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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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Heilmann-Clausen J, Christensen M, Frøslev T, Kjøller R. Taxonomy of Tricholoma in northern Europe based on ITS sequence data and morphological characters. PERSOONIA 2017; 38:38-57. [PMID: 29151626 PMCID: PMC5645187 DOI: 10.3767/003158517x693174] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/12/2016] [Indexed: 01/05/2023]
Abstract
Based on molecular and morphological data we investigated the taxonomy and phylogeny of the ectomycorrhizal genus Tricholoma in northern Europe. Our phylogenetic tree confirmed the presence of at least 72 well circumscribed species within the region. Of these, three species, viz. T. boreosulphurescens, T. bryogenum and T. ilkkae are described as new to science, based on morphological, distributional, ecological and molecular data. Several other terminal branches represent putative cryptic taxa nested within classical species or species groups. Molecular type studies and/or designation of sequenced neotypes are needed in these groups, before the taxonomy can be settled. In general our phylogenetic analysis supported previous suprageneric classification systems, but with some substantial changes. Most notably, T. virgatum and allies were found to belong to sect. Tricholoma rather than sect. Atrosquamosa, while T. focale was found to be clearly nested in sect. Genuina rather than in sect. Caligata. In total, ten sections are accepted, with five species remaining unassigned. The combination of morphological and molecular data showed pileus colour, pileipellis structure, presence of clamp connections and spore size to be rather conservative characters within accepted sections, while the presence of a distinct ring, and especially host selection were highly variable within these.
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Affiliation(s)
- J. Heilmann-Clausen
- University of Copenhagen, Natural History Museum of Denmark, Center for Macroecology, Evolution and Climate, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | | | - T.G. Frøslev
- University of Copenhagen, Natural History Museum of Denmark, Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - R. Kjøller
- University of Copenhagen, Institute of Biology, Section of Terrestrial Ecology, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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Feau N, Vialle A, Allaire M, Maier W, Hamelin RC. DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus. Mycologia 2017; 103:1250-66. [DOI: 10.3852/10-426] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nicolas Feau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P.O. Box 10380, Québec, QC, G1V 4C7 Canada
| | - Agathe Vialle
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P.O. Box 10380, Québec, QC, G1V 4C7 Canada; Centre d’étude de la forêt, Université Laval, Québec, QC, G1K 7P4 Canada
| | - Mathieu Allaire
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P.O. Box 10380, Québec, QC, G1V 4C7 Canada
| | - Wolfgang Maier
- Ruhr-Universität Bochum, Biodiversität und Evolution der Pflanzen, Geobotanik, Universitätsstraße 150, 44801 Bochum, Germany
| | - Richard C. Hamelin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P.O. Box 10380, Québec, QC, G1V 4C7 Canada, and Department of Forest Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4 Canada
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Molecular screening of xerophilic Aspergillus strains producing mycophenolic acid. Fungal Biol 2016; 121:103-111. [PMID: 28089042 DOI: 10.1016/j.funbio.2016.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/18/2016] [Accepted: 10/19/2016] [Indexed: 11/24/2022]
Abstract
Mycophenolic acid (MPA) is the fungal secondary metabolite displaying several biological properties. Up to now, screening of fungal strains producing MPA has mainly been the result of the search of this molecule in their culture medium by chemical methods. Here we developed a molecular approach by targeting the expression level of the MpaC gene encoding the polyketide synthase, one of the key enzymes involved in the MPA synthesis. Thirty xerophilic Aspergillus strains were identified using the RNA polymerase II subunit and the β-tubulin genes. Seven Aspergillus species were evidenced. The expression level of the MpaC gene was quantified and compared to the MPA production rate. Only Aspergillus pseudoglaucus and all the eight strains of this species produced MPA. While the MpaC gene was not expressed or weakly expressed in the MPA non-producing strains, all the A. pseudoglaucus strains presented a high level of expression of this gene. The highest expression level of the MpaC gene among the MPA non-producing strains was significantly lower than the lowest expression level of this gene in the MPA producing strains. To our knowledge, this is the first study that demonstrates the effectiveness of molecular approach for the screening of MPA-producing species.
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Dulla EL, Kathera C, Gurijala HK, Mallakuntla TR, Srinivasan P, Prasad V, Mopati RD, Jasti PK. Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J Mycol Med 2016; 26:291-297. [PMID: 27402509 DOI: 10.1016/j.mycmed.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/22/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022]
Abstract
Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification.
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Affiliation(s)
- E L Dulla
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - C Kathera
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - H K Gurijala
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India; Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - T R Mallakuntla
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P Srinivasan
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - V Prasad
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - R D Mopati
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P K Jasti
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India.
