ribosómica grande, un marcador filogenético popular en ciertos grupos, tuvieron una resolución de especies superior en algunos grupos taxonómicos, como los primeros linajes divergentes y las levaduras ascomicetas, pero por lo demás era ligeramente inferior al ITS. El ribosomal nuclear La subunidad pequeña tiene una resolución pobre a nivel de especie en los hongos. SU será propuesto formalmente para su adopción como el código de barras fúngico principal marcador al Consorcio para el Código de Barras de la Vida, con la posibilidad de que se desarrollen códigos de barras suplementarios para grupos taxonómicos estrechamente circunscritos., Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
- Published
- 2012
8. Molecular phylogeny reveals a core clade of Rhytismatales
- Author
-
David W. Minter, Duckchul Park, Henrik Lantz, and Peter R. Johnston
- Subjects
0106 biological sciences ,0301 basic medicine ,Leotiomycetes ,Physiology ,Molecular Sequence Data ,DNA, Mitochondrial ,Polymerase Chain Reaction ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Mellitiosporium ,Monophyly ,Ascomycota ,Polyphyly ,Botany ,Genetics ,DNA, Fungal ,Clade ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Sequence ,biology ,Cell Biology ,General Medicine ,030108 mycology & parasitology ,biology.organism_classification ,Helotiales ,Evolutionary biology ,Molecular phylogenetics ,Sequence Alignment ,Pezizomycotina - Abstract
Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.
- Published
- 2011
9. Diversity and distribution of fungal foliar endophytes in New Zealand Podocarpaceae
- Author
-
Duckchul Park, Peter R. Johnston, Barbara Paulus, and Sucheta Joshee
- Subjects
Dacrydium cupressinum ,Geography ,biology ,Ecology ,Fungi ,Podocarpus totara ,Prumnopitys ferruginea ,Biodiversity ,Plant Science ,Kunzea ,biology.organism_classification ,Endophyte ,Plant Leaves ,Tracheophyta ,Species Specificity ,Kunzea ericoides ,Botany ,Genetics ,Dacrycarpus dacrydioides ,Seasons ,Podocarpaceae ,Ecology, Evolution, Behavior and Systematics ,New Zealand ,Biotechnology - Abstract
The diversity and distribution of fungal endophytes in the leaves of four podocarps (Dacrydium cupressinum, Prumnopitys ferruginea, Dacrycarpus dacrydioides, and Podocarpus totara, all Podocarpaceae) and an angiosperm (Kunzea ericoides, Myrtaceae) occurring in close stands were studied. The effects of host species, locality, and season on endophyte assemblages were investigated. Host species was the major factor shaping endophyte assemblages. The spatial separation of sites and seasonal differences played significant but lesser roles. The mycobiota of each host species included both generalist and largely host-specialised fungi. The host-specialists were often observed at low frequencies on some of the other hosts. There was no clear evidence for family-level specialisation across the Podocarpaceae. Of the 17 species found at similar frequencies on several of the podocarp species, 15 were found also on Kunzea. Many of the endophytes isolated appear to represent species of fungi not previously recognised from New Zealand.
- Published
- 2009
10. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
- Author
-
Joseph W. Spatafora, Gi-Ho Sung, Peter R. Johnston, Valérie Hofstetter, Amy Y. Rossman, Soili Stenroos, Francesc López-Giráldez, Jolanta Miadlikowska, Richard C. Summerbell, Frank Kauff, Harrie J. M. Sipman, Paul Diederich, Pedro W. Crous, Jeffrey P. Townsend, David Hewitt, Peter D. Crittenden, Alga Zuccaro, Sung-Oui Suh, Franois Lutzoni, Rachael M. Andrie, Alexandra Rauhut, Karen Hansen, Brendan P. Hodkinson, Emily Fraker, Lizel Mostert, Robert Lücking, Donald H. Pfister, Kristin M. Trippe, Michael J. Wingfield, Wendy A. Untereiner, Kentaro Hosaka, H. Thorsten Lumbsch, Damien Ertz, P. Brandon Matheny, Meredith Blackwell, David M. Geiser, Burkhard Büdel, Cécile Gueidan, Anja Amtoft Wynns, Linda M. Ciufetti, Jack D. Rogers, Mahdi Arzanlou, Zheng Wang, David M. Hillis, Gregory Bonito, Paul S. Dyer, R. A. Shoemaker, Junta Sugiyama, André Aptroot, Jan Kohlmeyer, Brigitte Volkmann-Kohlmeyer, Kerry O'Donnell, Lisa A. Castlebury, Kristin R. Peterson, Mariette S. Cole, Conrad L. Schoch, Johannes Z. Groenewald, Rebecca Yahr, Gareth W. Griffith, Marieka Gryzenhout, James M. Trappe, G. Sybren de Hoog, Barbara Robbertse, Patrik Inderbitzin, and Evolutionary Biology (IBED, FNWI)
- Subjects
pezizomycotina ,Ancestral reconstruction ,Leotiomycetes ,rna-polymerase-ii ,Genes, Fungal ,Zoology ,Biology ,030308 mycology & parasitology ,03 medical and health sciences ,eukaryotes ,Ascomycota ,Phylogenetics ,morphology ,Genetics ,subunit ,Ecosystem ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Lecanoromycetes ,0303 health sciences ,cleistothecial fungi ,Phylogenetic tree ,Ecology ,Reproduction ,EPS-4 ,15. Life on land ,biology.organism_classification ,Laboratorium voor Phytopathologie ,classification ,Eurotiomycetes ,Laboratory of Phytopathology ,multiple sequence alignment ,fungal lineages ,Arthoniomycetes ,divergence ,Pezizomycotina - 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.
