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Shirouzu T, Uno K, Hosaka K, Hosoya T. Early-diverging wood-decaying fungi detected using three complementary sampling methods. Mol Phylogenet Evol 2016; 98:11-20. [PMID: 26850687 DOI: 10.1016/j.ympev.2016.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/17/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
Wood-decaying fungi are essential components of degradation systems in forest ecosystems. However, their species diversity and ecological features are largely unknown. Three methods are commonly used to investigate fungal diversity: fruiting body collection, culturing, and environmental DNA analysis. Because no single method fully characterises fungal diversity, complementary approaches using two or more methods are required. However, few studies have compared the different methods and determined the best way to characterise fungal diversity. To this end, we investigated wood-decomposing Dacrymycetes (Agaricomycotina, Basidiomycota) using a complementary approach combining fruiting body collection, culturing, and environmental DNA analysis, thereby offering an effective approach for investigating the diversity of saprotrophic mushrooms. Fruiting body collection, culturing, and environmental DNA analysis detected 11, 10, and 16 operational taxonomic units (OTUs; 25 OTUs in total) and identified three, seven, and seven novel lineages, respectively. The three methods were complementary to each other to detect greater Dacrymycetes diversity. The culturing and environmental DNA analysis identified three early-diverging lineages that were not identified in the fruiting body collection suggesting that diverse lineages lacking observable fruiting bodies remain undiscovered. Such lineages may be important to understand Dacrymycetes evolution. To detect early branches of Dacrymycetes more efficiently, we recommend a combined approach consisting of a primary environmental DNA survey to detect novel lineages and a secondary culture survey to isolate their living mycelia. This approach would be helpful for identifying otherwise-undetectable lineages, and could thus uncover missing links that are important for understanding the evolution of mushroom-forming fungi.
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Affiliation(s)
- Takashi Shirouzu
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Kunihiko Uno
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
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52
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Millanes AM, Diederich P, Wedin M. Cyphobasidium gen. nov., a new lichen-inhabiting lineage in the Cystobasidiomycetes (Pucciniomycotina, Basidiomycota, Fungi). Fungal Biol 2015; 120:1468-1477. [PMID: 27742100 DOI: 10.1016/j.funbio.2015.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/30/2015] [Accepted: 12/14/2015] [Indexed: 01/30/2023]
Abstract
Pucciniomycotina is a highly diverse group of fungi, showing a remarkably wide range of lifestyles and ecologies. However, lichen-inhabiting fungi are only represented by a few species included in the genera Chionosphaera and Cystobasidium, and their phylogenetic position has never been investigated. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA markers reveal that the lichenicolous members of Cystobasidium (C. hypogymniicola, C. usneicola) form a monophyletic group distinct from Cystobasidium and outside the Cystobasidiales. The new genus Cyphobasidium is consequently described to accommodate these lichen-inhabiting species. Cyphobasidium is characterized by producing conspicuous galls on the host lichen thalli, by having distinctive basidia that arise from a thick-walled, cup-like structure, the probasidium, that persists after the senescence of the actual basidium (meiosporangium), and by its lichenicolous occurrence on species of Hypogymnia and Usnea. Cyphobasidium is one of the few representatives of the Cystobasidiomycetes in which the sexual stage predominates in nature, whereas most species in the group are known only from an asexual yeast phase. This is the first time the position of lichen-inhabiting taxa within the Pucciniomycotina is investigated using molecular data.
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Affiliation(s)
- Ana M Millanes
- Universidad Rey Juan Carlos, Departmento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Mats Wedin
- Swedish Museum of Natural History, Department of Botany, P.O. Box 50007, SE-104 05 Stockholm, Sweden
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53
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Divakar PK, Crespo A, Wedin M, Leavitt SD, Hawksworth DL, Myllys L, McCune B, Randlane T, Bjerke JW, Ohmura Y, Schmitt I, Boluda CG, Alors D, Roca-Valiente B, Del-Prado R, Ruibal C, Buaruang K, Núñez-Zapata J, Amo de Paz G, Rico VJ, Molina MC, Elix JA, Esslinger TL, Tronstad IKK, Lindgren H, Ertz D, Gueidan C, Saag L, Mark K, Singh G, Dal Grande F, Parnmen S, Beck A, Benatti MN, Blanchon D, Candan M, Clerc P, Goward T, Grube M, Hodkinson BP, Hur JS, Kantvilas G, Kirika PM, Lendemer J, Mattsson JE, Messuti MI, Miadlikowska J, Nelsen M, Ohlson JI, Pérez-Ortega S, Saag A, Sipman HJM, Sohrabi M, Thell A, Thor G, Truong C, Yahr R, Upreti DK, Cubas P, Lumbsch HT. Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi. THE NEW PHYTOLOGIST 2015; 208:1217-1226. [PMID: 26299211 DOI: 10.1111/nph.13553] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 06/04/2023]
Abstract
We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
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Affiliation(s)
- Pradeep K Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Steven D Leavitt
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - David L Hawksworth
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Leena Myllys
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Bruce McCune
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331-2902, USA
| | - Tiina Randlane
- Institute of Ecology & Earth Sciences, University of Tartu, Lai Street 38, Tartu, 51005, Estonia
| | - Jarle W Bjerke
- Norwegian Institute for Nature Research (NINA), FRAM - High North Research Centre for Climate and the Environment, NO-9296, Tromsø, Norway
| | - Yoshihito Ohmura
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Imke Schmitt
- Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, 85 D-60438, Frankfurt, Germany
| | - Carlos G Boluda
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - David Alors
