Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for <i>Fungi</i>
Conrad L. SchochNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892;Keith A. SeifertBiodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6;Sabine M. HuhndorfDepartment of Botany, The Field Museum, Chicago, IL 60605; andVincent RobertCentraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW), 3508 AD, Utrecht, The NetherlandsJohn L. SpougeNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892;C. André LévesqueBiodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6;Wen ChenBiodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6;Elena BolchacovaKerstin VoigtJena Microbial Resource Collection, Institute of Microbiology, University of Jena & Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11 a, 07745 Jena, GermanyP.W. CrousCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsAndrew N. MillerUniversity of Illinois, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL 61820Michael J. WingfieldDepartment of Microbiology and Plant Pathology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South AfricaM. Catherine AimeLouisiana State University Agricultural Center, Department of Plant Pathology and Crop Physiology, Baton Rouge, LA 70803Kwang-Deuk AnJapan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, JapanFeng‐Yan BaiState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Bei-Chen-Xi Road, Chaoyang District, Beijing, 100101, ChinaRobert W. BarretoDepartamento de Fitopatologia, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, BrazilDominik BegerowRuhr-Universität Bochum, Geobotanik ND03/174, Universitätstr. 150, 44801 Bochum, GermanyMarie‐Josée BergeronLaurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 du PEPS, PO Box 10380, Stn. Sainte-Foy, Québec G1V 4C, Canada, 7Meredith BlackwellDepartment of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803Teun BoekhoutCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsMesfin BogaleDepartment of Biology, Brandon University, Brandon, Manitoba R7A 6A9, CanadaNattawut BoonyuenNational Center for Genetic Engineering and Biotechnology (BIOTEC),113 Paholyothin Road, Pathum Thani 12120, ThailandAna Rosa BurgazDepartamento de Biología Vegetal I, Facultad de Biología, Universidad Complutense de Madrid, Madrid 28040, SpainBart BuyckMuséum National d’Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, FranceLei CaiState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Bei-Chen-Xi Road, Chaoyang District, Beijing, 100101, ChinaQing CaiKey Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaGianluigi CardinaliDipartimento Biologia Applicata- Microbiologia, Università degli Studi di Perugia, Perugia, ItalyPriscila ChaverríUniversity of Maryland, Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, College Park, MD 20742B. J. CoppinsRoyal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UKAna CrespoDepartamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, SpainPilar CubasDepartamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, SpainCraig CummingsUlrike DammCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsZ. Wilhelm de BeerDepartment of Microbiology and Plant Pathology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South AfricaSybren de HoogCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsRuth Del‐PradoDepartamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, SpainBryn T. M. DentingerDepartment of Natural History, Royal Ontario Museum, and Department of Ecology and Evolutionary Biology, University of Toronto, 100 Queen's Park, Toronto, Ontario, M5S 2C6, CanadaJavier Diéguez‐UribeondoReal Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, SpainPradeep K. DivakarDepartamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, SpainBrian DouglasInstitute of Biological, Environmental and Rural Sciences, Prifysgol Aberystwyth, Aberystwyth, Ceredigion Wales SY23 3DD, UKMargarita DueñasReal Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, SpainTuan A. DuongDepartment of Genetics, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South AfricaUrsula EberhardtCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsJoan E. EdwardsInstitute of Biological, Environmental and Rural Sciences, Prifysgol Aberystwyth, Aberystwyth, Ceredigion Wales SY23 3DD, UKMostafa S. ElshahedDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074K. FliegerováInstitute of Animal Physiology and Genetics, Czech Academy of Sciences, v.v.i., Prague, Czech RepublicManohar R. FurtadoMiguel A. Garcı́aReal Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, SpainZai-Wei GeDipartimento Biologia Applicata- Microbiologia, Università degli Studi di Perugia, Perugia, ItalyGareth GriffithInstitute of Biological, Environmental and Rural Sciences, Prifysgol Aberystwyth, Aberystwyth, Ceredigion Wales SY23 3DD, UKKate GriffithsRoyal Botanic Gardens Melbourne, Birdwood Avenue, South Yarra, VIC 