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Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 2014; 9:e93560. [PMID: 24714189 PMCID: PMC3979922 DOI: 10.1371/journal.pone.0093560] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/07/2014] [Indexed: 12/27/2022] Open
Abstract
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
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Zara G, Ciani M, Domizio P, Zara S, Budroni M, Carboni A, Mannazzu I. A culture-independent PCR-based method for the detection of Lachancea thermotolerans in wine. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0647-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Chen WM, Chai HM, Zhou HM, Tian GT, Li SH, Zhao YC. Phylogenetic analysis of the Agrocybe aegerita multispecies complex in Southwest China inferred from ITS and mtSSU rDNA sequences and mating tests. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0437-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Yoon H, You YH, Woo JR, Park YJ, Kong WS, Lee BM, Kim JG. The mitochondrial genome of the white-rot fungus Flammulina velutipes. J GEN APPL MICROBIOL 2012; 58:331-7. [DOI: 10.2323/jgam.58.331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Prospects of molecular markers in Fusarium species diversity. Appl Microbiol Biotechnol 2011; 90:1625-39. [DOI: 10.1007/s00253-011-3209-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/17/2011] [Accepted: 02/17/2011] [Indexed: 11/26/2022]
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Moreau PA, Rochet J, Richard F, Chassagne F, Manzi S, Gardes M. Taxonomy ofAlnus-Associated Hypogeous Species ofAlpovaandMelanogaster(Basidiomycota, Paxillaceae) in Europe. CRYPTOGAMIE MYCOL 2011. [DOI: 10.7872/crym.v32.iss1.2012.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rochet J, Moreau PA, Manzi S, Gardes M. Comparative phylogenies and host specialization in the alder ectomycorrhizal fungi Alnicola, Alpova and Lactarius (Basidiomycota) in Europe. BMC Evol Biol 2011; 11:40. [PMID: 21306639 PMCID: PMC3045908 DOI: 10.1186/1471-2148-11-40] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/09/2011] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Mycorrhizal fungi form intimate associations with their host plants that constitute their carbon resource and habitat. Alnus spp. (Betulaceae) are known to host an exceptional species-poor and specialized ectomycorrhizal (ECM) fungal community compared to other tree species, but the host-specificity pattern and its significance in terms of fungal diversification and speciation remain poorly documented. The degree of parallel speciation, host switching, and patterns of biogeography were explored in the historical associations between alders and three ECM taxa of Basidiomycetes: Alnicola (Agaricales), Alpova (Boletales), and Lactarius (Russulales). The aim was to develop an evolutionary framework on host specificity and diversification of Basidiomycetes in this highly specialized plant-fungus symbiosis. RESULTS Sporocarps of Alnicola (220), Lactarius (61) and Alpova (29) were collected from stands of the four European alder species (A. alnobetula including the endemic subsp. suaveolens in Corsica, A. cordata, A. glutinosa, A. incana) in Western Europe (mainly in France and Austria), from 1995 to 2009. Specimens were morphologically identified to the species level. From these, 402 sequences of four DNA regions (ITS, rpb2, gpd, and the V9 domain of the mit-SSU rDNA) were successfully obtained and analyzed in addition with 89 sequences available in GenBank and UNITE databases. Phylogenetic analyses were conducted on all sequence data sets (individual and combined) using maximum likelihood reconstruction and Bayesian inference. Fungal phylogenies are compared and discussed in relation to the host, with a focus on species boundaries by associating taxonomic, systematic and molecular information. CONCLUSIONS Patterns of host specificity and phylogenies of Alnicola and Lactarius suggest coevolution as a basal factor of speciation in relation with the subgeneric diversification of Alnus, possibly due to the very selective pressure of the host. A second element of the historical associations between Alnus and its fungal symbionts is a host-dependent speciation (radiation without host change), here observed in Alnicola and Alpova in relation with Alnus subgen. Alnus. Finally host shifts from Alnus subgen. Alnus to A. alnobetula are found in most lineages of Alnicola (at least four times), Alpova (twice) and Lactarius (once), but they do not represent such a common event as could be expected by geographic proximity of trees from the two subgenera. However, active or very recent host extensions clearly occurred in Corsica, where some fungi usually associated with Alnus glutinosa on mainland Europe locally extend there to A. alnobetula subsp. suaveolens without significant genetic or morphological deviation.
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Affiliation(s)
- Juliette Rochet
- Université de Toulouse, UPS, UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, 31062 Toulouse Cedex 4, France
- CNRS, UMR 5174 EDB, 31062 Toulouse Cedex 4, France
| | - Pierre-Arthur Moreau
- Laboratoire de Botanique, Faculté des Sciences pharmaceutiques et biologiques, Univ Lille Nord de France, 59006 Lille Cedex, France
| | - Sophie Manzi
- Université de Toulouse, UPS, UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, 31062 Toulouse Cedex 4, France
- CNRS, UMR 5174 EDB, 31062 Toulouse Cedex 4, France
| | - Monique Gardes
- Université de Toulouse, UPS, UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, 31062 Toulouse Cedex 4, France
- CNRS, UMR 5174 EDB, 31062 Toulouse Cedex 4, France
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Jargeat P, Martos F, Carriconde F, Gryta H, Moreau PA, Gardes M. Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota). Mol Ecol 2010; 19:5216-30. [PMID: 21044190 DOI: 10.1111/j.1365-294x.2010.04863.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.
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Affiliation(s)
- Patricia Jargeat
- Université de Toulouse, UPS, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique); 118 route de Narbonne, F-31062 Toulouse, France.
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Molitor C, Inthavong B, Sage L, Geremia RA, Mouhamadou B. Potentiality of thecox1â gene in the taxonomic resolution of soil fungi. FEMS Microbiol Lett 2010; 302:76-84. [DOI: 10.1111/j.1574-6968.2009.01839.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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