Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Conrad L. Schoch, Keith A. Seifert, Sabine Huhndorf, Vincent Robert, John L. Spouge, C. André Levesque, Wen Chen, Elena Bolchacova, Kerstin Voigt, Pedro W. Crous, Andrew N. Miller, Michael J. Wingfield, M. Catherine Aime, Kwang Deuk An, Feng Yan Bai, Robert W. Barreto, Dominik Begerow, Marie Josée Bergeron, Meredith Blackwell, Teun BoekhoutMesfin Bogale, Nattawut Boonyuen, Ana R. Burgaz, Bart Buyck, Lei Cai, Qing Cai, G. Cardinali, Priscila Chaverri, Brian J. Coppins, Ana Crespo, Paloma Cubas, Craig Cummings, Ulrike Damm, Z. Wilhelm de Beer, G. Sybren de Hoog, Ruth Del-Prado, Bryn Dentinger, Javier Diéguez-Uribeondo, Pradeep K. Divakar, Brian Douglas, Margarita Dueñas, Tuan A. Duong, Ursula Eberhardt, Joan E. Edwards, Mostafa S. Elshahed, Katerina Fliegerova, Manohar Furtado, Miguel A. García, Zai Wei Ge, Gareth W. Griffith, K. Griffiths, Johannes Z. Groenewald, Marizeth Groenewald, Martin Grube, Marieka Gryzenhout, Liang Dong Guo, Ferry Hagen, Sarah Hambleton, Richard C. Hamelin, Karen Hansen, Paul Harrold, Gregory Heller, Cesar Herrera, Kazuyuki Hirayama, Yuuri Hirooka, Hsiao Man Ho, Kerstin Hoffmann, Valérie Hofstetter, Filip Högnabba, Peter M. Hollingsworth, Seung Beom Hong, Kentaro Hosaka, Jos Houbraken, Karen Hughes, Seppo Huhtinen, Kevin D. Hyde, Timothy James, Eric M. Johnson, Joan E. Johnson, Peter R. Johnston, E. B.Gareth Jones, Laura J. Kelly, Paul M. Kirk, Dániel G. Knapp, Urmas Kõljalg, Gábor M. Kovács, Cletus P. Kurtzman, Sara Landvik, Steven D. Leavitt, Audra S. Liggenstoffer, Kare Liimatainen, Lorenzo Lombard, J. Jennifer Luangsa-ard, H. Thorsten Lumbsch, Harinad Maganti, Sajeewa S.N. Maharachchikumbura, María P. Martin, Tom W. May, Alistair R. McTaggart, Andrew S. Methven, Wiel Meyer, Jean Marc Moncalvo, Suchada Mongkolsamrit, László G. Nagy, R. Henrik Nilsson, Tuula Niskanen, Ildikó Nyilasi, Gen Okada, Izumi Okane, Ibai Olariaga, Jürgen Otte, Tamás Papp, Duckchul Park, Tamás Petkovits, Raquel Pino-Bodas, William Quaedvlieg, Huzefa A. Raja, Dirk Redecker, Tara L. Rintoul, Constantino Ruibal, Jullie M. Sarmiento-Ramírez, Imke Schmitt, Arthur Schüßler, Carol Shearer, Kozue Sotome, Franck O.P. Stefani, Soili Stenroos, Benjamin Stielow, Herbert Stockinger, Satinee Suetrong, Sung Oui Suh, Gi Ho Sung, Motofumi Suzuki, Kazuaki Tanaka, Leho Tedersoo, M. Teresa Telleria, Eric Tretter, Wendy A. Untereiner, Hector Urbina, Csaba Vágvölgyi, Agathe Vialle, Thuy Duong Vu, Grit Walther, Qi Ming Wang, Yan Wang, Bevan S. Weir, Michael Weiß, Merlin M. White, Jianping Xu, Rebecca Yahr, Zhu L. Yang, Andrey Yurkov, Juan Carlos Zamora, Ning Zhang, Wen Ying Zhuang, David Schindel

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)6241-6246
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number16
DOIs
StatePublished - Apr 17 2012

Keywords

  • DNA barcoding
  • Fungal biodiversity

ASJC Scopus subject areas

  • General

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