- Published
- 2009
11. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex
- Author
-
Peter R. Johnston, Deanna A. Sutton, Pedro W. Crous, Seogchan Kang, R. P. Baayen, David M. Geiser, Patrick Colyer, Kerstin Skovgaard, Matthew G. Cromey, Monica L. Elliott, Sean Bithell, Ron Riley, Randy C. Ploetz, Theo van der Lee, Cécile Gueidan, H. Corby Kistler, Kerry O'Donnell, Jean H. Juba, Michael James Davis, Anthony E. Glenn, Stacy Sink, Brice A. J. Sarver, Antonio Moretti, Cees Waalwijk, Hye-Seon Kim, and Nicholas C. Zitomer
- Subjects
0106 biological sciences ,fragment-length-polymorphisms ,computer.software_genre ,01 natural sciences ,ribosomal dna ,Conserved sequence ,Intergenic region ,Peptide Elongation Factor 1 ,Fusarium ,DNA, Fungal ,Mycological Typing Techniques ,Conserved Sequence ,Phylogeny ,f-sp cubense ,Genetics ,0303 health sciences ,Cross Infection ,Database ,Phylogenetic tree ,EPS-4 ,Fungal genetics ,genetic diversity ,Plants ,intergenic spacer region ,phylogenetic diversity ,Databases, Nucleic Acid ,nectria-haematococca ,Sequence analysis ,Biology ,Microbiology ,DNA, Ribosomal ,Evolution, Molecular ,03 medical and health sciences ,Species Specificity ,Phylogenetics ,DNA, Ribosomal Spacer ,RNA, Ribosomal, 18S ,Humans ,discontinuous distribution ,Ribosomal DNA ,Plant Diseases ,Biointeracties and Plant Health ,Base Sequence ,030306 microbiology ,EF-1 alpha ,Mycotoxins ,Genealogical discordance ,IGS rDNA ,Sequence Analysis, DNA ,Ribosomal RNA ,vegetative compatibility groups ,DNA Fingerprinting ,Laboratorium voor Phytopathologie ,Mycoses ,Laboratory of Phytopathology ,fungus fusarium ,PRI Biointeractions en Plantgezondheid ,computer ,Sequence Alignment ,010606 plant biology & botany - Abstract
We constructed a two-locus database, comprising partial translation elongation factor (EF-1 alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex (FOSC). Of the 850 isolates typed, 101 EF-1 alpha, 203 IGS rDNA, and 256 two-locus sequence types (STs) were differentiated. Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant. This analysis also revealed that the 26 STs associated with human mycoses were genetically diverse, including several which appear to be nosocomial in origin. A congruence analysis, comparing partial EF-1 alpha and IGS rDNA bootstrap consensus, identified a significant number of conflicting relationships dispersed throughout the bipartitions, suggesting that some of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework
- Published
- 2009
- Full Text
- View/download PDF
12. Fusarium dactylidis sp. nov., a novel nivalenol toxin-producing species sister to F. pseudograminearum isolated from orchard grass (Dactylis glomerata) in Oregon and New Zealand
- Author
-
Mark Busman, Todd J. Ward, David M. Geiser, Peter R. Johnston, Amy C. Kelly, Takayuki Aoki, Kerry O'Donnell, Susan P. McCormick, and Martha M. Vaughan
- Subjects
0106 biological sciences ,0301 basic medicine ,Fusarium ,Physiology ,Trichothecene ,Molecular Sequence Data ,01 natural sciences ,Zea mays ,Conidium ,03 medical and health sciences ,chemistry.chemical_compound ,Oregon ,Botany ,Genetics ,Mycotoxin ,Dactylis ,Molecular Biology ,Zearalenone ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Triticum ,Plant Diseases ,biology ,Host (biology) ,food and beverages ,Cell Biology ,General Medicine ,Mycotoxins ,Spores, Fungal ,biology.organism_classification ,030104 developmental biology ,Dactylis glomerata ,chemistry ,Trichothecenes ,010606 plant biology & botany ,New Zealand - Abstract
The B trichothecene toxin-producing clade (B clade) of Fusarium includes the etiological agents of Fusarium head blight, crown rot of wheat and barley and stem and ear rot of maize. B clade isolates also have been recovered from several wild and cultivated grasses, including Dactylis glomerata (orchard grass or cock's foot), one of the world's most important forage grasses. Two isolates from the latter host are formally described here as F. dactylidis. Phenotypically F. dactylidis most closely resembles F. ussurianum from the Russian Far East. Both species produce symmetrical sporodochial conidia that are similar in size and curved toward both ends. However, conidia of F. ussurianum typically end in a narrow apical beak while the apical cell of F. dactylidis is acute. Fusarium dactylidis produced nivalenol mycotoxin in planta as well as low but detectable amounts of the estrogenic mycotoxin zearalenone in vitro. Results of a pathogenicity test revealed that F. dactylidis induced mild head blight on wheat.
