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Li T, Mao N, Fu H, Zhang Y, Fan L. Five New Species of the Genus Hymenogaster (Hymenogastraceae, Agaricales) from Northern China. J Fungi (Basel) 2024; 10:272. [PMID: 38667943 PMCID: PMC11051317 DOI: 10.3390/jof10040272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, five new species from China, Hymenogaster latisporus, H. minisporus, H. papilliformis, H. perisporius, and H. variabilis, are described and illustrated based on morphological and molecular evidence. Hymenogaster latisporus was distinguished from other species of the genus by the subglobose, broad ellipsoidal, ovoid basidiospores (average = 13.7 μm × 11.6 μm) with sparse verrucose and ridge-like ornamentation (1-1.2 μm high); H. minisporus by the ellipsoidal to broadly ellipsoidal and small basidiospores (average = 11.7 μm × 9.5 μm); H. papilliformis was characterized by the whitish to cream-colored basidiomes, and broadly fusiform to citriform basidiospores with a pronounced apex (2-3 μm, occasionally up to 4 μm high), papillary, distinct warts and ridges, and pronounced appendix (2-3 μm long); H. perisporius by the dirty white to pale yellow basidiomes, broad ellipsoidal to ellipsoidal, and yellow-brown to dark-brown basidiospores with warts and gelatinous perisporium; H. variabilis by the peridium with significant changes in thickness (167-351 μm), and broad ellipsoidal to subglobose basidiospores ornamented with sparse warts and ridges. An ITS/LSU-based phylogenetic analysis supported the erection of the five new species. A key for Hymenogaster species from northern China is provided.
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Affiliation(s)
- Ting Li
- Department of Life Sciences, National Natural History Museum of China, Tianqiaonandajie 126, Beijing 100050, China;
| | - Ning Mao
- College of Life Science, Capital Normal University, Xisanhuanbeilu 105, Beijing 100048, China; (N.M.); (H.F.); (Y.Z.)
| | - Haoyu Fu
- College of Life Science, Capital Normal University, Xisanhuanbeilu 105, Beijing 100048, China; (N.M.); (H.F.); (Y.Z.)
| | - Yuxin Zhang
- College of Life Science, Capital Normal University, Xisanhuanbeilu 105, Beijing 100048, China; (N.M.); (H.F.); (Y.Z.)
| | - Li Fan
- College of Life Science, Capital Normal University, Xisanhuanbeilu 105, Beijing 100048, China; (N.M.); (H.F.); (Y.Z.)
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2
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Cervantes CR, Montes JR, Rosas U, Arias S. Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae). Mol Phylogenet Evol 2023; 187:107891. [PMID: 37517507 DOI: 10.1016/j.ympev.2023.107891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/15/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.
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Affiliation(s)
- Cristian R Cervantes
- Unidad de Síntesis en Sistemática y Evolución, Instituto de Biología, Circuito Exterior s.n., Ciudad Universitaria, Ciudad de México 04510, México; Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México.
| | - José-Rubén Montes
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
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3
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Hurdeal VG, Longcore JE, Gareth Jones EB, Rabern Simmons D, Hyde KD, Gentekaki E. Integrative approach to species delimitation in Rhizophydiales: Novel species of Angulomyces, Gorgonomyces, and Terramyces from northern Thailand. Mol Phylogenet Evol 2023; 180:107706. [PMID: 36657624 DOI: 10.1016/j.ympev.2023.107706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
The Chytridiomycota is a phylum of zoosporic eufungi that inhabit terrestrial, freshwater, and oceanic habitats. Within the phylum, the Rhizophydiales contains several monotypic families theorized to hold a diverse assemblage of fungi yet to be discovered and properly described. Based on morphology alone, many species in this order are difficult or impossible to identify. In this study, we isolated three chytrids from northern Thailand. Phylogenetic analyses placed the isolates in three monotypic genera within Rhizophydiales. Intrageneric genetic distances in the internal transcribed spacer (ITS) ranged between 1.5 and 8.5%. Angulomyces solicola sp. nov. is characterized by larger sporangia, spores, and fewer discharge papilla than A.argentinensis; Gorgonomyces thailandicus sp. nov. has larger zoospores and fewer discharge papillae in culture compared to G. haynaldii; Terramyces chiangraiensis sp. nov. produces larger sporangia than T. subangulosum. We delimited species of Angulomyces, Gorgonomyces and Terramyces using a tripartite approach that employed phylogeny, ITS genetic distances and Poisson tree processes (PTP). Results of these approaches suggest more than one species in each genus. This study contributes to the knowledge of chytrids, an understudied group in Thailand and worldwide.