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Beatriz Roca-Valiente
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Ruth Del-Prado
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Constantino Ruibal
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Kawinnat Buaruang
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
- Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok, 10240, Thailand
| | - Jano Núñez-Zapata
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Guillermo Amo de Paz
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Víctor J Rico
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - M Carmen Molina
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/ Tulipón s/n., 28933, Móstoles, Madrid, Spain
| | - John A Elix
- Research School of Chemistry, Australian National University, Building 137, Canberra, ACT, 2601, Australia
| | - Theodore L Esslinger
- Department of Biological Sciences Dept. 2715, North Dakota State University, PO Box 6050, Fargo, ND, 58108-6050, USA
| | - Inger Kristin K Tronstad
- Tromsø University Museum, University of Tromsø - The Arctic University of Norway, PO Box 6050, Langnes, NO-9037, Tromsø, Norway
| | - Hanna Lindgren
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Damien Ertz
- Department of Bryophytes-Thallophytes, Domaine de Bouchout, National Botanic Garden of Belgium, 1860, Meise, Belgium
| | - Cécile Gueidan
- Department of Botany, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Lauri Saag
- Institute of Ecology & Earth Sciences, University of Tartu, Lai Street 38, Tartu, 51005, Estonia
| | - Kristiina Mark
- Institute of Ecology & Earth Sciences, University of Tartu, Lai Street 38, Tartu, 51005, Estonia
| | - Garima Singh
- Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre BiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Sittiporn Parnmen
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
- Department of Medical Sciences, Ministry of Public Health, Tivanon Road, Nonthaburi, 11000, Thailand
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung, Menzinger Str. 67 D-80638, München, Germany
| | - Michel Navarro Benatti
- Instituto de Botânica, Núcleo de Pesquisa em Micologia, Caixa Postal 68041, 04045-972, São Paulo, SP, Brazil
| | - Dan Blanchon
- Biodiversity and Animal Welfare Research Group, Department of Natural Sciences, Unitec Institute of Technology, Private Bag 92025, Auckland, 1142, New Zealand
| | - Mehmet Candan
- Department of Biology, Faculty of Science, Anadolu University, EskiŞehir, Turkey
| | - Philippe Clerc
- Conservatoire et Jardin botaniques de la Ville de Genève, CP 60, 1292, Chambésy, Switzerland
| | - Trevor Goward
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Holteigasse 6, 8010, Graz, Austria
| | - Brendan P Hodkinson
- Grice Lab, Department of Dermatology, University of Pennsylvania, BRB 1046A, 421 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, 540-742, Korea
| | | | - Paul M Kirika
- Botany Department, National Museums of Kenya, PO Box 45166-00100, Nairobi, Kenya
| | - James Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Jan-Eric Mattsson
- School of Life Sciences, Södertörn University, SE-141 89, Huddinge, Sweden
| | - María Inés Messuti
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA) - CONICET, Universidad del Comahue, Quintral 1250, 8400, Sán Carlos de Bariloche, Río Negro, Argentina
| | | | - Matthew Nelsen
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Jan I Ohlson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Sergio Pérez-Ortega
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, c/ Serrano 115, E-28006, Madrid, Spain
| | - Andres Saag
- Institute of Ecology & Earth Sciences, University of Tartu, Lai Street 38, Tartu, 51005, Estonia
| | - Harrie J M Sipman
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - Mohammad Sohrabi
- Iranian Research Organization for Science and Technology (IROST), 15815-115, Tehran, Iran
| | - Arne Thell
- Biologal Museum, Lund University, Box 117, SE-22100, Lund, Sweden
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-750 07, Uppsala, Sweden
| | - Camille Truong
- Conservatoire et Jardin botaniques de la Ville de Genève, CP 60, 1292, Chambésy, Switzerland
| | - Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Dalip K Upreti
- National Botanical Research Institute (CSIR), Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
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54
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Liu XZ, Wang QM, Theelen B, Groenewald M, Bai FY, Boekhout T. Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses. Stud Mycol 2015; 81:1-26. [PMID: 26955196 PMCID: PMC4777771 DOI: 10.1016/j.simyco.2015.08.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The Tremellomycetes (Basidiomycota) contains a large number of unicellular and dimorphic fungi with stable free-living unicellular states in their life cycles. These fungi have been conventionally classified as basidiomycetous yeasts based on physiological and biochemical characteristics. Many currently recognised genera of these yeasts are mainly defined based on phenotypical characters and are highly polyphyletic. Here we reconstructed the phylogeny of the majority of described anamorphic and teleomorphic tremellomycetous yeasts using Bayesian inference, maximum likelihood, and neighbour-joining analyses based on the sequences of seven genes, including three rRNA genes, namely the small subunit of the ribosomal DNA (rDNA), D1/D2 domains of the large subunit rDNA, and the internal transcribed spacer regions (ITS 1 and 2) of rDNA including 5.8S rDNA; and four protein-coding genes, namely the two subunits of the RNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB). With the consideration of morphological, physiological and chemotaxonomic characters and the congruence of phylogenies inferred from analyses using different algorithms based on different data sets consisting of the combined seven genes, the three rRNA genes, and the individual protein-coding genes, five major lineages corresponding to the orders Cystofilobasidiales, Filobasidiales, Holtermanniales, Tremellales, and Trichosporonales were resolved. A total of 45 strongly supported monophyletic clades with multiple species and 23 single species clades were recognised. This phylogenetic framework will be the basis for the proposal of an updated taxonomic system of tremellomycetous yeasts that will be compatible with the current taxonomic system of filamentous basidiomycetes accommodating the ‘one fungus, one name’ principle.