- Published
- 2015
13. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data
- Author
-
Joseph W. Spatafora, Susumu Takamatsu, Peter R. Johnston, Zheng Wang, and David S. Hibbett
- Subjects
0106 biological sciences ,0301 basic medicine ,Leotiomycetes ,Physiology ,Sequence Homology ,DNA, Ribosomal ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Ascomycota ,RNA, Ribosomal, 28S ,Botany ,RNA, Ribosomal, 18S ,Genetics ,Sclerotiniaceae ,Geoglossaceae ,Cluster Analysis ,DNA, Fungal ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,biology ,Phylogenetic tree ,Computational Biology ,Cell Biology ,General Medicine ,030108 mycology & parasitology ,Erysiphales ,biology.organism_classification ,RNA, Ribosomal, 5.8S ,Helotiales ,Evolutionary biology ,Geoglossum ,Phylogenetic nomenclature - Abstract
Phylogenetic relationships of one of the largest nonlichen-forming ascomycetous groups, the Leotiomycetes, were inferred from genes encoding three rDNA regions (SSU+LSU+5.8S rDNA). A dataset was prepared with rDNA sequences data from 108 isolates, among which we sampled 85 taxa representing four orders and 16 families in the Leotiomycetes. Equally weighted parsimony and Bayesian analyses were performed. Bootstrap proportion and Bayesian posterior probability under the GTR+gamma+iota model were estimated along the branches. Based on our results the Leotiomycetes is relatively well defined as a class and it includes the Cyttariales, Erysiphales, Helotiales, Rhytismatales and two families of uncertain position, Myxotrichaceae and Pseudeurotiaceae. The placements of the Thelebolales and Ascocorticiaceae are not examined and are accepted as tentative in the Leotiomycetes. Our results agree with previous studies to remove the Geoglossaceae, including Geoglossum, Trichoglossum and Sarcoleotia, from the Leotiomycetes. Positions of the Erysiphales and Rhytismatales in the Leotiomycetes are confirmed. The Helotiales and Myxotrichaceae are paraphyletic. Close relationships are supported strongly among the Hemiphacidiaceae, Rutstroemiaceae and Sclerotiniaceae, among Loramycetaceae, the northern hemisphere Vibrisseaceae, the Dark Septate Endophyte fungus Phialocephala fortinii and Mollisia cinerea, and between species of Bulgaria and Phadidiopycnis. Sequence data of rDNA regions are not adequate to resolve the relationships among major groups of the Leotiomycetes.
- Published
- 2006
14. Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny
- Author
-
Peter R. Johnston, David S. Hibbett, Manfred Binder, Conrad L. Schoch, Joseph W. Spatafora, and Zheng Wang
- Subjects
Leotiomycetes ,Models, Statistical ,biology ,biology.organism_classification ,Leotiomyceta ,Biological Evolution ,DNA, Ribosomal ,Monophyly ,Helotiales ,Ascomycota ,Phylogenetics ,Evolutionary biology ,Geoglossum ,Molecular phylogenetics ,Botany ,Genetics ,Fruiting Bodies, Fungal ,DNA, Fungal ,Molecular Biology ,Ecosystem ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Pezizomycotina - Abstract
The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales.