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Affiliation(s)
- Vedprakash G Hurdeal
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, ME 04469-5722, USA
| | - E B Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - D Rabern Simmons
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Eleni Gentekaki
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.
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Fedosov A, Achaz G, Gontchar A, Puillandre N. MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Mol Ecol Resour 2022; 22:2038-2053. [DOI: 10.1111/1755-0998.13590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Leninsky prospect 33 119071 Moscow Russia
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
- UMR7206 Eco‐Anthropologie Université de Paris‐CNRS‐MNHN Paris
- UMR7241 Centre Interdisciplinaire de Recherche en Biologie Collége de France‐CNRS‐INSERM Paris
| | - Andrey Gontchar
- Molecular Immunology Laboratory Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Samory Mashela street 1 117997 Moscow Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
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Komur P, Chachuła P, Kapusta J, Wierzbowska IA, Rola K, Olejniczak P, Mleczko P. What determines species composition and diversity of hypogeous fungi in the diet of small mammals? A comparison across mammal species, habitat types and seasons in Central European mountains. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Santolamazza-Carbone S, Iglesias-Bernabé L, Sinde-Stompel E, Gallego PP. Ectomycorrhizal fungal community structure in a young orchard of grafted and ungrafted hybrid chestnut saplings. MYCORRHIZA 2021; 31:189-201. [PMID: 33502579 PMCID: PMC7910378 DOI: 10.1007/s00572-020-01015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Ectomycorrhizal (ECM) fungal community of the European chestnut has been poorly investigated, and mostly by sporocarp sampling. We proposed the study of the ECM fungal community of 2-year-old chestnut hybrids Castanea × coudercii (Castanea sativa × Castanea crenata) using molecular approaches. By using the chestnut hybrid clones 111 and 125, we assessed the impact of grafting on ECM colonization rate, species diversity, and fungal community composition. The clone type did not have an impact on the studied variables; however, grafting significantly influenced ECM colonization rate in clone 111. Species diversity and richness did not vary between the experimental groups. Grafted and ungrafted plants of clone 111 had a different ECM fungal species composition. Sequence data from ITS regions of rDNA revealed the presence of 9 orders, 15 families, 19 genera, and 27 species of ECM fungi, most of them generalist, early-stage species. Thirteen new taxa were described in association with chestnuts. The basidiomycetes Agaricales (13 taxa) and Boletales (11 taxa) represented 36% and 31%, of the total sampled ECM fungal taxa, respectively. Scleroderma citrinum, S. areolatum, and S. polyrhizum (Boletales) were found in 86% of the trees and represented 39% of total ECM root tips. The ascomycete Cenococcum geophilum (Mytilinidiales) was found in 80% of the trees but accounted only for 6% of the colonized root tips. These results could help to unveil the impact of grafting on fungal symbionts, improving management of chestnut agro-ecosystems and production of edible fungal species.
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Affiliation(s)
- Serena Santolamazza-Carbone
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain.
