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Irinyi L, Meyer W. DNA barcoding of human and animal pathogenic fungi: the ISHAM-ITS database. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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202
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Visagie CM, Houbraken J, Frisvad JC, Hong SB, Klaassen CHW, Perrone G, Seifert KA, Varga J, Yaguchi T, Samson RA. Identification and nomenclature of the genus Penicillium. Stud Mycol 2014; 78:343-71. [PMID: 25505353 PMCID: PMC4261876 DOI: 10.1016/j.simyco.2014.09.001] [Citation(s) in RCA: 463] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Penicillium is a diverse genus occurring worldwide and its species play important roles as decomposers of organic materials and cause destructive rots in the food industry where they produce a wide range of mycotoxins. Other species are considered enzyme factories or are common indoor air allergens. Although DNA sequences are essential for robust identification of Penicillium species, there is currently no comprehensive, verified reference database for the genus. To coincide with the move to one fungus one name in the International Code of Nomenclature for algae, fungi and plants, the generic concept of Penicillium was re-defined to accommodate species from other genera, such as Chromocleista, Eladia, Eupenicillium, Torulomyces and Thysanophora, which together comprise a large monophyletic clade. As a result of this, and the many new species described in recent years, it was necessary to update the list of accepted species in Penicillium. The genus currently contains 354 accepted species, including new combinations for Aspergillus crystallinus, A. malodoratus and A. paradoxus, which belong to Penicillium section Paradoxa. To add to the taxonomic value of the list, we also provide information on each accepted species MycoBank number, living ex-type strains and provide GenBank accession numbers to ITS, β-tubulin, calmodulin and RPB2 sequences, thereby supplying a verified set of sequences for each species of the genus. In addition to the nomenclatural list, we recommend a standard working method for species descriptions and identifications to be adopted by laboratories working on this genus.
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Affiliation(s)
- C M Visagie
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - J Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - J C Frisvad
- Department of Systems Biology, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - S-B Hong
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, Korea
| | - C H W Klaassen
- Medical Microbiology & Infectious Diseases, C70 Canisius Wilhelmina Hospital, 532 SZ Nijmegen, The Netherlands
| | - G Perrone
- Institute of Sciences of Food Production, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
| | - K A Seifert
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - J Varga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Közép fasor 52, Hungary
| | - T Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
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203
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Visagie CM, Hirooka Y, Tanney JB, Whitfield E, Mwange K, Meijer M, Amend AS, Seifert KA, Samson RA. Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Stud Mycol 2014; 78:63-139. [PMID: 25492981 PMCID: PMC4255536 DOI: 10.1016/j.simyco.2014.07.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As part of a worldwide survey of the indoor mycobiota, dust was collected from nine countries. Analyses of dust samples included the culture-dependent dilution-to-extinction method and the culture-independent 454-pyrosequencing. Of the 7 904 isolates, 2 717 isolates were identified as belonging to Aspergillus, Penicillium and Talaromyces. The aim of this study was to identify isolates to species level and describe the new species found. Secondly, we wanted to create a reliable reference sequence database to be used for next-generation sequencing projects. Isolates represented 59 Aspergillus species, including eight undescribed species, 49 Penicillium species of which seven were undescribed and 18 Talaromyces species including three described here as new. In total, 568 ITS barcodes were generated, and 391 β-tubulin and 507 calmodulin sequences, which serve as alternative identification markers.
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Affiliation(s)
- C M Visagie
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - Y Hirooka
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - J B Tanney
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - E Whitfield
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - K Mwange
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - M Meijer
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - A S Amend
- Department of Botany, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA
| | - K A Seifert
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
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204
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Hawksworth DL, van den Hoeven-Verweij M. News. IMA Fungus 2014. [DOI: 10.1007/bf03449450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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205
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Epitypification and neotypification: guidelines with appropriate and inappropriate examples. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0315-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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206
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Rampersad SN. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. SPRINGERPLUS 2014; 3:684. [PMID: 25512885 PMCID: PMC4254888 DOI: 10.1186/2193-1801-3-684] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
Abstract
The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of member species which are of quarantine importance is impacted by a number of factors that negatively affect species identification. Structural information of the rRNA marker may be considered to be a conserved marker which can be used as supplementary information for possible species identification. The difficulty in using ITS rDNA sequences for identification lies in the low level of sequence variation at the intra-specific level and the generation of artificially-induced sequence variation due to errors in polymerization of the ITS array during DNA replication. Type and query ITS sequences were subjected to sequence analyses prior to generation of predicted consensus secondary structures, including the pattern of nucleotide polymorphisms and number of indel haplotypes, GC content, and detection of artificially-induced sequence variation. Data pertaining to structure stability, the presence of conserved motifs in secondary structures and mapping of all sequences onto the consensus C. gloeosporioides sensu stricto secondary structure for ITS1, 5.8S and ITS2 markers was then carried out. Motifs that are evolutionarily conserved among eukaryotes were found for all ITS1, 5.8S and ITS2 sequences. The sequences exhibited conserved features typical of functional rRNAs. Generally, polymorphisms occurred within less conserved regions and were seen as bulges, internal and terminal loops or non-canonical G–U base-pairs within regions of the double stranded helices. Importantly, there were also taxonomic motifs and base changes that were unique to specific taxa and which may be used to support intra-specific identification of members of the C. gloeosporioides sensu lato species complex.