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Affiliation(s)
- X-Z Liu
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Q-M Wang
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - B Theelen
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - M Groenewald
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - F-Y Bai
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - T Boekhout
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
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55
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Lindgren H, Diederich P, Goward T, Myllys L. The phylogenetic analysis of fungi associated with lichenized ascomycete genus Bryoria reveals new lineages in the Tremellales including a new species Tremella huuskonenii hyperparasitic on Phacopsis huuskonenii. Fungal Biol 2015; 119:844-56. [DOI: 10.1016/j.funbio.2015.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 11/25/2022]
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56
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Takashima M, Manabe RI, Iwasaki W, Ohyama A, Ohkuma M, Sugita T. Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species. PLoS One 2015; 10:e0131217. [PMID: 26241762 PMCID: PMC4524599 DOI: 10.1371/journal.pone.0131217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 05/30/2015] [Indexed: 02/07/2023] Open
Abstract
The order Trichosporonales (Tremellomycotina, Basidiomycota) includes various species that have clinical, agricultural and biotechnological value. Thus, understanding why and how evolutionary diversification occurred within this order is extremely important. This study clarified the phylogenetic relationships among Tricosporonales species. To select genes suitable for phylogenetic analysis, we determined the draft genomes of 17 Trichosporonales species and extracted 30 protein-coding DNA sequences (CDSs) from genomic data. The CDS regions of Trichosporon asahii and T. faecale were identified by referring to mRNA sequence data since the intron positions of the respective genes differed from those of Cryptococcus neoformans (outgroup) and are not conserved within this order. A multiple alignment of the respective gene was first constructed using the CDSs of T. asahii, T. faecale and C. neoformans, and those of other species were added and aligned based on codons. The phylogenetic trees were constructed based on each gene and a concatenated alignment. Resolution of the maximum-likelihood trees estimated from the concatenated dataset based on both nucleotide (72,531) and amino acid (24,173) sequences were greater than in previous reports. In addition, we found that several genes, such as phosphatidylinositol 3-kinase TOR1 and glutamate synthase (NADH), had good resolution in this group (even when used alone). Our study proposes a set of genes suitable for constructing a phylogenetic tree with high resolution to examine evolutionary diversification in Trichosporonales. These can also be used for epidemiological and biogeographical studies, and may also serve as the basis for a comprehensive reclassification of pleomorphic fungi.
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Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Ri-ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumiku, Yokohama, Kanagawa, 230-0045, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Yayoi, Bunkyoku, Tokyo, 113-0032, Japan
| | - Akira Ohyama
- Planning, in silico biology, inc., SOHO Station 706, 24-8 Yamashita-cho, Naka-ku, Yokohama, Kanagawa, 231-0023 Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan
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57
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Molecular Phylogenetic Analysis of Ballistoconidium-Forming Yeasts in Trichosporonales (Tremellomycetes): A Proposal for Takashimella gen. nov. and Cryptotrichosporon tibetense sp. nov. PLoS One 2015. [PMID: 26200459 PMCID: PMC4511645 DOI: 10.1371/journal.pone.0132653] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bullera species in the Trichosporonales (Tremellomycetes, Agaricomycotina) are phylogenetically distinct from Bullera alba (teleomorph: Bulleromyces albus), the type species of Bullera that belongs to Tremellales. In the present study, the three Bullera species, namely Bullera formosensis, Bullera koratensis and Bullera lagerstroemiae, and Cryptococcus tepidarius belonging to the Trichosporonales are transferred into a new genus Takashimella gen. nov. (MycoBank No. MB 810672) based on sequence analysis of the small subunit (SSU) rRNA gene, the D1/D2 domains of large subunit (LSU) rRNA gene and the ITS+5.8S rRNA gene sequences. In addition, the genus Cryptotrichosporon is emended to accommodate a novel ballistoconidium-forming species of the Trichosporonales, which is named as Cryptotrichosporon tibetense (type strain CGMCC 2.02614T = CBS 10455T). The MycoBank number of this new species is MB 810688.
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58
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Kurtzman CP, Mateo RQ, Kolecka A, Theelen B, Robert V, Boekhout T. Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways. FEMS Yeast Res 2015; 15:fov050. [PMID: 26136514 DOI: 10.1093/femsyr/fov050] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 01/02/2023] Open
Abstract
Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.
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Affiliation(s)
- Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Raquel Quintilla Mateo
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Anna Kolecka
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Bart Theelen
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Vincent Robert
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
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59
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Liu XZ, Wang QM, Göker M, Groenewald M, Kachalkin A, Lumbsch H, Millanes A, Wedin M, Yurkov A, Boekhout T, Bai FY. Towards an integrated phylogenetic classification of the Tremellomycetes. Stud Mycol 2015; 81:85-147. [PMID: 26955199 PMCID: PMC4777781 DOI: 10.1016/j.simyco.2015.12.001] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.