- CITACA - Agri-Food Research and Transfer Cluster, University of Vigo, Ourense, Spain.
| | - Laura Iglesias-Bernabé
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain
| | | | - Pedro Pablo Gallego
- Applied Plant & Soil Biology, Plant Biology and Soil Science Department, Biology Faculty, University of Vigo, E-36310, Vigo, Spain
- CITACA - Agri-Food Research and Transfer Cluster, University of Vigo, Ourense, Spain
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7
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Mleczko P, Kozak M, Karpowicz F. New Records of Rare Hypogeous Fungi from Poland (Central Europe). ACTA MYCOLOGICA 2021. [DOI: 10.5586/am.5529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Investigations carried out in recent years have provided new data on the localities of some rare hypogeous fungi in Central Europe. In this study, we present new localities of <em>Leucangium carthusianum</em>, <em>Melanogaster luteus</em>, and <em>Rhizopogon </em><em>melanogastroides</em>, two of which are new for Poland. Sporocarps of <em>L. carthusianum </em>were found in seven new localities in mixed and coniferous forests in the Western Carpathians as well as in Sudetes. In Poland, the species was also recorded in a mixed forest in the Kraków-Częstochowa Upland. Fir, <em>Abies alba</em>, accompanied the fungus in almost all known localities. Three localities of <em>M. luteus </em>were found in the Polish Western and Eastern Carpathians in <em>Alnus incana </em>communities mostly associated with streams. Knowledge of the distribution of this species in Europe is incomplete due to the complicated taxonomic history; nevertheless, it is regarded as rare, despite its wide distribution. One new locality of <em>R. melanogastroides </em>recorded in the Tatra Mts, Western Carpathians, is the fourth known to date. This species is mostly associated with <em>Pinus mugo </em>in high mountain localities (the Alps, the Tatra Mts). In this study, detailed descriptions and illustrations of the macro- and micromorphological features of the species are provided.
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Marjanović Ž, Nawaz A, Stevanović K, Saljnikov E, Maček I, Oehl F, Wubet T. Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests. Microorganisms 2020; 8:E1331. [PMID: 32878332 PMCID: PMC7563819 DOI: 10.3390/microorganisms8091331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T.macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.
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Affiliation(s)
- Žaklina Marjanović
- Institute for Multidisciplinary Research, Belgrade University, Kneza Višeslava 1, 11030 Belgrade, Serbia
| | - Ali Nawaz
- Helmholtz Centre for Environmental Research—UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany;
| | - Katarina Stevanović
- Faculty of Biology, University of Belgrade, Studentski Trg 3, 11000 Belgrade, Serbia;
| | - Elmira Saljnikov
- Soil Science Institute, Teodora Drajzera 7, 11000 Belgrade, Serbia;
| | - Irena Maček
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research—UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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9
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Namulawa VT, Mutiga S, Musimbi F, Akello S, Ngángá F, Kago L, Kyallo M, Harvey J, Ghimire S. Assessment of Fungal Contamination in Fish Feed from the Lake Victoria Basin, Uganda. Toxins (Basel) 2020; 12:toxins12040233. [PMID: 32272644 PMCID: PMC7232351 DOI: 10.3390/toxins12040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/28/2020] [Accepted: 04/02/2020] [Indexed: 12/17/2022] Open
Abstract
The emergence of commercial fish farming has stimulated the establishment of fish feed factories in Uganda. However, no information is available on the safety of the feed, mainly due to lack of mycotoxin testing facilities and weak regulatory systems. A study was carried out to examine fungal colonization and mycotoxin contamination in fish feed samples (n = 147) of different types collected from nine fish farms (n = 81) and seven fish feed factories (n = 66) in the Lake Victoria Basin (LVB). Fungi were isolated in potato dextrose agar, grouped into morphotypes and representative isolates from each morphotype were identified based on the internal transcribed spacer (ITS) region of ribosomal DNA sequences. Aflatoxin B1 (AFB1) and total fumonisin (combinations of B1, B2 and B3; hereinafter named fumonisin) levels in feed samples were determined by enzyme-linked immunosorbent assay (ELISA). A wide range of fungi, including toxigenic Aspergillus flavus and Fusarium verticillioides, were isolated from the fish feed samples. AFB1 was detected in 48% of the factory samples and in 63% of the farm samples, with toxin levels <40 and >400 µg/kg, respectively. Similarly, 31% of the factory samples and 29% of the farm samples had fumonisin contamination ranging between 0.1 and 4.06 mg/kg. Pellets and powder had higher mycotoxin contamination compared to other commercially available fish feed types. This study shows AFB1 as a potential fish feed safety issue in the LVB and suggests a need for more research on mycotoxin residues in fish fillets.