- Published
- 2006
15. Characterization of diversity inColletotrichum acutatumsensu latoby sequence analysis of two gene introns, mtDNA and intron RFLPs, and mating compatibility
- Author
-
James C. Correll, Peter R. Johnston, John C. Guerber, and Bo Liu
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,biology ,Phylogenetic tree ,Physiology ,Sequence analysis ,Cell Biology ,General Medicine ,030108 mycology & parasitology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Colletotrichum acutatum ,Sensu ,Phylogenetics ,Polyphyly ,Clade ,Molecular Biology ,Genetic isolate ,Ecology, Evolution, Behavior and Systematics - Abstract
A diverse collection of isolates identified as Colletotrichum acutatum, including a range of fruit-rot and foliar pathogens, was examined for mtDNA RFLPs and RFLPs and sequence variation of a 900-bp intron of the glutamine synthetase (GS) gene and a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase (GPDH) gene. RFLPs of mtDNA, RFLPs of the 900-bp GS intron and sequence analysis of each intron identified the same seven distinct molecular groups, or clades, within C. acutatum sensu lato. Sequence analysis produced highly concordant tree topologies with definitive phylogenetic relationships within and between the clades. The clades might represent phylogenetically distinct species within C. acutatum sensu lato. Mating tests also were conducted to assess sexual compatibility with tester isolates known to outcross to form the teleomorph Glomerella acutata. Mating compatibility was identified within one clade, C, and between two phylogenetically distinct clades, C and J4. The C clade represented isolates from a wide range of hosts and geographic origins. J4 clade contained isolates from Australia or New Zealand recovered from fruit rot and pine seedlings with terminal crook disease. That isolates in two phylogenetically distinct clades were capable of mating suggests that genetic isolation occurred before reproductive isolation. No other isolates were sexually compatible with the mating testers, which also were in groups C and J4. Certain clades identified by mtDNA and intron analysis (D1, J3 and J6) appeared to represent relatively host-limited populations. Other clades (C1, F1 and J4) contained isolates from a wide range of hosts. Isolates described as C. acutatum f. sp. pineum were clearly polyphyletic.
- Published
- 2003
16. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- Author
-
Dirk Redecker, Johannes Z. Groenewald, B. Stielow, Ibai Olariaga, Wendy A. Untereiner, Steven D. Leavitt, Scott Federhen, Samantha C. Karunarathna, Pedro W. Crous, Katerina Fliegerova, Jianping Xu, Ana Crespo, M. Teresa Telleria, Soili Stenroos, Martha J. Powell, Sajeewa S. N. Maharachchikumbura, Gianluigi Cardinali, Laszlo Irinyi, Hiran A. Ariyawansa, Javier Diéguez Uribeondo, Andrew M. Minnis, Paul M. Kirk, Zai-Wei Ge, Duong Vu, Richard C. Hamelin, Conrad L. Schoch, Jian-Kui Liu, Wieland Meyer, Kevin D. Hyde, Csaba Vágvölgyi, Bryn T. M. Dentinger, Ning Zhang, Dhanushka Udayanga, Tamás Petkovits, Qing Cai, Cletus P. Kurtzman, Raquel Pino-Bodas, Jie Chen, Michael Weiß, Karl-Henrik Larsson, Leho Tedersoo, María P. Martín, Peter M. Letcher, Gábor M. Kovács, Liang-Dong Guo, Kazuaki Tanaka, Bhushan Shrestha, Andrew N. Miller, Krishna V. Subbarao, Nicolas Feau, Urmas Kõljalg, Huzefa A. Raja, D. Jean Lodge, Karen K. Nakasone, Jean-Marc Moncalvo, Nalin N. Wijayawardene, Sung-Oui Suh, Cécile Gueidan, Teun Boekhout, Wen Ying Zhuang, Marieka Gryzenhout, Jullie M. Sarmiento-Ramírez, Bart Buyck, H. Thorsten Lumbsch, Marizeth Groenewald, Seung-Beom Hong, Keith A. Seifert, Peter R. Johnston, Janet Jennifer Luangsa-ard, Barbara Robbertse, Kessy Abarenkov, Dimuthu S. Manamgoda, Z. Wilhelm de Beer, Pradeep K. Divakar, Tuula Niskanen, Patrik Inderbitzin, M. Catherine Aime, Bevan S. Weir, Sarah Hambleton, Zhu L. Yang, R. Henrik Nilsson, Kare Liimatainen, Cobus M. Visagie, Krisztina Krizsán, Michael J. Wingfield, Ulrike Damm, Gareth W. Griffith, Donald M. Walker, Tamás Papp, Vincent Robert, Miguel A. García, Valérie Hofstetter, Martin I. Bidartondo, Karen Hansen, Margarita Dueñas, Jos Houbraken, Karen W. Hughes, Kerstin Voigt, Giuseppina Mulè, Martin Grube, Ekaphan Kraichak, National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), NLM, National Institutes of Health, CBS-KNAW Fungal Biodiversity Centre, Department of Pharmaceutical Sciences – Microbiology, Università degli Studi di Perugia (UNIPG), Molecular Mycology Research Laboratory, University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The Westmead Institute for Medical Research, Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki, Ecology and Evolutionary Biology, University of Tennessee System, Illinois Natural History Survey, University of Illinois System-University of Illinois System, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, University of Tartu, Department of Botany and Plant Pathology, Oregon State University (OSU), Institute of Excellence in Fungal Research and School of Science, Mae Fah Luang University [Thaïlande] (MFU), Imperial College London, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), School of Science, Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Museum of Natural History Görlitz, Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UPSpace), Real Jardin Botanico (RJB), Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia (UBC), Czech Academy of Sciences [Prague] (CAS), Department of Biology, Northern Arizona University [Flagstaff], Aberystwyth University, Institute of Plant Sciences, Karl Franzens University, Department of Plant Sciences, University of California, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food [Ottawa] (AAFC), Department of Botany, National University of Ireland [Galway] (NUI Galway), Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, Agroscope, Korean Agricultural Culture Collection, National Academy of Agricultural Science, Davis Department of Plant Pathology, Manaaki Whenua – Landcare Research [Lincoln], Institute of Biology, Department of Plant Anatomy, Eötvös Loránd University (ELTE), Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Science and Education, Field Museum, Department of Microbiology [Szeged], University of Szeged [Szeged], Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research (NCAUR), United States Department of Agriculture (USDA)-United States Department of Agriculture (USDA), The Natural History Museum [London] (NHM), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Plant Biology, Department of Biosciences, Forest Service, United States Department of Agriculture, Biotec - National Center for Genetic Engineering and Biotechnology, Department of Medical Microbiology and Immunology [Göteborg], University of Gothenburg (GU), Department of Natural History, Royal Ontario Museum, Department of Ecology Evolutionary Biology, University of Toronto, Institute of Sciences of Food Production (ISPA), Consiglio Nazionale delle Ricerche (CNR), Northern Research Station, U.S. Forest Service, Center for Forest Mycology Research (CFMR), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, Department of Chemistry and Biochemistry, University of California [Los Angeles] (UCLA), University of California-University of California, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Life Science and Biotechnology, Sungkyunkwan University [Suwon] (SKKU), Mycology and Botany Program, American Type Culture Collection (ATCC), Faculty of Agriculture and Life Science, University of Maribor, Natural History Museum, University of Kansas [Lawrence] (KU), University of California [Davis] (UC Davis), Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Department of Natural Sciences, University of Findlay, Institute of Evolution and Ecology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, McMaster University, Kunming Institute of Botany [CAS] (KIB), Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), National Center for Biotechnology Information, National Library of Medicine, Schoch, Conrad L., Département Systématique et Evolution, Muséum national d'Histoire naturelle (MNHN), Chinese Academy of Sciences, Kunming Institute of Botany, Universidad Complutense de Madrid [Madrid] (UCM), Czech Academy of Sciences [Prague] (ASCR), Landcare Research, United States Department of Agriculture - USDA (USA)-United States Department of Agriculture - USDA (USA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Friedrich-Schiller-Universität Jena, Eberhard Karls Universität Tübingen, National Center for Biotechnology Information ( NCBI ), National Institutes of Health ( NIH ), Università degli Studi di Perugia, Westmead Institute for Medical Research, Department of Biological and Environmental Sciences, University of Tennessee, Oregon State University ( OSU ), Mae Fah Luang University [Thaïlande] ( MFU ), Muséum National d’Histoire Naturelle ( MNHN ), Universidad Complutense de Madrid [Madrid] ( UCM ), Forestry and Agricultural Biotechnology Institute ( FABI ), University of Pretoria ( UPSpace ), Real Jardin Botanico ( RJB ), University of British Columbia ( UBC ), Czech Academy of Sciences [Prague] ( ASCR ), Commonwealth Scientific and Industrial Research Organisation [Canberra] ( CSIRO ), Chinese Academy of Sciences [Changchun Branch] ( CAS ), Agriculture and Agri-Food Canada ( AAFC ), National University of Ireland [Galway] ( NUI Galway ), Eotvos Lorand University, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences [Budapest], National Center for Agricultural Utilization Research, The Open University [Milton Keynes] ( OU ), University of Gothenburg ( GU ), Institute of Sciences of Food Production, Center for Forest Mycology Research ( CFMR ), Botanical Museum, Finnish Museum of Natural History, University of California at Los Angeles [Los Angeles] ( UCLA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Sungkyunkwan University, American Type Culture Collection ( ATCC ), University of Kansas [Lawrence] ( KU ), University of California Davis, Leibniz Institute for Natural Product Research and Infection Biology, Rutgers University (State University of New Jersey), Università degli Studi di Perugia = University of Perugia (UNIPG), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Pretoria [South Africa], University of California (UC), Agriculture and Agri-Food (AAFC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and University of California (UC)-University of California (UC)
- Subjects