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Key Words
- A. cacaoliposimilis (J.L. Zhou, S.O. Suh & Gujjari) Kachalkin, A.M. Yurkov & Boekhout
- A. dehoogii (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. domesticum (Sugita, A. Nishikawa & Shinoda) A.M. Yurkov & Boekhout
- A. dulcitum (Berkhout) A.M. Yurkov & Boekhout
- A. gamsii (Middelhoven, Scorzetti, Sigler & Fell) A.M. Yurkov & Boekhout
- A. gracile (Weigmann & A. Wolff) A.M. Yurkov & Boekhout
- A. laibachii (Windisch) A.M. Yurkov & Boekhout
- A. lignicola (Diddens) A.M. Yurkov & Boekhout
- A. loubieri (Morenz) A.M. Yurkov & Boekhout
- A. montevideense (L.A. Queiroz) A.M. Yurkov & Boekhout
- A. mycotoxinivorans (O. Molnár, Schatzm. & Prillinger) A.M. Yurkov & Boekhout
- A. scarabaeorum (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. siamense (Nakase, Jindam., Sugita & H. Kawas.) Kachalkin, A.M. Yurkov & Boekhout
- A. sporotrichoides (van Oorschot) A.M. Yurkov & Boekhout
- A. vadense (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. veenhuisii (Middelhoven, Scorzetti & Fell) A.M. Yurkov & Boekhout
- A. wieringae (Middelhoven) A.M. Yurkov & Boekhout
- A. xylopini (S.O. Suh, Lee, Gujjari & Zhou) Kachalkin, A.M. Yurkov & Boekhout
- Apiotrichumbrassicae (Nakase) A.M. Yurkov & Boekhout
- Bandonia A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bandoniamarina (van Uden & Zobell) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. foliicola (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. hainanense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. panici (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. pseudovariabile (F.Y. Bai, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. sanyaense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. setariae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. siamense (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. variabile (Nakase & M. Suzuki) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bu. wuzhishanense (Q.M. Wang, F.Y. Bai, Boekhout & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleraceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidiaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Bulleribasidiumbegoniae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Carc. polyporina (D.A. Reid) A.M. Yurkov
- Carcinomycesarundinariae (Fungsin, M. Takash. & Nakase) A.M. Yurkov
- Carlosrosaea A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Carlosrosaeavrieseae (Landell, Brandão, Safar, Gomes, Félix, Santos, Pagani, Ramos, Broetto, Mott, Valente & Rosa) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cr. luteus (Roberts) Boekhout, Liu, Bai & M. Groenew.
- Cryptococcusdepauperatus (Petch) Boekhout, Liu, Bai & M. Groenew.
- Cu. curvatus (Diddens & Lodder) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. cutaneum (de Beurmann, Gougerot & Vaucher) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. cyanovorans (Motaung, Albertyn, J.L.F. Kock et Pohl) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. daszewskae (Takash., Sugita, Shinoda & Nakase) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. debeurmannianum (Sugita, Takash., Nakase & Shinoda) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. dermatis (Sugita, Takash., Nakase, Ichikawa, Ikeda & Shinoda) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. guehoae (Middelhoven, Scorzettii & Fell) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. haglerorum (Middelhoven, Á. Fonseca, S.C. Carreiro, Pagnocca & O.C. Bueno) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. jirovecii (Frágner) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. moniliiforme (Weigmann & A. Wolff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. mucoides (E. Guého & M.T. Smith) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. oleaginosus (J.J. Zhou, S.O. Suh & Gujjari) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. smithiae (Middelhoven, Scorzetti, Sugita & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cu. terricola (Sugita, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cutaneotrichosporon X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Cutaneotrichosporonarboriformis (Sugita, M. Takash., Sano, Nishim., Kinebuchi, S. Yamag. & Osanai) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Dimennazyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Dimennazyma cistialbidi (Á. Fonseca, J. Inácio & Spenc.-Mart.) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Effuseotrichosporon A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Effuseotrichosporon vanderwaltii (Motaung, Albertyn, Kock, C.F. Lee, S.O. Suh, M. Blackwell & C.H. Pohl) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. magnum (Lodder & Kreger-van Rij) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. oeirense (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. stepposum (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fil. wieringae (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Filobasidium chernovii (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fon. mujuensis (K.S. Shin & Y.H. Park) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fon. tronadorensis (V. De Garcia, Zalar, Brizzio, Gunde-Cim. & van Brook) A.M. Yurkov
- Fonsecazyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Fonsecazyma betulae (K. Sylvester, Q.M. Wang, C. T. Hittinger) A.M. Yurkov, A.V. Kachalkin & Boekhout
- Gelidatrema A.M. Yurkov, X.Z. Liu, F.Y. Bai
- Gelidatrema spencermartinsiae (Garcia, Brizzio, Boekhout, Theelen, Libkind & van Broock) A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. armeniaca (Á. Fonseca & J. Inácio) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. bromeliarum (Landell & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gen. tibetensis (F.Y. Bai & Q.M. Wang) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Genolevuria amylolytica (Á. Fonseca, J. Inácio & Spenc.-Mart.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. agrionensis (Russo, Libkind, Samp. & van Broock) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. gastrica (Reiersöl & di Menna) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. gilvescens (Chernov & Babeva) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. iberica (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Gof. metallitolerans (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Goffeauzyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Goffeauzyma aciditolerans (Gadanho & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Haglerozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Haglerozymachiarellii (Pagnocca, Legaspe, Rodrigues & Ruivo) A. M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Het. bachmannii (Diederich & M.S. Christ.) Millanes & Wedin
- Het. physciacearum (Diederich) Millanes & Wedin
- Heterocephalacriaarrabidensis (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Itersoniliapannonica (Niwata, Takash., Tornai-Lehoczki, T. Deák & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Jelly fungi