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Affiliation(s)
- Victoria Tibenda Namulawa
- National Agricultural Research Organization, Aquaculture Research & Development Center, P.O. Box 530, Kampala 00256, Uganda;
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
- Correspondence:
| | - Samuel Mutiga
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
- Department of Plant Pathology, University of Arkansas, Fayetteville, NC 72701, USA
| | - Fred Musimbi
- National Agricultural Research Organization, Aquaculture Research & Development Center, P.O. Box 530, Kampala 00256, Uganda;
| | - Sundy Akello
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
| | - Fredrick Ngángá
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
| | - Leah Kago
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
| | - Martina Kyallo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
| | - Jagger Harvey
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
- Feed the Future Innovation Lab for the Reduction of Post-Harvest Loss, and Department of Plant Pathology; Kansas State University, Manhattan, KS 66506, USA
| | - Sita Ghimire
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA–ILRI) Hub, P.O. Box 30709-00100, Nairobi 00100, Kenya; (S.M.); (S.A.); (F.N.); (L.K.); (M.K.); (J.H.); (S.G.)
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Ectomycorrhizal fungi of exotic Carya ovata in the context of surrounding native forests on Central European sites. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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11
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Sousa JO, Suz LM, García MA, Alfredo DS, Conrado LM, Marinho P, Ainsworth AM, Baseia IG, Martín MP. More than one fungus in the pepper pot: Integrative taxonomy unmasks hidden species within Myriostoma coliforme (Geastraceae, Basidiomycota). PLoS One 2017; 12:e0177873. [PMID: 28591150 PMCID: PMC5462367 DOI: 10.1371/journal.pone.0177873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/01/2017] [Indexed: 11/18/2022] Open
Abstract
Since the nineteenth century, Myriostoma has been regarded as a monotypic genus with a widespread distribution in north temperate and subtropical regions. However, on the basis of morphological characters and phylogenetic evidence of DNA sequences of the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), four species are now delimited: M. areolatum comb. & stat. nov., M. calongei sp. nov., M. capillisporum comb. & stat. nov., and M. coliforme. Myriostoma coliforme is typified by selecting a lectotype (iconotype) and a modern sequenced collection as an epitype. The four species can be discriminated by a combination of morphological characters, such as stomatal form, endoperidial surface texture, and basidiospore size and ornamentation.
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Affiliation(s)
- Julieth O. Sousa
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Laura M. Suz
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, England
| | - Miguel A. García
- Department of Biology, University of Toronto, Mississagua, Ontario, Canada
| | - Donis S. Alfredo
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Luana M. Conrado
- Graduação em Ciências Biológicas, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Paulo Marinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Iuri G. Baseia
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - María P. Martín
- Departamento de Micología, Real Jardín Botánico-CSIC, Plaza de Murillo 2, Madrid, Spain
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13
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Sheedy EM, Van de Wouw AP, Howlett BJ, May TW. Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia. Mycologia 2017; 105:547-63. [DOI: 10.3852/12-266] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Tom W. May
- Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, Victoria 3141, Australia
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14
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Wang QM, Yurkov A, Göker M, Lumbsch H, Leavitt S, Groenewald M, Theelen B, Liu XZ, Boekhout T, Bai FY. Phylogenetic classification of yeasts and related taxa within Pucciniomycotina. Stud Mycol 2016; 81:149-89. [PMID: 26951631 PMCID: PMC4777780 DOI: 10.1016/j.simyco.2015.12.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.