3141, AustraliaJ.Z. GroenewaldCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsMarizeth GroenewaldCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsMartín GrubeInstitut für Pflanzenwissenschaften, Karl-Franzens-Universität Graz, Holteigasse 6, 8010 Graz, AustriaMarieka GryzenhoutDepartment of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South AfricaLiang‐Dong GuoState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Bei-Chen-Xi Road, Chaoyang District, Beijing, 100101, ChinaFerry HagenCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsSarah HambletonRichard C. HamelinLaurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 du PEPS, PO Box 10380, Stn. Sainte-Foy, Québec G1V 4C, Canada, 7Karen HansenDepartment of Cryptogamic Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, SwedenPaul HarroldRoyal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UKGregory HellerLouisiana State University Agricultural Center, Department of Plant Pathology and Crop Physiology, Baton Rouge, LA 70803Cesar S. HerreraUniversity of Maryland, Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, College Park, MD 20742Kazuyuki HirayamaFaculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, JapanYuuri HirookaUniversity of Maryland, Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, College Park, MD 20742Hsiao-Man HoDepartment of Science Education, National Taipei University of Education, Taipei 10642, TaiwanKerstin HoffmannJena Microbial Resource Collection, Institute of Microbiology, University of Jena & Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11 a, 07745 Jena, GermanyValérie HofstetterAgroscope Changins-Wädenswil Research Station ACW, Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, CP 1012, CH-1260 Nyon, SwitzerlandFilip HögnabbaBotanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, FinlandPeter M. HollingsworthRoyal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UKSeung‐Beom HongKorean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, 441-707, KoreaKentaro HosakaNational Museum of Nature and Science, Tsukuba, JapanJos HoubrakenCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsKaren W. HughesEcology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920Seppo HuhtinenHerbarium, University of Turku, FI-20014 University of Turku, FinlandKevin D. HydeBotany and Microbiology Department, College of Science, King Saud University, P.O. Box: 2455, Riyadh 1145, Saudi ArabiaTimothy Y. JamesDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109Eric M. JohnsonBoise State University, Department of Biological Sciences, 1910 University Dr., Boise, ID 83725Joan E. JohnsonInstitute of Biological, Environmental and Rural Sciences, Prifysgol Aberystwyth, Aberystwyth, Ceredigion Wales SY23 3DD, UKPeter R. JohnstonLandcare Research, Private Bag 92170, Auckland 1142, New ZealandE. B. Gareth JonesNational Center for Genetic Engineering and Biotechnology (BIOTEC),113 Paholyothin Road, Pathum Thani 12120, ThailandLaura J. KellyJodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UKPaul M. KirkCABI-UK, Bakeham Lane, Egham, Surrey TW20 9TY, UKDániel G. KnappEötvös Loránd University, Institute of Biology, Department of Plant Anatomy, Pázmány Péter sétány 1/c, 1117 Budapest, HungaryUrmas KõljalgInstitute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu 51005, EstoniaGábor M. KovácsEötvös Loránd University, Institute of Biology, Department of Plant Anatomy, Pázmány Péter sétány 1/c, 1117 Budapest, HungaryCletus P. KurtzmanNational Center for Agricultural Utilization Research, ARS, USDA, 1815 N. University St, Peoria, ILSara LandvikFungal Screening, Novozymes A/S, Krogshoejvej 36, DK-2880 Bagsvaerd, DenmarkSteven D. LeavittDepartment of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605Audra S. LiggenstofferDepartment of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74074Kare LiimatainenUniversity of Helsinki, Plant Biology, Department of Biosciences, P.O. Box 65, 00014, FinlandLorenzo LombardCentraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The NetherlandsJanet Jennifer Luangsa-ardNational Center for Genetic Engineering and Biotechnology (BIOTEC),113 Paholyothin Road, Pathum Thani 12120, ThailandH. Thorsten LumbschDepartment of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605Harinad B. MagantiDepartment of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, CanadaSajeewa S. N. MaharachchikumburaMae Fah Luang University, 57100 Chiang Rai, ThailandMaría P. MartínReal Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, SpainTom W. MayRoyal Botanic Gardens Melbourne, Birdwood Avenue, South Yarra, VIC 3141, AustraliaAlistair R. McTaggartLouisiana State University Agricultural Center, Department of Plant Pathology and Crop Physiology, Baton Rouge, LA 70803Andrew S. MethvenDeppartment of Biology, Eastern Illinois University, Charleston, IL 61920
2012en
ABI
Аннотация
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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