[SDV]Life Sciences [q-bio] ,sequence analyses ,ribosomal dna ,Intergenic region ,0807 Library And Information Studies ,Databases, Genetic ,RefSeq ,Cluster Analysis ,donnée de séquence moléculaire ,DNA, Fungal ,Genetics ,DNA, Intergenic ,Genes, Fungal ,Molecular Sequence Annotation ,Fungi ,Sequence Analysis, DNA ,Medicine (all) ,Phylogenetic tree ,EPS-4 ,3. Good health ,internal transcribed spacer ,Fungal ,Identification (biology) ,Original Article ,General Agricultural and Biological Sciences ,Life Sciences & Biomedicine ,Sequence Analysis ,Information Systems ,specimen ,life ,Sequence analysis ,arbuscular mycorrhizal fungi ,interspecific hybridization ,Computational biology ,Biology ,General Biochemistry, Genetics and Molecular Biology ,DNA sequencing ,Databases ,Genetic ,evolution ,Internal transcribed spacer ,species complex ,Science & Technology ,Intergenic ,[ SDV ] Life Sciences [q-bio] ,barcode ,0804 Data Format ,DNA ,Laboratorium voor Phytopathologie ,MATHEMATICAL & COMPUTATIONAL BIOLOGY ,référence ,Genes ,Laboratory of Phytopathology ,identification - Abstract
DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi., B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine
- Published
- 2014
17. Morphological and molecular analysis of Colletotrichum acutatum sensu lato
- Author
-
Peter R. Johnston, Kim M. Plummer, R. Lardner, and Michael N. Pearson
- Subjects
biology ,Phylogenetic tree ,Plant Science ,biology.organism_classification ,RAPD ,Colletotrichum acutatum ,Sensu ,Genetic distance ,Chemotaxonomy ,Botany ,Genetics ,Taxonomy (biology) ,Ecology, Evolution, Behavior and Systematics ,Biotechnology ,Specific identification - Abstract
The genetic relationships between several morphological groups recognized within Colletotrichum acutatum sensu lato were investigated using RAPD analysis and vegetative compatibility analysis. Isolates were examined from fruit rots originating in New Zealand and Australia, from Lupinus spp. in New Zealand, Canada, France and the U.K., and from Pinus radiata in New Zealand and Australia. The genetic distinctness of the groups recognized morphologically is confirmed. Two genetically distinct groups of C. acutatum-like pathogens are recognized from lupin, one comprising isolates from New Zealand and the U.K., the other isolates from Canada and France. C. acutatum f. sp. pineum isolates from New Zealand and Australia form two genetically distinct groups.
- Published
- 1999
18. Leaf endophytes of manuka (Leptospermum scoparium)
- Author
-
Peter R. Johnston
- Subjects
Pioneer species ,Phyllosticta ,biology ,food and beverages ,Plant Science ,biology.organism_classification ,Endophyte ,Leptospermum ,Leptospermum scoparium ,Common species ,Kunzea ericoides ,Botany ,Genetics ,Kunzea ,Ecology, Evolution, Behavior and Systematics ,Biotechnology - Abstract
The diversity and frequency of leaf endophytic fungi occurring in naturally regenerating and planted stands of manuka were investigated at several sites. A restricted and characteristic range of species was isolated from all sites, although marked differences were noted between natural and planted stands. In natural stands a Phyllosticta species was the single dominant endophyte. This fungus appears to be host species specific, as it was not isolated from the closely related kanuka (Kunzea ericoides) in mixed, even-aged stands of manuka and kanuka. The frequency of the Phyllosticta sp. fluctuated greatly between individual trees across single stands. No obvious environmental or other gradients were recognized which could explain this patchy distribution. The Phyllosticta sp., along with the two next most common species in natural stands, Diploceras leptospermi and an unidentified coelomycete, were absent from most of the planted stands sampled, and at very low frequencies when present. Although several of the planted stands were close to natural stands and had been established for several years, the difference between them has been maintained. The most common endophytes in planted stands were Botryosphaeria and Alternaria spp. These species, found at low levels in natural stands, are likely to be ‘opportunistic’ endophytes. They are probably also characteristic of the epiphytic mycota, invading only the living leaves of plants under stress. The difference in leaf endophyte communities between planted and natural stands of manuka may be an indication of wider differences in the microbial communities of the respective stands, and could prove significant for site restoration projects. Such projects using nursery-raised manuka plants as a pioneer species may be establishing stands lacking much of the natural diversity of manuka communities for extended periods following establishment.
- Published
- 1998
19. Relationships amongColletotrichumisolates from fruit-rots assessed using rDNA sequences
- Author
-
Derek Jones and Peter R. Johnston
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Colletotrichum coccodes ,Colletotrichum musae ,010603 evolutionary biology ,01 natural sciences ,Glomerella cingulata ,03 medical and health sciences ,Colletotrichum acutatum ,Phylogenetics ,Botany ,Genetic variation ,Genetics ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,biology ,Colletotrichum orbiculare ,food and beverages ,Cell Biology ,General Medicine ,030108 mycology & parasitology ,biology.organism_classification ,body regions ,Horticulture ,Colletotrichum - Abstract
Isolates of Colletotrichum associated with fruit rots in New Zealand were used to test the applicability of morphological, cultural, and rDNA sequence data to clarify relationships within this genu...