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Key Words
- B. aurantiaca (Saito) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. kluyveri-nielii (van der Walt) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. ogasawarensis (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. phyllomatis (van der Walt & Y. Yamada) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. salicina (B.N. Johri & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. syzygii (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. taupoensis (Hamam. & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- B. yamatoana (Nakase, M. Suzuki & M. Itoh) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ballistosporomycessasicola (Nakase & M. Suzuki) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Bannoabischofiae (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozymaarctica (Vishniac & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaarmeniaca (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. diffluens (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. eucalyptica (C.H. Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. falcata (Nakase, M. Itoh & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. foliorum (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. griseoflava (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. lophatheri (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. philyla (van der Walt, Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. retinophila (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. terpenoidalis (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymafushanensis (Nakase, F.L. Lee & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeacycloclastica (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiopsislactophilus (Nakase, M. Itoh, M. Suzuki & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiumportillonense (F. Laich, I. Vaca & R. Chávez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- E. yunnanense (F.Y. Bai, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Erythrobasidiumelongatum (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozymainositophila (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fungi
- GMYC approach
- H. singularis (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoa Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoalignophila (Dill, C. Ramírez & González) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazymalactosa (Hasegawa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyunia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyuniasakaguchii (Sugita, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- K. miscanthi (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. phyllada (van der Walt & Y. Yamada) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. sorbi (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. subrosea (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. thailandica (Fungsin, Hamam. & Nakase ) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. yuccicola (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- Kondoachangbaiensis (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- M. magnisporus (Nakase, Tsuzuki, F.L. Lee, Sugita, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. orientis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. pini (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycesbloemfonteinensis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycetaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Molecular phylogeny
- O. straminea (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- O. yarrowii (Á. Fonseca & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozymasilvestris (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. buffonii (C. Ramírez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. corallina (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. dimennae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. glacialis (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. himalayensis (Shivaji, Bhadra & Rao) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. linderae (Nakase, M. Takash. & Hamam.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. musae (M. Takash., S.O. Suh & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- P. novozealandica (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. producta (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. psychrophila (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. pustula (Buhagiar) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. subbrunnea (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferiapsychrophenolica (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozymacoprosmicola (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phylogenetic rank boundary optimisation
- Pseudobensingtonia F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudobensingtoniaingoldii (Nakase & Itoh.) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudohyphozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pseudohyphozymabogoriensis (Deinema) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pucciniomycotina
- R. azoricus (J.P. Samp. & Gadanho) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. babjevae (Golubev) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. colostri (T. Castelli) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diobovata (S.Y. Newell & I.L. Hunter) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diospyroris (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. dracophylli (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. kratochvilovae (Hamam., Sugiy. & Komag.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. lusitaniae (Á. Fonseca & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. microsporus (Higham ex Fell, Blatt & Statzell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. nylandii (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. odoratus (J.P. Samp., Á. Fonseca & Valério) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. paludigena (Fell & Tallman) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. poonsookiae (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. pyrrosiae (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. rubra (Nakase, Oakada & Sugiy.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. ruineniae (Holzschu, Tredick & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. sphaerocarpa (S.Y. Newell & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. toruloides (I. Banno) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus fluvialis (Fell, Kurtzman, Tallman & J.D. Buck) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodotorulaalborubescens (Derx) Q.M. Wang, F.Y. Bai, Groenew. & Boekhout
