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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
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Document Title
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Author
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, Miller AN, Wingfield MJ, Aime MC, An KD, Bai FY, Barreto RW, Begerow D, Bergeron MJ, Blackwell M, Boekhout T, Bogale M, Boonyuen N, Burgaz AR, Buyck B, Cai L, Cai Q, Cardinali G, Chaverri P, Coppins BJ, Crespo A, Cubas P, Cummings C, Damm U, de Beer ZW, de Hoog GS, Del-Prado R, Dentinger B, Dieguez-Uribeondo J, Divakar PK, Douglas B, Duenas M, Duong TA, Eberhardt U, Edwards JE, Elshahed MS, Fliegerova K, Furtado M, Garcia MA, Ge ZW, Griffith GW, Griffiths K, Groenewald JZ, Groenewald M, Grube M, Gryzenhout M, Guo LD, Hagen F, Hambleton S, Hamelin RC, Hansen K, Harrold P, Heller G, Herrera G, Hirayama K, Hirooka Y, Ho HM, Hoffmann K, Hofstetter V, Hognabba F, Hollingsworth PM, Hong SB, Hosaka K, Houbraken J, Hughes K, Huhtinen S, Hyde KD, James T, Johnson EM, Johnson JE, Johnston PR, Jones EB, Kelly LJ, Kirk PM, Knapp DG, Koljalg U, Kovacs GM, Kurtzman CP, Landvik S, Leavitt SD, Liggenstoffer AS, Liimatainen K, Lombard L, Luangsa-Ard JJ, Lumbsch HT, Maganti H, Maharachchikumbura SS, Martin MP, May TW, McTaggart AR, Methven AS, Meyer W, Moncalvo JM, Mongkolsamrit S, Nagy LG, Nilsson RH, Niskanen T, Nyilasi I, Okada G, Okane I, Olariaga I, Otte J, Papp T, Park D, Petkovits T, Pino-Bodas R, Quaedvlieg W, Raja HA, Redecker D, Rintoul TL, Ruibal C, Sarmiento-Ramirez JM, Schmitt I, Schussler A, Shearer C, Sotome K, Stefani FOP, Stenroos S, Stielow B, Stockinger H, Suetrong S, Suh SO, Sung GH, Suzuki M, Tanaka K, Tedersoo L, Telleria MT, Tretter E, Untereiner WA, Urbina H, Vagvolgyi C, Vialle A, Vu TD, Walther G, Wang QM, Wang Y, Weir BS, Weiss M, White MM, Xu J, Yahr R, Yang ZL, Yurkov A, Zamora JC, Zhang N, Zhuang WY, Schindel D
Name from Authors Collection
Scopus Author ID
16319823700
Scopus Author ID
16319823700
Scopus Author ID
16319823700
Affiliations
National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Agriculture & Agri Food Canada; Field Museum of Natural History (Chicago); Thermo Fisher Scientific; Friedrich Schiller University of Jena; Hans Knoll Institute (HKI); Illinois Natural History Survey; University of Illinois System; University of Illinois Urbana-Champaign; University of Pretoria; Louisiana State University System; Louisiana State University; RIKEN; Chinese Academy of Sciences; Universidade Federal de Vicosa; Ruhr University Bochum; Natural Resources Canada; Canadian Forest Service; Louisiana State University System; Louisiana State University; Utrecht University; Utrecht University Medical Center; Brandon University; National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC); Complutense University of Madrid; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Museum National d'Histoire Naturelle (MNHN); UDICE-French Research Universities; Sorbonne Universite; Chinese Academy of Sciences; Kunming Institute of Botany, CAS; University of Perugia; University System of Maryland; University of Maryland College Park; Complutense University of Madrid; Royal Botanic Gardens, Kew; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Real Jardin Botanico de Madrid; Aberystwyth University; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC); Institute of Biological, Environmental, Rural & Sciences (IBERS); University of Pretoria; Oklahoma State University System; Oklahoma State University - Stillwater; Czech Academy of Sciences; Institute of Animal Physiology & Genetics of the Czech Academy of Sciences; University of Graz; University of the Free State; Swedish Museum of Natural History; Hirosaki University; National Taipei University of Education; Swiss Federal Research Station Agroscope; University of Helsinki; Rural Development Administration (RDA), Republic of Korea; National Museum of Nature and Science; University of Tennessee System; University of Tennessee Knoxville; University of Turku; Mae Fah Luang University; King Saud University; University of Michigan System; University of Michigan; Landcare Research - New Zealand; Eotvos Lorand University; University of Tartu; Tartu University Institute of Ecology & Earth Sciences; United States Department of Agriculture (USDA); Novozymes; University of Helsinki; McMaster University; Eastern Illinois University; University of Sydney; Westmead Institute for Medical Research; Royal Ontario Museum; University of Toronto; Szeged University; University of Gothenburg; Senckenberg Biodiversitat & Klima- Forschungszentrum (BiK-F); Senckenberg Gesellschaft fur Naturforschung (SGN); University of North Carolina; University of North Carolina Greensboro; INRAE; Institut Agro; AgroSup Dijon; Universite de Bourgogne; Goethe University Frankfurt; University of Munich; University of Illinois System; University of Illinois Urbana-Champaign; Tottori University; National Institute of Horticultural & Herbal Science (NIHHS), Republic of Korea; Rural Development Administration (RDA), Republic of Korea; University of Tartu; Idaho; Boise State University; Eberhard Karls University of Tubingen; Rutgers State University New Brunswick; Smithsonian Institution; Smithsonian National Museum of Natural History
Type
Article
Source Title
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Year
2012
Volume
109
Issue
16
Page
6241-6246
Open Access
Bronze, Green Published
Publisher
NATL ACAD SCIENCES
DOI
10.1073/pnas.1117018109
Format
Abstract
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.
Keyword
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Alfred P. Sloan Foundation; National Library of Medicine at the National Institutes of Health; Life Technologies Corporation; BBSRC [BBS/E/W/10964A01B] Funding Source: UKRI; Biotechnology and Biological Sciences Research Council [BBS/E/W/10964A01B] Funding Source: researchfish; NATIONAL LIBRARY OF MEDICINE [ZIALM200883] Funding Source: NIH RePORTER; Office Of The Director [0814361] Funding Source: National Science Foundation; Grants-in-Aid for Scientific Research [11J03316] Funding Source: KAKEN
Publication Source
WOS