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

Author
item SCHOCH, CONRAD - National Institutes Of Health (NIH)
item SEIFERT, KEITH - Agri Food - Canada
item HUHNDORF, SABINE - Field Museum Natural History
item ROBERT, VINCENT - Fungal Biodiversity
item SPOUGE, JOHN - National Institutes Of Health (NIH)
item BOLCHACOVA, ELENA - Life Technologies Corporation
item VOIGT, KERSTIN - Leibniz Institute
item CHEN, WEN - Agri Food - Canada
item MILLER, ANDREW - University Of Illinois
item WINGFIELD, MICHAEL - University Of Pretoria
item AIME, M. CATHERINE - Louisiana State University
item AN, KWANG-DEUK - Riken Bioresource Center
item BAI, FENG-YAN - Chinese Academy Of Sciences
item BARRETO, ROBERT - Universidade Federal De Vicosa
item BEGEROW, DOMINIK - University Of Bochum
item BERGERON, MARIE-JOSEE - Canadian Forest Service
item BLACKWELL, MEREDITH - Louisana State University
item BOEKHOUT, TEUN - Fungal Biodiversity
item BOGALE, MESFIN - Brandon University
item BOONYUEN, NATTAWUT - National Center For Genetic Engineering And Biotechnology (BIOTEC)
item BURGAZ, ANA - Complutense University Of Madrid (UCM)
item OLARIAGA, IBAI - The Swedish Museum Of Natural History
item CAI, LEI - Chinese Academy Of Sciences
item CARDINALI, G - University Of Perugia
item CHAVERRI, PRISCILA - University Of Maryland
item COPPINS, BRIAN - Royal Botanical Gardens
item CRESPO, ANA - Complutense University Of Madrid (UCM)
item CROUS, PEDRO - Fungal Biodiversity
item CUBAS, PALOMA - Complutense University Of Madrid (UCM)
item DAMM, ULRIKE - Fungal Biodiversity
item DE BEER, Z. WILHELM - University Of Pretoria
item DE HOOG, G. SYBREN - Fungal Biodiversity
item DEL-PRADO, RUTH - Complutense University Of Madrid (UCM)
item DENTINGER, BRYN - Royal Botanical Gardens
item DUONG, TUAN - University Of Pretoria
item DIVAKAR, PRADEEP - Complutense University Of Madrid (UCM)
item MAHARACHCHIKUMBURA, SAJEEWA - Mae Fah Luan University
item OKANE, IZUMI - National Institute Of Technology And Evaluation (NITE)
item OTTE, JURGEN - Biodiversity And Climate Research Centre (BIK-F)
item EBERHARDT, URSULA - Fungal Biodiversity
item ELSHAHED, MOSTAFA - Oklahoma State University
item FLIEGEROVA, KATERINA - Academy Of Sciences Of The Czech Republic (ASCR)
item RAJA, HUZEFA - University Of North Carolina
item GE, ZAI-WEI - Chinese Academy Of Sciences
item SCHMITT, IMKE - Goethe University
item REDECKER, DIRK - Universite De Bourgogne
item GROENEWALD, JOHANNES - Fungal Biodiversity
item GROENEWALD, MARIZETH - Fungal Biodiversity
item GRUBE, MARTIN - Universitat Graz
item GRYZENHOUT, MARIEKA - University Of The Free State
item GUO, LIANG-DONG - Chinese Academy Of Sciences
item HAGEN, FERRY - Fungal Biodiversity
item HAMBLETON, SARAH - Agri Food - Canada
item HAMELIN, RICHARD - Canadian Forest Service
item HANSEN, KAREN - The Swedish Museum Of Natural History
item HARROLD, PAUL - Royal Botanical Gardens
item HELLER, GREGORY - Louisana State University
item HIRAYAMA, KAZUYUKI - Hirosaki University
item SHEARER, CAROL - University Of Illinois
item HOFFMAN, KERSTIN - Leibniz Institute
item HOFSTETTER, VALERIE - Agroscope
item HOGNABBA, FILIP - University Of Helsinki
item SCHUBLER, ARTHUR - Ludwig-Maximilians University
item SOTOME, KOZUE - Tottori University
item SUH, SUNG-OUI - American Type Culture Collections
item HOUBRAKEN, JOS - Fungal Biodiversity
item HUGHES, KAREN - University Of Tennessee
item HUHTINEN, SEPPO - University Of Turku
item HYDE, KEVIN - Mae Fah Luan University
item JAMES, TIMOTHY - University Of Michigan
item PARK, DUCKHUL - Landcare Research
item JOHNSTON, PETER - Landcare Research
item JONES, E.B. GARETH - National Center For Genetic Engineering And Biotechnology (BIOTEC)
item KELLY, LAURA - Royal Botanical Gardens
item KIRK, PAUL - Commonwealth Agricultural Bureau International (CABI)
item KNAPP, DANIEL - Eotvos Lorand University
item KOLJALG, URMAS - University Of Tartu
item KOVACS, GABOR - Eotvos Lorand University
item Kurtzman, Cletus
item LANDVIK, SARA - Novozymes
item LEAVITT, STEVEN - Field Museum Natural History
item LEVESQUE, C ANDRE - Agri Food - Canada
item LIGGENSTOFFER, AUDRA - Oklahoma State University
item LIIMATAINEN, KARE - University Of Helsinki
item LOMBARD, LORENZO - Fungal Biodiversity
item LUANGSA-ARD, J. JENNIFER - National Center For Genetic Engineering And Biotechnology (BIOTEC)
item LUMBSCH, H. THORSTEN - Field Museum Natural History
item MAGANTI, HARINAD - McMaster University
item SCHINDEL, DAVID - Smithsonian Institute
item TRETTER, ERIC - Boise State University
item WEIB, MICHAEL - University Of Tubingen
item MCTAGGART, ALISTAIR - Louisana State University
item METHVEN, ANDREW - Eastern Illinois University
item MEYER, WIELAND - University Of Sydney
item MONCALVO, JEAN-MARC - University Of Toronto
item MONGKOLSAMRIT, S - National Center For Genetic Engineering And Biotechnology (BIOTEC)
item NAGY, LASZLO - University Of Szeged

