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United States Department of Agriculture

Agricultural Research Service


Location: Mycotoxin Prevention and Applied Microbiology Research

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

item Schoch, Conrad
item Seifert, Keith
item Huhndorf, Sabine
item Robert, Vincent
item Spouge, John
item Bolchacova, Elena
item Voigt, Kerstin
item Chen, Wen
item Miller, Andrew
item Wingfield, Michael
item Aime, M. Catherine
item An, Kwang-deuk
item Bai, Feng-yan
item Barreto, Robert
item Begerow, Dominik
item Bergeron, Marie-josee
item Blackwell, Meredith
item Boekhout, Teun
item Bogale, Mesfin
item Boonyuen, Nattawut
item Burgaz, Ana
item Olariaga, Ibai
item Cai, Lei
item Cardinali, G
item Chaverri, Priscila
item Coppins, Brian
item Crespo, Ana
item Crous, Pedro
item Cubas, Paloma
item Damm, Ulrike
item De Beer, Z. Wilhelm
item De Hoog, G. Sybren
item Del-prado, Ruth
item Dentinger, Bryn
item Duong, Tuan
item Divakar, Pradeep
item Maharachchikumbura, Sajeewa
item Okane, Izumi
item Otte, Jurgen
item Eberhardt, Ursula
item Elshahed, Mostafa
item Fliegerova, Katerina
item Raja, Huzefa
item Ge, Zai-wei
item Schmitt, Imke
item Redecker, Dirk
item Groenewald, Johannes
item Groenewald, Marizeth
item Grube, Martin
item Gryzenhout, Marieka
item Guo, Liang-dong
item Hagen, Ferry
item Hambleton, Sarah
item Hamelin, Richard
item Hansen, Karen
item Harrold, Paul
item Heller, Gregory
item Hirayama, Kazuyuki
item Shearer, Carol
item Hoffman, Kerstin
item Hofstetter, Valerie
item Hognabba, Filip
item Schubler, Arthur
item Sotome, Kozue
item Suh, Sung-oui
item Houbraken, Jos
item Hughes, Karen
item Huhtinen, Seppo
item Hyde, Kevin
item James, Timothy
item Park, Duckhul
item Johnston, Peter
item Jones, E.b. Gareth
item Kelly, Laura
item Kirk, Paul
item Knapp, Daniel
item Koljalg, Urmas
item Kovacs, Gabor
item Kurtzman, Cletus
item Landvik, Sara
item Leavitt, Steven
item Levesque, C Andre
item Liggenstoffer, Audra
item Liimatainen, Kare
item Lombard, Lorenzo
item Luangsa-ard, J. Jennifer
item Lumbsch, H. Thorsten
item Maganti, Harinad
item Schindel, David
item Tretter, Eric
item Weib, Michael
item Mctaggart, Alistair
item Methven, Andrew
item Meyer, Wieland
item Moncalvo, Jean-marc
item Mongkolsamrit, S
item Nagy, Laszlo

Submitted to: Proceedings of the National Academy of Sciences
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.

Last Modified: 10/17/2017
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