- Ko. distylii (Hamam., Kuroy. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. fuzhouensis (J.Z. Yue) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. lichenicola (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai
- Ko. mexicana (Lopandic, O. Molnár & Prillinger) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ko. ogasawarensis (Hamam., Kuroy. & Nakase) X.Z. Liu, F.Y. Bai, Groenew. & Boekhout
- Ko. sichuanensis (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaellachinensis (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kockovaellaprillingeri (Prillinger, G. Kraep. & Lopandic) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kr. tahquamenonensis (Wang, Hulfachor, Sylvester and Hittinger) A.M. Yurkov
- Krasilnikovozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Krasilnikovozymahuempii (C. Ramírez & A. E. González) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. dejecticola (Thanh, Hai & Lachance) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. dendrophila (Van der Walt & D.B. Scott) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. pini (Golubev & Pfeiffer) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kw. shivajii (S.R. Ravella, S.A. James, C.J. Bond, I.N. Roberts, K. Cross, Retter & P.J. Hobbs) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Kwoniellabestiolae (Thanh, Hai & Lachance) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- M. Groenew. & Boekhout
- M. cryoconiti (Margesin & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- M. niccombsii (Thomas-Hall) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Morphology
- Mrakiaaquatica (E.B.G. Jones & Slooff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Mrakiaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Multigene phylogeny
- Naem. microspora (Lloyd) Millanes & Wedin
- Naemateliaaurantialba (Bandoni & M. Zang) Millanes & Wedin
- Naemateliaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. albida (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. albidosimilis (Vishniac & Kurtzman) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. antarctica (Vishniac & Kurtzman) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. bhutanensis (Goto & Sugiy.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. cerealis (Passoth, A.-C. Andersson, Olstorpe, Theelen, Boekhout & Schnürer) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. diffluens (Zach) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. friedmannii (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. liquefaciens (Saito & M. Ota) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. onofrii (Turchetti, Selbmann & Zucconi) A.M. Yurkov
- Nag. randhawae (Z.U. Khan, S.O. Suh. Ahmad, F. Hagen, Fell, Kowshik, Chandy & Boekhout) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. uzbekistanensis (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nag. vaughanmartiniae (Turchetti, Blanchette & Arenz) A.M. Yurkov
- Nag. vishniacii (Vishniac & Hempfling) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Naganishiaadeliensis (Scorzetti, I. Petrescu, Yarrow & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Niel. melastomae (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Nielozymaformosana (Nakase, Tsuzuki, F.L. Lee & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- P. mycophaga (G.W. Martin) Millanes & Wedin
- Pap. aspenensis (K. Ferreira-Paim, T.B. Ferreira, L. Andrade-Silva, D.J. Mora, D.J. Springer, J. Heitman, F.M. Fonseca, D. Matos, M.S.C. Melhem & M.L. Silva-Vergara) X.Z. Liu, F.Y. Bai, A.M. Yurkov & Boekhout
- Pap. aurea (Saito) M. Takash., Sugita, Shinoda & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. baii (A.M. Yurkov, M.A. Guerreiro & Á. Fonseca) A.M. Yurkov
- Pap. flavescens (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. fonsecae (V. de García, Zalar, Braizzio, Gunde-Cim. & van Brollck) A.M. Yurkov
- Pap. frias (V. de García, Zalar, Braizzio, Gunde-Cim. & van Brollck) A.M. Yurkov
- Pap. fuscus (J.P. Samp., J. Inácio, Fonseca & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. hoabinhensis (D.T. Luong, M. Takash., Ty. Dung & Nakase) A.M. Yurkov
- Pap. japonica (J.P. Samp., Fonseca & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. laurentii (Kuff.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. mangalensis (Fell, Statzell & Scorzett) A.M. Yurkov
- Pap. nemorosus (Golubev, Gadanho, J.P. Samp. & N.W. Golubev) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. perniciosus (Golubev, Gadanho, J.P. Samp. & N.W. Golubev) X.Z. Liu, F.Y. Bai
- Pap. pseudoalba (Nakase & M. Suzuki) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. rajasthanensis (Saluja & G.S. Prasad) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. ruineniae (A.M. Yurkov, M.A. Guerreiro & Á. Fonseca) A.M. Yurkov
- Pap. taeanensis (K.S. Shin & Y.H. Park) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. terrestris (Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pap. wisconsinensis (Crestani, Landell, Faganello, Vainstein, Vishniac & P. Valente) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Papiliotremaanemochoreius (C.H. Pohl, Kock, P.W.J. van Wyk & Albertyn) F.Y. Bai, M. Groenew. & Boekhout
- Ph. mycetophiloides (Kobayasi) Millanes & Wedin
- Ph. neofoliacea (Chee J. Chen) Millanes & Wedin
- Ph. simplex (H.S. Jacks. & G.W. Martin) Millanes & Wedin
- Ph. skinneri (Phaff & Carmo Souza) A.M. Yurkov & Boekhout
- Phaeotremellaceae A.M. Yurkov & Boekhout
- Phaeotremellafagi (Middelhoven & Scorzetti) A.M. Yurkov & Boekhout
- Pis. cylindrica (Á. Fonseca, Scorzetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pis. fildesensis (T. Zhang & L.-Y. Yu) A.M. Yurkov
- Pis. filicatus (Golubev & J.P. Samp.) Kachalkin
- Pis. silvicola (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, Groenew. & Boekhout
- Pis. sorana (Hauerslev) A.M. Yurkov
- Pis. taiwanensis (Nakase, Tsuzuki & M. Takash.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Piskurozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Piskurozymacapsuligena (Fell, Statzell, I.L. Hunter & Phaff) A.M. Yurkov
- Piskurozymaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ps. lacticolor (Satoh & Makimura) A.M. Yurkov
- Ps. moriformis (Berk.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Ps. nivalis (Chee J. Chen) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Pseudotremella X.Z. Liu, F.Y. Bai, A.M. Yurkov, M. Groenew. & Boekhout
- Pseudotremellaallantoinivorans (Middelhoven) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- R. complexa (Landell, Pagnocca, Sette, Passarini, Garcia, Ribeiro, Lee, Brandao, Rosa & Valente) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. fermentans (Lee) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. glucofermentans (S.O. Suh & Blackwell) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. nanyangensis (F.L. Hui & Q.H. Niu) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. noutii (Boekhout, Fell, Scorzett & Theelen) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. tunnelae (Boekhout, Fell, Scorzetti & Theelen) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- R. visegradensis (Peter & Dlauchy) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Ranks
