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

Schoch, Conrad L.; Seifert, Keith A.; Huhndorf, Sabine; Robert, Vincent; Spouge, John L.; Levesque, C. André; Chen, Wen; Bolchacova, Elena; Voigt, Kerstin; Crous, Pedro W.; Miller, Andrew N.; Wingfield, Michael J.; Aime, M. Catherine; An, Kwang-Deuk; Bai, Feng-Yan; Barreto, Robert W.; Begerow, Dominik; Bergeron, Marie-Josée; Blackwell, Meredith; Boekhout, Teun

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

Resource type

Journal article

Creator (person)

Schoch, Conrad L.

Seifert, Keith A.

Huhndorf, Sabine

Robert, Vincent

Spouge, John L.

Levesque, C. André

Chen, Wen

Bolchacova, Elena

Voigt, Kerstin

Crous, Pedro W.

Miller, Andrew N.

Wingfield, Michael J.

Aime, M. Catherine

An, Kwang-Deuk

Bai, Feng-Yan

Barreto, Robert W.

Begerow, Dominik

Bergeron, Marie-Josée

Blackwell, Meredith

Boekhout, Teun

Bogale, Mesfin

Boonyuen, Nattawut

Burgaz, Ana R.

Buyck, Bart

Cai, Lei

Cai, Qing

Cardinali, G.

Chaverri, Priscila

Coppins, Brian J.

Crespo, Ana

Cubas, Paloma

Cummings, Craig

Damm, Ulrike

de Beer, Z. Wilhelm

de Hoog, G. Sybren

Del-Prado, Ruth

Dentinger, Bryn

Diéguez-Uribeondo, Javier

Divakar, Pradeep K.

Douglas, Brian

ORCID

Dueñas, Margarita

Duong, Tuan A.

Eberhardt, Ursula

Edwards, Joan E.

Elshahed, Mostafa S.

Fliegerova, Katerina

Furtado, Manohar

García, Miguel A.

Ge, Zai-Wei

Griffith, Gareth W.

Griffiths, K.

Groenewald, Johannes Z.

Groenewald, Marizeth

Grube, Martin

Gryzenhout, Marieka

Guo, Liang-Dong

Hagen, Ferry

Hambleton, Sarah

Hamelin, Richard C.

Hansen, Karen

Harrold, Paul

Heller, Gregory

Herrera, Cesar

Hirayama, Kazuyuki

Hirooka, Yuuri

Ho, Hsiao-Man

Hoffmann, Kerstin

Hofstetter, Valérie

Högnabba, Filip

Hollingsworth, Peter M.

Hong, Seung-Beom

Hosaka, Kentaro

Houbraken, Jos

Hughes, Karen

Huhtinen, Seppo

Hyde, Kevin D.

James, Timothy

Johnson, Eric M.

Johnson, Joan E.

Johnston, Peter R.

Jones, E.B. Gareth

Kelly, Laura J.

ORCID

Kirk, Paul M.

ORCID

Knapp, Dániel G.

Kõljalg, Urmas

Kovács, Gábor M.

Kurtzman, Cletus P.

Landvik, Sara

Leavitt, Steven D.

Liggenstoffer, Audra S.

Liimatainen, Kare

ORCID

Lombard, Lorenzo

Luangsa-ard, J. Jennifer

Lumbsch, H. Thorsten

Maganti, Harinad

Maharachchikumbura, Sajeewa S. N.

Martin, María P.

May, Tom W.

McTaggart, Alistair R.

Methven, Andrew S.

Meyer, Wieland

Moncalvo, Jean-Marc

Mongkolsamrit, Suchada

Nagy, László G.

Nilsson, R. Henrik

Niskanen, Tuula

ORCID

Nyilasi, Ildikó

Okada, Gen

Okane, Izumi

Olariaga, Ibai

Otte, Jürgen

Papp, Tamás

Park, Duckchul

Petkovits, Tamás

Pino-Bodas, Raquel

ORCID

Quaedvlieg, William

Raja, Huzefa A.

Redecker, Dirk

Rintoul, Tara L.

Ruibal, Constantino

Sarmiento-Ramírez, Jullie M.

Schmitt, Imke

Schüßler, Arthur

Shearer, Carol

Sotome, Kozue

Stefani, Franck O.P.

Stenroos, Soili

Stielow, Benjamin

Stockinger, Herbert

Suetrong, Satinee

Suh, Sung-Oui

Sung, Gi-Ho

Suzuki, Motofumi

Tanaka, Kazuaki

Tedersoo, Leho

Telleria, M. Teresa

Tretter, Eric

Untereiner, Wendy A.

Urbina, Hector

Vágvölgyi, Csaba

Vialle, Agathe

Vu, Thuy Duong

Walther, Grit

Wang, Qi-Ming

Wang, Yan

Weir, Bevan S.

Weiß, Michael

White, Merlin M.

Xu, Jianping

Yahr, Rebecca

Yang, Zhu L.

Yurkov, Andrey

Zamora, Juan-Carlos

Zhang, Ning

Zhuang, Wen-Ying

Schindel, David

Date published

April 17, 2012

Abstract

Six DNA regions were evaluated as potential DNA barcodes for , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome 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.

Creator (organisation)

Fungal Barcoding Consortium

Fungal Barcoding Consortium Author List