- Published
- 1997
20. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST
- Author
-
Peter R. Johnston, Pedro W. Crous, Takayuki Aoki, Vincent Robert, Kerry O'Donnell, David M. Geiser, Stephen A. Rehner, Richard A. Humber, Alejandro P. Rooney, Bongsoo Park, and Seogchan Kang
- Subjects
0106 biological sciences ,0301 basic medicine ,fujikuroi species complex ,Insecta ,Nematoda ,Physiology ,01 natural sciences ,rpb2 ,Fusarium ,DNA, Fungal ,Mycological Typing Techniques ,Clade ,Acari ,Phylogeny ,Soil Microbiology ,Phylogenetic tree ,biology ,EPS-4 ,food and beverages ,General Medicine ,030108 mycology & parasitology ,contact-lens ,recognition ,rna-polymerase-ii ,Genotype ,Genes, Fungal ,Molecular Sequence Data ,010603 evolutionary biology ,DNA sequencing ,03 medical and health sciences ,Botany ,evolution ,Genetics ,Animals ,Typing ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Genetic diversity ,model ,Base Sequence ,gene genealogies ,Genetic Variation ,Cell Biology ,biology.organism_classification ,Laboratorium voor Phytopathologie ,Phylogenetic diversity ,Genetic Loci ,Evolutionary biology ,Laboratory of Phytopathology ,solani ,Multilocus sequence typing ,fungi ,Sequence Alignment ,Multilocus Sequence Typing - Abstract
We constructed several multilocus DNA sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed in the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to facilitate molecular identifications of unknowns via the FUSARIUM-ID and Fusarium MLST online databases and analysis packages. Analyses of a 190-taxon two-locus dataset, which included 159 isolates from insects, indicated that: 1) insect-associated fusaria were nested within 10 species complexes spanning the phylogenetic breadth of Fusarium, 2) novel, putatively unnamed insecticolous species were nested within 8/10 species complexes, and 3) Latin binomials could be applied with confidence to only 18/58 phylogenetically distinct fusaria associated with pest insects. Phylogenetic analyses of an 82-taxon three-locus dataset nearly fully resolved evolutionary relationships among the 10 clades containing insecticolous fusaria. Multilocus typing of isolates within four species complexes identified surprisingly high genetic diversity in that 63/65 of the fusaria typed represented newly discovered haplotypes. The DNA sequence data, together with corrected ABI sequence chromatograms and alignments, have been uploaded to the following web-accessible sites dedicated to identifying fusaria: FUSARIUM-ID (http://isolate.fusariumdb.org) at The Pennsylvania State University's Department of Plant Pathology and Fusarium MLST (http://www.cbs.knaw.nl/fusarium) at the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center.
- Published
- 2012
21. Gibberella tumida sp. nov. — teleomorph of Fusarium tumidum from gorse in New Zealand
- Author
-
Peter R. Johnston and P.G. Broadhurst
- Subjects
biology ,Introduced species ,Plant Science ,Fungi imperfecti ,biology.organism_classification ,Ulex europaeus ,Spore ,Ascospore ,Botany ,Genetics ,Gibberella ,Taxonomy (biology) ,Fusarium tumidum ,Ecology, Evolution, Behavior and Systematics ,Biotechnology - Abstract
Single-ascospore isolates from perithecia belonging to a species of Gibberella found on diseased gorse ( Ulex europaeus ) plants produced an anamorph in culture identified as Fusarium tumidum . A teleomorph has not previously been reported for F. tumidum and it is described as Gibberella tumida sp. nov. ascospore size distinguishing it from all previously described species.
- Published
- 1994
22. Phylogenetics of Lophodermium from pine
- Author
-
Elena R. Alvarez-Buylla, Jeffrey K. Stone, Ignacio H. Chapela, David S. Gernandt, Sol Ortiz-García, Peter R. Johnston, and Rodolfo Salas-Lizana
- Subjects
0106 biological sciences ,0301 basic medicine ,biology ,Physiology ,Cell Biology ,General Medicine ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Terriera ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Sister group ,Elytroderma ,Botany ,Genetics ,Lophodermium ,Internal transcribed spacer ,Clade ,Molecular Biology ,Ribosomal DNA ,Ecology, Evolution, Behavior and Systematics - Abstract
Lophodermium comprises ascomycetous fungi that are both needle-cast pathogens and asymptomatic endophytes on a diversity of plant hosts. It is distinguished from other genera in the family Rhytismataceae by its filiform ascospores and ascocarps that open by a longitudinal slit. Nucleotide sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were used to infer phylogenetic relationships within Lophodermium. Twenty-nine sequences from approximately 11 species of Lophodermium were analyzed together with eight sequences from isolates thought to represent six other genera of Rhytismataceae: Elytroderma, Lirula, Meloderma, Terriera, Tryblidiopsis and Colpoma. Two putative Meloderma desmazieresii isolates occurred within the Lophodermium clade but separate from one another, one grouped with L. indianum and the other with L. nitens. An isolate of Elytroderma deformans also occurred within the Lophodermium clade but on a solitary branch. The occurrence of these genera within the Lophodermium clade might be due to problems in generic concepts in Rhytismataceae, such as emphasis on spore morphology to delimit genera, to difficulty of isolating Rhytismataceae needle pathogens from material that also is colonized by Lophodermium or to a combination of both factors. We also evaluated the congruence of host distribution and several morphological characters on the ITS phylogeny. Lophodermium species from pine hosts formed a monophyletic sister group to Lophodermium species from more distant hosts from the southern hemisphere, but not to L. piceae from Picea. The ITS topology indicated that Lophodermium does not show strict cospeciation with pines at deeper branches, although several closely related isolates have closely related hosts. Pathogenic species occupy derived positions in the pine clade, suggesting that pathogenicity has evolved from endophytism. A new combination is proposed, Terriera minor (Tehon) P.R. Johnst.