- Ruinenia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaclavata (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. oryzae (F.Y. Bai & Y.M. Cai) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. foliicola (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. gracilis (Derx) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. johnsonii (Nyland) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. lamellibrachiae (Nagah., Hamam., Nakase & Horikoshi) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. marina (Phaff, Mrak & Williams) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. meli (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. novozelandica (W.B. Kendr. & X.D. Gong) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. pilati (F.H. Jacob, Faure-Raynaud & Berton) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. pulcherrima (J.E. Wright) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. symmetrica (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. tsugae (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vanillica (J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vermiculata (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiacladiensis (Fell, Statzell & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozymaingeniosa (Di Menna) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia cresolica (Middelhoven & Spaaij) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozymacrocea (Shifrine & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spiculogloeomycetes Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sporobolomyceslongiusculus (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sterigmatomyceshyphaenes (Har. & Pat.) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- Symmetrospora Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporacoprosmae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Taxonomy
- Trigonosporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Trigonosporomyceshylophilus (van der Walt, van der Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozymaferulica (J.P. Samp. & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ustilentylomagraminis (Rodr. Mir. & Diem) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxula Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxulajavanica (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Y. sonckii (Hopsu-Havu, Tunnela & Yarrow) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamycesrosulatus (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yeasts
- Yunzhangia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yunzhangiaauriculariae (Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
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Affiliation(s)
- Q.-M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - A.M. Yurkov
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - M. Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - H.T. Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - S.D. Leavitt
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - M. Groenewald
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Theelen
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - X.-Z. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - T. Boekhout
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Correspondence: T. Boekhout; F.-Y. Bai
| | - F.-Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence: T. Boekhout; F.-Y. Bai
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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: 287] [Impact Index Per Article: 31.9] [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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Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units. Fungal Biol 2014; 118:559-78. [DOI: 10.1016/j.funbio.2013.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 11/18/2022]
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17
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Verkley G, Dukik K, Renfurm R, Göker M, Stielow J. Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota). PERSOONIA 2014; 32:25-51. [PMID: 25264382 PMCID: PMC4150078 DOI: 10.3767/003158514x679191] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 08/08/2013] [Indexed: 11/25/2022]
Abstract
Based on analyses of concatenated internal transcribed spacer regions of the nrDNA operon (ITS), large subunit rDNA (LSU), γ-actin and β-tubulin gene sequences the taxonomy of coniothyrium-like fungi belonging in the family Montagnulaceae, order Pleosporales, was re-assessed. Two new genera are proposed, Alloconiothyrium, to accommodate A. aptrootii sp. nov., and Dendrothyrium for D. longisporum sp. nov. and D. variisporum sp. nov. One new species is described in Paraconiothyrium, viz. Parac. archidendri sp. nov., while two species so far classified in Paraconiothyrium are transferred to Paraphaeosphaeria, viz. Paraph. minitans comb. nov. and Paraph. sporulosa comb. nov. In Paraphaeosphaeria five new species are described based on asexual morphs, viz. Paraph. arecacearum sp. nov., Paraph. neglecta sp. nov., Paraph. sardoa sp. nov., Paraph. verruculosa sp. nov., and Paraph. viridescens sp. nov. Macro- and micromorphological characteristics are fully described.
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Affiliation(s)
- G.J.M. Verkley
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - K. Dukik
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - R. Renfurm
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - M. Göker
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - J.B. Stielow
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
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18
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19
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Cruz D, Suárez JP, Kottke I, Piepenbring M. Cryptic species revealed by molecular phylogenetic analysis of sequences obtained from basidiomata of Tulasnella. Mycologia 2014; 106:708-22. [PMID: 24874921 DOI: 10.3852/12-386] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Delimitation of species and the search for a proper threshold for defining phylogenetic species in fungi are under discussion. In this study, morphological and molecular data are correlated to delimit species of Tulasnella, the most important mycobionts of Orchidaceae, which suffer from poor taxonomy. Resupinate basidiomata of Tulasnella species were collected in Ecuador and Germany, and 11 specimens (seven from Ecuador, four from Germany) were assigned to traditional species concepts by use of morphological keys. The specimens were compared by micro-anatomical examination with 75 specimens of Tulasnella borrowed from fungaria to obtain better insights on variation of characters. Sequences of the ITS region (127) were obtained after cloning from the fresh basidiomata and from pure cultures. Proportional variability of ITS sequences was analyzed within and among the cultures and the specimens designated to different morphospecies. Results suggested an intragenomic variation of less than 2%, an intraspecific variation of up to 4% and an interspecific divergence of more than 9% in Tulasnella. Cryptic species in Tulasnella, mostly from Ecuador, were revealed by phylogenetic analyses with 4% intraspecific divergence as a minimum threshold for delimiting species. Conventional diagnostic morphological characters appeared insufficient for species characterization. Arguments are presented for molecular delimitation of the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. cf. pinicola, T. tomaculum and T. violea.