- Rhynchogastremaaquatica (Brandao, Valente, Pimenta & Rosa) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Sait. ninhbinhensis (Luong, Takash., Dung & Nakase) A.M. Yurkov
- Sait. paraflava (Golubev & J.P. Samp.) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sait. podzolica (Babeva & Reshetova) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Saitozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Saitozymaflava (Saito) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sol. fuscescens (Golubev) A.M. Yurkov
- Sol. keelungensis (C.F. Chang & S.M. Liu) A.M. Yurkov
- Sol. phenolicus (Á. Fonseca, Scorzetti & Fell) A.M. Yurkov
- Sol. terreus (Di Menna) A.M. Yurkov
- Sol. terricola (T.A. Pedersen) A.M. Yurkov
- Solicoccozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Solicoccozymaaeria (Saito) A.M. Yurkov
- Sugitazyma A.M. Yurkov, X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Sugitazymamiyagiana (Nakase, Itoh, Takem. & Bandoni) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Tausoniapullulans (Lindner) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Taxonomy
- Tremellayokohamensis (Alshahni, Satoh & Makimura) A.M. Yurkov
- Tremellomycetes
- Trimorphomycessakaeraticus (Fungsin, M. Takash. & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew., Boekhout & A.M. Yurkov
- Trimorphomycetaceae X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Van. meifongana (C.F. Lee) Kachalkin, A.M. Yurkov & Boekhout
- Van. nantouana (C.F. Lee) Kachalkin, A.M. Yurkov & Boekhout
- Van. thermophila (Vogelmann, Chaves & Hertel) Kachalkin, A.M. Yurkov & Boekhout
- Vanrijafragicola (M. Takash., Sugita, Shinoda & Nakase) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. dimennae (Fell & Phaff) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. foliicola (Q.M. Wang & F.Y. Bai) A.M. Yurkov
- Vis. globispora (B.N. Johri & Bandoni) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. heimaeyensis (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. nebularis (Vishniac) A.M. Yurkov
- Vis. peneaus (Phaff, Mrak & O.B. Williams) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. psychrotolerans (V. de García, Zalar, Brizzio, Gunde-Cim. & van Broock) A.M. Yurkov
- Vis. taibaiensis (Q.M. Wang & F.Y. Bai) A.M. Yurkov
- Vis. tephrensis (Vishniac) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vis. victoriae (M.J. Montes, Belloch, Galiana, M.D. García, C. Andrés, S. Ferrer, Torr.-Rodr. & J. Guinea) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozyma X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Vishniacozymacarnescens (Verona & Luchetti) X.Z. Liu, F.Y. Bai, M. Groenew. & Boekhout
- Yeasts
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Affiliation(s)
- X.-Z. Liu
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - Q.-M. Wang
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - M. Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - M. Groenewald
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
| | - A.V. Kachalkin
- Faculty of Soil Science, Lomonosov Moscow State University, Moscow 119991, Russia
| | - H.T. Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - A.M. Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain
| | - M. Wedin
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden
| | - A.M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig 38124, Germany
| | - T. Boekhout
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, PR China
| | - F.-Y. Bai
- State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands
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Kües U, Navarro-González M. How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development. FUNGAL BIOL REV 2015. [DOI: 10.1016/j.fbr.2015.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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61
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Yurkov A, Guerreiro MA, Sharma L, Carvalho C, Fonseca Á. Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales). PLoS One 2015; 10:e0120400. [PMID: 25811603 PMCID: PMC4374795 DOI: 10.1371/journal.pone.0120400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/21/2015] [Indexed: 02/06/2023] Open
Abstract
Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.
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Affiliation(s)
- Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- * E-mail:
| | - Marco A. Guerreiro
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Lav Sharma
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Cláudia Carvalho
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Álvaro Fonseca
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Sharma R, Gassel S, Steiger S, Xia X, Bauer R, Sandmann G, Thines M. The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. BMC Genomics 2015; 16:233. [PMID: 25887949 PMCID: PMC4393869 DOI: 10.1186/s12864-015-1380-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
Background Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota. Results The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned. Conclusions The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1380-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Sören Gassel
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Sabine Steiger
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Robert Bauer
- Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| | - Gerhard Sandmann
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
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Hagen F, Khayhan K, Theelen B, Kolecka A, Polacheck I, Sionov E, Falk R, Parnmen S, Lumbsch HT, Boekhout T. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex. Fungal Genet Biol 2015; 78:16-48. [PMID: 25721988 DOI: 10.1016/j.fgb.2015.02.009] [Citation(s) in RCA: 473] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 02/12/2015] [Accepted: 02/15/2015] [Indexed: 02/08/2023]
Abstract
Phylogenetic analysis of 11 genetic loci and results from many genotyping studies revealed significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus neoformans species complex. Genealogical concordance, coalescence-based, and species tree approaches supported the presence of distinct and concordant lineages within the complex. Consequently, we propose to recognize the current C. neoformans var. grubii and C. neoformans var. neoformans as separate species, and five species within C. gattii. The type strain of C. neoformans CBS132 represents a serotype AD hybrid and is replaced. The newly delimited species differ in aspects of pathogenicity, prevalence for patient groups, as well as biochemical and physiological aspects, such as susceptibility to antifungals. MALDI-TOF mass spectrometry readily distinguishes the newly recognized species.