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2012
Publication Date: 4/17/2012
Citation: Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Bolchacova, E., Voigt, K., Chen, W., Miller, A.N., Wingfield, M.J., Aime, M., An, K., Bai, F., Barreto, R.W., Begerow, D., Bergeron, M., Blackwell, M., Boekhout, T., Bogale, M., Boonyuen, N., Burgaz, A.R., Olariaga, I., Cai, L., Cardinali, G., Chaverri, P., Coppins, B.J., Crespo, A., Crous, P.W., Cubas, P., Damm, U., De Beer, Z., De Hoog, G., Del-Prado, R., Dentinger, B., Duong, T.S., Divakar, P.K., Maharachchikumbura, S.S., Okane, I., Otte, J., Eberhardt, U., Elshahed, M.S., Fliegerova, K., Raja, H.A., Ge, Z., Schmitt, I., Redecker, D., Groenewald, J.Z., Groenewald, M., Grube, M., Gryzenhout, M., Guo, L., Hagen, F., Hambleton, S., Hamelin, R.C., Hansen, K., Harrold, P., Heller, G., Hirayama, K., Shearer, C., Hoffman, K., Hofstetter, V., Hognabba, F., Schubler, A., Sotome, K., Suh, S., Houbraken, J., Hughes, K., Huhtinen, S., Hyde, K.D., James, T., Park, D., Johnston, P.R., Jones, E., Kelly, L.J., Kirk, P.M., Knapp, D.G., Koljalg, U., Kovacs, G.M., Kurtzman, C.P., Landvik, S., Leavitt, S.D., Levesque, C., Liggenstoffer, A.S., Liimatainen, K., Lombard, L., Luangsa-Ard, J., Lumbsch, H., Maganti, H., Schindel, D., Tretter, E., Weib, M., Mctaggart, A.R., Methven, A.S., Meyer, W., Moncalvo, J., Mongkolsamrit, S., Nagy, L.G., et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences. 109(16):6241-6246.

Interpretive Summary: The Consortium for the Barcode of Life (CBOL) has been striving to have a gene sequence barcode for all of earth’s species. The requirement is a gene sequence of approximately 600 nucleotides that can identify all species, or groups of closely related species, for a particular group of organisms, and the gene sequence must be easy to determine using a fixed set of DNA sequencing primers. The fungi have remained the only major group of organisms for which a barcode gene was yet to be selected. The Fungal Working Group of CBOL tested six different genes that are commonly used to compare fungi for their utility as barcode genes. Following extensive analysis of all major fungal groups, it was decided to use the Internal Transcribed Spacer (ITS) of the cellular ribosomal RNA repeat. Of the genes tested, this sequence is the easiest to determine and often resolves individual species. There is also an extensive database of ITS sequences for many groups of fungi. The benefit to barcoding fungi using a single gene is that species can be quickly identified and as new species are characterized, the ITS sequence will be added to the database. Use of this system will allow rapid identification of human and plant pathogenic fungi as well as those used in pest biocontrol and in biotechnology.

Technical Abstract: Six DNA regions were evaluated in a multi-national, multi-laboratory consortium as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life. 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 regions from the nuclear ribosomal RNA cistron were compared, together with regions of three representative protein coding genes, RPB1, RPB2 and MCM7. Although the protein coding gene regions often had a higher percent of correct identification compared to ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. The nuclear ribosomal small subunit (SSU) has poor species-level resolution in fungi. The internal transcribed spacer (ITS) region has the highest probability of successful identification of the regions within the ribosomal cistron across the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit (LSU), a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the yeasts, but was otherwise slightly inferior to the ITS. ITS will be formally proposed for adoption by the Consortium for the Barcode of Life as the primary fungal barcode marker, with the possibility that supplementary barcodes may be proposed for particular, narrowly circumscribed taxonomic groups.