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Affiliation(s)
- Darío Cruz
- Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, San Cayetano Alto s/n C.P. 11 01 608, Loja, Ecuador
| | - Juan Pablo Suárez
- Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, San Cayetano Alto s/n C.P. 11 01 608, Loja, Ecuador
| | - Ingrid Kottke
- Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, San Cayetano Alto s/n C.P. 11 01 608, Loja, EcuadorInstitute of Evolution and Ecology, Evolutionary Ecology of Plants, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany
| | - Meike Piepenbring
- Institute of Ecology, Evolution and Diversity, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany
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20
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Merényi Z, Varga T, Geml J, Orczán ÁK, Chevalier G, Bratek Z. Phylogeny and phylogeography of the Tuber brumale aggr. MYCORRHIZA 2014; 24 Suppl 1:S101-S113. [PMID: 24604084 DOI: 10.1007/s00572-014-0566-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 02/05/2014] [Indexed: 06/03/2023]
Abstract
The Tuber brumale (winter truffle) is a black truffle reported from most European countries, belonging to the Melanosporum group. Its significance in the economy is ambivalent as the winter truffle has been shown to be a frequent contaminant species in the orchards of the Perigord truffle and occasionally in those of the summer truffle, yet owing to its delicate fragrance, its trade is worthy of note. The phylogeny and phylogeography of economically important truffles are relatively well-explored; however, no thorough research has been published on these aspects of the winter truffle. Therefore, here, we report the first phylogeographic analyses based on samples representing the entire distribution of the species. ITS sequences were used in this survey for haplotype and coalescent analyses, while phylogenetic analyses were based on the ITS, LSU and PKC loci. According to all loci, the samples clustered into two big clades imply the existence of two phylogenetic species. Based on our results, one of these appears to be endemic to the Carpathian Basin. In the other more widespread species, two main phylogeographic groups can be distinguished that show east-west separation with a zone of overlap in the Carpathian Basin, suggesting that they survived the latest glacial period in separate refugia.
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Affiliation(s)
- Zsolt Merényi
- Institute of Biology, Department of Plant Physiology and Molecular Plant Biology, Eötvös Loránd University, Budapest, Hungary
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21
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Salgado-Salazar C, Rossman AY, Chaverri P. Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota). PLoS One 2013; 8:e76737. [PMID: 24204665 PMCID: PMC3799981 DOI: 10.1371/journal.pone.0076737] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/29/2013] [Indexed: 11/29/2022] Open
Abstract
The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.
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Affiliation(s)
- Catalina Salgado-Salazar
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America
| | - Amy Y. Rossman
- Systematic Mycology and Microbiology Laboratory, Agriculture Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, United States of America
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22
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Carstens BC, Pelletier TA, Reid NM, Satler JD. How to fail at species delimitation. Mol Ecol 2013; 22:4369-83. [PMID: 23855767 DOI: 10.1111/mec.12413] [Citation(s) in RCA: 642] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/29/2022]
Abstract
Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293, USA.
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23
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Tsykun T, Rigling D, Prospero S. A new multilocus approach for a reliable DNA-based identification of Armillaria species. Mycologia 2013; 105:1059-76. [PMID: 23449075 DOI: 10.3852/12-209] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this paper we highlight and critically discuss limitations to molecular methods for identification of fungi via the example of the basidiomycete genus Armillaria. We analyzed a total of 144 sequences of three DNA regions commonly used for identifying fungi (ribosomal IGS-1 and ITS regions, translation elongation factor-1 alpha gene) from 48 specimens of six Armillaria species occurring in Europe (A. cepistipes, A. ostoyae, A. gallica, A. borealis, A. mellea, A. tabescens). Species were identified by comparing newly obtained sequences with those from the NCBI database, phylogenetic analyses and PCR-RFLP analyses of the three regions considered. When analyzed separately, no single gene region could unambiguously identify all six Armillaria species because of low interspecific and high intrasequence variability. We therefore developed a multilocus approach, which involves the stepwise use of the three regions. Following this scheme, all six species could be clearly discriminated. Our study suggests that, to improve the reliability of DNA-based techniques for species identification, multiple genes or intergenic regions should be analyzed.