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Affiliation(s)
- Ferry Hagen
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Kantarawee Khayhan
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Bart Theelen
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands
| | - Anna Kolecka
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands
| | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Edward Sionov
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel; Department of Food Quality & Safety, Institute for Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel; Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Sittiporn Parnmen
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Teun Boekhout
- CBS-KNAW Fungal Biodiversity Centre, Basidiomycete and Yeast Research, Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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Mittelbach M, Yurkov AM, Nocentini D, Nepi M, Weigend M, Begerow D. Nectar sugars and bird visitation define a floral niche for basidiomycetous yeast on the Canary Islands. BMC Ecol 2015; 15:2. [PMID: 25638173 PMCID: PMC4318194 DOI: 10.1186/s12898-015-0036-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies on the diversity of yeasts in floral nectar were first carried out in the late 19th century. A narrow group of fermenting, osmophilous ascomycetes were regarded as exclusive specialists able to populate this unique and species poor environment. More recently, it became apparent that microorganisms might play an important role in the process of plant pollination. Despite the importance of these nectar dwelling yeasts, knowledge of the factors that drive their diversity and species composition is scarce. RESULTS In this study, we linked the frequencies of yeast species in floral nectars from various host plants on the Canary Islands to nectar traits and flower visitors. We estimated the structuring impact of pollination syndromes (nectar volume, sugar concentration and sugar composition) on yeast diversity.The observed total yeast diversity was consistent with former studies, however, the present survey yielded additional basidiomycetous yeasts in unexpectedly high numbers. Our results show these basidiomycetes are significantly associated with ornithophilous flowers. Specialized ascomycetes inhabit sucrose-dominant nectars, but are surprisingly rare in nectar dominated by monosaccharides. CONCLUSIONS There are two conclusions from this study: (i) a shift of floral visitors towards ornithophily alters the likelihood of yeast inoculation in flowers, and (ii) low concentrated hexose-dominant nectar promotes colonization of flowers by basidiomycetes. In the studied floral system, basidiomycete yeasts are acknowledged as regular members of nectar. This challenges the current understanding that nectar is an ecological niche solely occupied by ascomycetous yeasts.
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Affiliation(s)
- Moritz Mittelbach
- />Department of Geobotany, - LS Evolution & Biodiversity of Plants, Ruhr-University Bochum, ND 1/150 / Universitaetsstr. 150, 44780 Bochum, Germany
| | - Andrey M Yurkov
- />Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Massimo Nepi
- />Department of Life Sciences, University of Siena, Siena, Italy
| | - Maximilian Weigend
- />Nees Institute for biodiversity of plants, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Dominik Begerow
- />Department of Geobotany, - LS Evolution & Biodiversity of Plants, Ruhr-University Bochum, ND 1/150 / Universitaetsstr. 150, 44780 Bochum, Germany
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Two yeast species Cystobasidium psychroaquaticum f.a. sp. nov. and Cystobasidium rietchieii f.a. sp. nov. isolated from natural environments, and the transfer of Rhodotorula minuta clade members to the genus Cystobasidium. Antonie van Leeuwenhoek 2014; 107:173-85. [DOI: 10.1007/s10482-014-0315-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
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Park CH, Kim KM, Elvebakk A, Kim OS, Jeong G, Hong SG. Algal and Fungal Diversity in Antarctic Lichens. J Eukaryot Microbiol 2014; 62:196-205. [DOI: 10.1111/jeu.12159] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/24/2014] [Accepted: 06/14/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chae Haeng Park
- Division of Polar Life Sciences; Korea Polar Research Institute; 26 Songdomirae-ro Yeonsu-gu Incheon 406-840 Korea
- School of Biological Sciences; College of Natural Science; Seoul National University; 599 Gwanak-ro Gwanak-gu Seoul Korea
| | - Kyung Mo Kim
- Biological Resource Center; Korea Research Institute of Bioscience and Biotechnology; 125 Gwahak-ro Yuseong-gu Daejeon Korea
| | - Arve Elvebakk
- Tromsø University Museum; University of Tromsø; N-9037 Tromsø Norway
| | - Ok-Sun Kim
- Division of Polar Life Sciences; Korea Polar Research Institute; 26 Songdomirae-ro Yeonsu-gu Incheon 406-840 Korea
| | - Gajin Jeong
- School of Biological Sciences; College of Natural Science; Seoul National University; 599 Gwanak-ro Gwanak-gu Seoul Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences; Korea Polar Research Institute; 26 Songdomirae-ro Yeonsu-gu Incheon 406-840 Korea
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Millanes AM, Truong C, Westberg M, Diederich P, Wedin M. Host switching promotes diversity in host-specialized mycoparasitic fungi: uncoupled evolution in the Biatoropsis-usnea system. Evolution 2014; 68:1576-93. [PMID: 24495034 DOI: 10.1111/evo.12374] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/24/2014] [Indexed: 12/15/2022]
Abstract
Fungal mycoparasitism-fungi parasitizing other fungi-is a common lifestyle in some basal lineages of the basidiomycetes, particularly within the Tremellales. Relatively nonaggressive mycoparasitic fungi of this group are in general highly host specific, suggesting cospeciation as a plausible speciation mode in these associations. Species delimitation in the Tremellales is often challenging because morphological characters are scant. Host specificity is therefore a great aid to discriminate between species but appropriate species delimitation methods that account for actual diversity are needed to identify both specialist and generalist taxa and avoid inflating or underestimating diversity. We use the Biatoropsis-Usnea system to study factors inducing parasite diversification. We employ morphological, ecological, and molecular data-methods including genealogical concordance phylogenetic species recognition (GCPSR) and the general mixed Yule-coalescent (GMYC) model-to assess the diversity of fungi currently assigned to Biatoropsis usnearum. The degree of cospeciation in this association is assessed with two cophylogeny analysis tools (ParaFit and Jane 4.0). Biatoropsis constitutes a species complex formed by at least seven different independent lineages and host switching is a prominent force driving speciation, particularly in host specialists. Combining ITS and nLSU is recommended as barcode system in tremellalean fungi.
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Affiliation(s)
- Ana M Millanes
- Departamento de Biología y Geología, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain.
