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United States Department of Agriculture

Agricultural Research Service

Research Project: MANAGEMENT AND GENETIC CHARACTERIZATION OF AGRICULTURAL AND BIOTECHNOLOGICAL MICROBIAL RESOURCES Title: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Authors
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: February 24, 2012
Publication Date: April 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: 10/24/2014
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