- Published
- 2010
23. Claviradulomyces, a new genus of Odontotremataceae from West African rainforest
- Author
-
Harry C, Evans, Peter R, Johnston, Duckchul, Park, Robert W, Barreto, Dartanhã J, Soares, and Dartanhã R, Soares
- Subjects
Molecular Sequence Data ,Rainforest ,Endophyte ,Ghana ,Trees ,Ascomycota ,Species Specificity ,Phylogenetics ,Botany ,Genetics ,DNA, Fungal ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Plant Diseases ,biology ,Acuminate ,Claviradulomyces ,Sequence Analysis, DNA ,Spores, Fungal ,biology.organism_classification ,Erythroxylaceae ,Plant disease ,Erythroxylum ,Infectious Diseases ,Cote d'Ivoire ,Plant Bark ,Taxonomy (biology) - Abstract
A new genus, Claviradulomyces, morphologically typical of Odontotremataceae, is proposed to accommodate the new species Claviradulomyces dabeicola. The genus is characterised by its ornamented periphysoids, and long-cylindric, sigmoid, acuminate ascospores. Genetically, C. dabeicola falls within the Ostropales, but the Odontotremataceae have been very poorly sampled genetically and their phylogenetic relationship within the order is unclear. C. dabeicola has been collected consistently and exclusively on the rainforest tree Erythroxylum mannii in the Cote d'Ivoire and Ghana, where it is associated with bark abnormalities on branches and stems of living trees.
- Published
- 2009
24. Corrigendum to 'Claviradulomyces, a new genus of Odontotremataceae from West African rainforest', Fungal Biology 114 (1): pp. 41–48 (2010)
- Author
-
Peter R. Johnston, Harry C. Evans, Robert W. Barreto, D. J. Soares, and Duckchul Park
- Subjects
West african ,Infectious Diseases ,biology ,Genus ,Ecology ,Odontotremataceae ,Genetics ,Zoology ,Claviradulomyces ,Rainforest ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics - Published
- 2010
25. Phylogenetics of Lophodermium from Pine
- Author
-
Sol Ortiz-Garcia, David S. Gernandt, Jeffrey K. Stone, Peter R. Johnston, Ignacio H. Chapela, Rodolfo Salas-Lizana, and Elena R. Alvarez-Buylla
- Subjects
Physiology ,Genetics ,Cell Biology ,General Medicine ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Published
- 2003
26. Characterization of Diversity in Colletotrichum acutatum sensu lato by Sequence Analysis of Two Gene Introns, mtDNA and Intron RFLPs, and Mating Compatibility
- Author
-
John C. Guerber, Bo Liu, James C. Correll, and Peter R. Johnston
- Subjects
Physiology ,Genetics ,Cell Biology ,General Medicine ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Published
- 2003
27. Relationships among Colletotrichum Isolates from Fruit-Rots Assessed Using rDNA Sequences
- Author
-
Peter R. Johnston and Derek Jones
- Subjects
Physiology ,Genetics ,Cell Biology ,General Medicine ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics - Published
- 1997
28. Structure and taxonomic significance of the ascus in the Coryneliaceae
- Author
-
Peter R. Johnston and David W. Minter
- Subjects
Coryneliales ,biology ,Coryneliaceae ,Tripospora ,Caliciopsis ,Zoology ,Plant Science ,biology.organism_classification ,Lagenulopsis ,Botany ,Genetics ,Taxonomy (biology) ,Elongation ,Ecology, Evolution, Behavior and Systematics ,Single family ,Biotechnology - Abstract
Asci of most members of the Coryneliaceae were examined. All species of Corynelia, Coryneliospora Fitzpatrickiella, Lagenulopsis , and Tripospora , and representative species of Caliciopsis and Coryneliopsis were studied by light microscopy. Two species of Corynelia were also examined using transmission electron microscopy. Except in Coryneliopsis , all had asci with more than one functional wall layer with the outer layer breaking during ascus elongation, long before ascospores are ready to be released. It is concluded that the order Coryneliales, containing the single family Coryneliaceae, should be retained, and that Coryneliopsis should probably be removed from the family.
- Published
- 1989
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.