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68
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Lichenicolous fungi of the genus Abrothallus (Dothideomycetes: Abrothallales ordo nov.) are sister to the predominantly aquatic Janhulales. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0269-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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69
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Dhami MK, Weir BS, Taylor MW, Beggs JR. Diverse honeydew-consuming fungal communities associated with scale insects. PLoS One 2013; 8:e70316. [PMID: 23922978 PMCID: PMC3724830 DOI: 10.1371/journal.pone.0070316] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated with the keystone insect-honeydew systems of New Zealand's native forests and suggests there is much to learn about sooty mould communities.
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Affiliation(s)
- Manpreet K Dhami
- Centre for Microbial Innovation, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Molecular and genetic evidence for a tetrapolar mating system in the basidiomycetous yeast Kwoniella mangrovensis and two novel sibling species. EUKARYOTIC CELL 2013; 12:746-60. [PMID: 23524993 DOI: 10.1128/ec.00065-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Kwoniella mangrovensis has been described as a sexual species with a bipolar mating system. Phylogenetic analysis of multiple genes places this species together with Kwoniella heveanensis in the Kwoniella clade, a sister clade to that containing two pathogenic species of global importance, Cryptococcus neoformans and Cryptococcus gattii, within the Tremellales. Recent studies defining the mating type loci (MAT) of species in these clades showed that, with the exception of C. neoformans and C. gattii, which are bipolar with a single biallelic multigene MAT locus, several other species feature a tetrapolar mating system with two unlinked loci (homeodomain [HD] and pheromone/receptor [P/R] loci). We characterized several strains from the original study describing K. mangrovensis; two MAT regions were amplified and sequenced: the STE20 gene (P/R locus) and the divergently transcribed SXI1 and SXI2 genes (HD locus). We identified five different mating types with different STE20/SXI allele combinations that together with results of mating experiments demonstrate that K. mangrovensis is not bipolar but instead has a tetrapolar mating system. Sequence and gene analysis for a 43-kb segment of the K. mangrovensis type strain MAT locus revealed remarkable synteny with the homologous K. heveanensis MAT P/R region, providing new insights into slower evolution of MAT loci in the Kwoniella compared to the Cryptococcus clade of the Tremellales. The study of additional isolates from plant substrates in Europe and Botswana using a combination of multilocus sequencing with MAT gene analysis revealed two novel sibling species that we name Kwoniella europaea and Kwoniella botswanensis and which appear to also have tetrapolar mating systems.
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Hansen K, Perry BA, Dranginis AW, Pfister DH. A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits. Mol Phylogenet Evol 2013; 67:311-35. [PMID: 23403226 DOI: 10.1016/j.ympev.2013.01.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 01/24/2013] [Accepted: 01/29/2013] [Indexed: 10/27/2022]
Abstract
Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1α (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. l., whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades (- and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts.
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Affiliation(s)
- Karen Hansen
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
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Werth S, Millanes AM, Wedin M, Scheidegger C. Lichenicolous fungi show population subdivision by host species but do not share population history with their hosts. Fungal Biol 2012; 117:71-84. [PMID: 23332835 DOI: 10.1016/j.funbio.2012.11.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/22/2012] [Accepted: 11/24/2012] [Indexed: 11/29/2022]
Abstract
Lichenicolous fungi are a species-rich biological group growing on lichen thalli. Here, we analyze the genetic structure of the lichenicolous basidiomycete Tremella lobariacearum and three host species (Lobaria pulmonaria, Lobaria macaronesica, and Lobaria immixta) in Macaronesia. We used ordination and analysis of molecular variance to investigate the structuring of genetic variation, and a simulation test to investigate whether rDNA haplotypes of T. lobariacearum were significantly associated with host species. To investigate the evolutionary and demographic history of the lichenicolous fungus and its hosts, we used coalescent samplers to generate trees, and Bayesian skyline plots. We found that the hosts were most important in structuring populations of the lichenicolous species. Despite their wide geographic distribution, the same haplotypes of T. lobariacearum consistently associated with a given host species. Our results suggest that the Lobaria hosts create a selective environment for the lichenicolous fungus. Both the pathogen and the host populations exhibited substantial genetic structure. However, evolutionary and demographic histories differed between the parasite and its hosts, as evidenced by different divergence times and tree topologies.
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Affiliation(s)
- Silke Werth
- Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland.
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Valente P, Boekhout T, Landell MF, Crestani J, Pagnocca FC, Sette LD, Passarini MRZ, Rosa CA, Brandão LR, Pimenta RS, Ribeiro JR, Garcia KM, Lee CF, Suh SO, Péter G, Dlauchy D, Fell JW, Scorzetti G, Theelen B, Vainstein MH. Bandoniozyma gen. nov., a genus of fermentative and non-fermentative tremellaceous yeast species. PLoS One 2012; 7:e46060. [PMID: 23056233 PMCID: PMC3467267 DOI: 10.1371/journal.pone.0046060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. METHODOLOGY/PRINCIPAL FINDINGS The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. CONCLUSIONS/SIGNIFICANCE In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364(T) = DBVPG 4489(T)), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20(T) = CBS 12527(T) = ATCC MYA-4876(T)), Bandoniozyma complexa sp. nov. (CBS 11570(T) = ATCC MYA-4603(T) = MA28a(T)), Bandoniozyma fermentans sp. nov. (CBS 12399(T) = NU7M71(T) = BCRC 23267(T)), Bandoniozyma glucofermentans sp. nov. (CBS 10381(T) = NRRL Y-48076(T) = ATCC MYA-4760(T) = BG 02-7-15-015A-1-1(T)), Bandoniozyma tunnelae sp. nov. (CBS 8024(T) = DBVPG 7000(T)), and Bandoniozyma visegradensis sp. nov. (CBS 12505(T) = NRRL Y-48783(T) = NCAIM Y.01952(T)).
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Affiliation(s)
- Patricia Valente
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Rio Grande do Sul, Porto Alegre-RS, Brazil.
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