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24
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Makonde HM, Boga HI, Osiemo Z, Mwirichia R, Stielow JB, Göker M, Klenk HP. Diversity of Termitomyces associated with fungus-farming termites assessed by cultural and culture-independent methods. PLoS One 2013; 8:e56464. [PMID: 23437139 PMCID: PMC3577893 DOI: 10.1371/journal.pone.0056464] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/09/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Fungus-cultivating termites make use of an obligate mutualism with fungi from the genus Termitomyces, which are acquired through either vertical transmission via reproductive alates or horizontally transmitted during the formation of new mounds. Termitomyces taxonomy, and thus estimating diversity and host specificity of these fungi, is challenging because fruiting bodies are rarely found. Molecular techniques can be applied but need not necessarily yield the same outcome than morphological identification. METHODOLOGY Culture-dependent and culture-independent methods were used to comprehensively assess host specificity and gut fungal diversity. Termites were identified using mitochondrial cytochrome oxidase II (COII) genes. Twenty-three Termitomyces cultures were isolated from fungal combs. Internal transcribed spacer (ITS) clone libraries were constructed from termite guts. Presence of Termitomyces was confirmed using specific and universal primers. Termitomyces species boundaries were estimated by cross-comparison of macromorphological and sequence features, and ITS clustering parameters accordingly optimized. The overall trends in coverage of Termitomyces diversity and host associations were estimated using Genbank data. RESULTS AND CONCLUSION Results indicate a monoculture of Termitomyces in the guts as well as the isolation sources (fungal combs). However, cases of more than one Termitomyces strains per mound were observed since mounds can contain different termite colonies. The newly found cultures, as well as the clustering analysis of GenBank data indicate that there are on average between one and two host genera per Termitomyces species. Saturation does not appear to have been reached, neither for the total number of known Termitomyces species nor for the number of Termitomyces species per host taxon, nor for the number of known hosts per Termitomyces species. Considering the rarity of Termitomyces fruiting bodies, it is suggested to base the future taxonomy of the group mainly on well-characterized and publicly accessible cultures.
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Affiliation(s)
- Huxley M. Makonde
- Microbiology, Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Hamadi I. Boga
- Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Zipporah Osiemo
- Zoology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Romano Mwirichia
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | - Markus Göker
- Microbiology, Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Hans-Peter Klenk
- Microbiology, Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
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Hoffmannoscypha, a novel genus of brightly coloured, cupulate Pyronemataceae closely related to Tricharina and Geopora. Mycol Prog 2012. [DOI: 10.1007/s11557-012-0875-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Salgado-Salazar C, Rossman A, Samuels GJ, Capdet M, Chaverri P. Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes. Mycologia 2012; 104:1325-50. [PMID: 22778168 DOI: 10.3852/12-055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thelonectria is a recently established genus of common and ubiquitous fungi on woody hosts, previously placed in the genus Neonectria. Thelonectria coronata and T. veuillotiana occur sympatrically in tropical, subtropical and temperate regions. Previous taxonomic studies including T. coronata and T. veuillotiana suggested these fungi could represent species complexes; however, the morphological features used to define species exhibited few differences useful for testing this hypothesis. To assess the status of T. coronata and T. veuillotiana, phylogenetic analyses of six genomic regions were combined with a morphological examination of specimens. A multi-gene phylogeny reconstructed with maximum parsimony, maximum likelihood and Bayesian approaches identified five phylogenetic groups in T. coronata and six in T. veuillotiana. As is common for cryptic species, unequivocal diagnostic morphological characters could not be identified; however, average values of morphological traits correspond to the phylogenetic groups. An increased number of non-synonymous/synonymous substitutions in the β-tubu-lin gene and a decreased or absent production of conidia were detected within the T. coronata complex, possibly indicating the homothallic nature of these isolates. T. coronata and T. veuillotiana and related species are described and illustrated here; a dichotomous key to all species is provided.
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Affiliation(s)
- Catalina Salgado-Salazar
- University of Maryland, Department of Plant Science and Landscape Architecture, College Park, MD 20742, USA.
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Genea mexicana, sp. nov., and Geopora tolucana, sp. nov., new hypogeous Pyronemataceae from Mexico, and the taxonomy of Geopora reevaluated. Mycol Prog 2011. [DOI: 10.1007/s11557-011-0781-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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