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Affiliation(s)
- Sephra N Rampersad
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, West Indies, Trinidad and Tobago
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207
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Abstract
Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species. For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria. The NCBI Taxonomy Database (http://www.ncbi.nlm.nih.gov/taxonomy) now includes annotation of type material that we use to flag sequences from type in GenBank and in Genomes. This has important implications for many NCBI resources, some of which are outlined below.
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Affiliation(s)
- Scott Federhen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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208
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Ariyawansa HA, Tanaka K, Thambugala KM, Phookamsak R, Tian Q, Camporesi E, Hongsanan S, Monkai J, Wanasinghe DN, Mapook A, Chukeatirote E, Kang JC, Xu JC, McKenzie EHC, Jones EBG, Hyde KD. A molecular phylogenetic reappraisal of the Didymosphaeriaceae (= Montagnulaceae). FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0305-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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209
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210
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Crous PW, Giraldo A, Hawksworth DL, Robert V, Kirk PM, Guarro J, Robbertse B, Schoch CL, Damm U, Trakunyingcharoen T, Groenewald JZ. The Genera of Fungi: fixing the application of type species of generic names. IMA Fungus 2014; 5:141-60. [PMID: 25083414 PMCID: PMC4107892 DOI: 10.5598/imafungus.2014.05.01.14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/06/2014] [Indexed: 10/26/2022] Open
Abstract
To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the "Without-prejudice List of Protected Generic Names of Fungi" (see IMA Fungus 4(2): 381-443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.
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Affiliation(s)
- Pedro W Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; ; Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ; Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alejandra Giraldo
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - David L Hawksworth
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, Madrid 28040, Spain ; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK ; Mycology Section, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK
| | - Vincent Robert
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Paul M Kirk
- Mycology Section, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK ; State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut and IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Tarragona, Spain
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Ulrike Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Thippawan Trakunyingcharoen
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Johannes Z Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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211
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Samson R, Visagie C, Houbraken J, Hong SB, Hubka V, Klaassen C, Perrone G, Seifert K, Susca A, Tanney J, Varga J, Kocsubé S, Szigeti G, Yaguchi T, Frisvad J. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud Mycol 2014; 78:141-73. [PMID: 25492982 PMCID: PMC4260807 DOI: 10.1016/j.simyco.2014.07.004] [Citation(s) in RCA: 645] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aspergillus comprises a diverse group of species based on morphological, physiological and phylogenetic characters, which significantly impact biotechnology, food production, indoor environments and human health. Aspergillus was traditionally associated with nine teleomorph genera, but phylogenetic data suggest that together with genera such as Polypaecilum, Phialosimplex, Dichotomomyces and Cristaspora, Aspergillus forms a monophyletic clade closely related to Penicillium. Changes in the International Code of Nomenclature for algae, fungi and plants resulted in the move to one name per species, meaning that a decision had to be made whether to keep Aspergillus as one big genus or to split it into several smaller genera. The International Commission of Penicillium and Aspergillus decided to keep Aspergillus instead of using smaller genera. In this paper, we present the arguments for this decision. We introduce new combinations for accepted species presently lacking an Aspergillus name and provide an updated accepted species list for the genus, now containing 339 species. To add to the scientific value of the list, we include information about living ex-type culture collection numbers and GenBank accession numbers for available representative ITS, calmodulin, β-tubulin and RPB2 sequences. In addition, we recommend a standard working technique for Aspergillus and propose calmodulin as a secondary identification marker.
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Affiliation(s)
- R.A. Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - C.M. Visagie
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - J. Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - S.-B. Hong
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, South Korea
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - C.H.W. Klaassen
- Medical Microbiology & Infectious Diseases, C70 Canisius Wilhelmina Hospital, 532 SZ Nijmegen, The Netherlands
| | - G. Perrone
- Institute of Sciences of Food Production National Research Council, 70126 Bari, Italy
| | - K.A. Seifert
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - A. Susca
- Institute of Sciences of Food Production National Research Council, 70126 Bari, Italy
| | - J.B. Tanney
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - J. Varga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - S. Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - G. Szigeti
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8673, Japan
| | - J.C. Frisvad
- Department of Systems Biology, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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