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, G. 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, T. 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, C. 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 journalArticle

2162 Citations (Scopus)

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
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
Publication statusPublished - Apr 17 2012

Fingerprint

Genetic Markers
Fungi
Minichromosome Maintenance Proteins
Large Ribosome Subunits
Small Ribosome Subunits
Nuclear RNA
Ascomycota
Ribosomal RNA
DNA
Electron Transport Complex IV
Introns
Open Reading Frames
Genes
Yeasts
Polymerase Chain Reaction
Proteins
RNA polymerase II largest subunit

Keywords

  • DNA barcoding
  • Fungal biodiversity

ASJC Scopus subject areas

  • General

Cite this

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; 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; 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.; Kirk, Paul M.; Knapp, Dániel G.; Kõljalg, Urmas; Kovács, G.; Kurtzman, Cletus P.; Landvik, Sara; Leavitt, Steven D.; Liggenstoffer, Audra S.; Liimatainen, Kare; 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, Wiel; Moncalvo, Jean Marc; Mongkolsamrit, Suchada; Nagy, László G.; Nilsson, R. Henrik; Niskanen, Tuula; Nyilasi, Ildikó; Okada, Gen; Okane, Izumi; Olariaga, Ibai; Otte, Jürgen; Papp, T.; Park, Duckchul; Petkovits, Tamás; Pino-Bodas, Raquel; 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, C.; 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.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 16, 17.04.2012, p. 6241-6246.

Research output: Contribution to journalArticle

Schoch, CL, Seifert, KA, Huhndorf, S, Robert, V, Spouge, JL, Levesque, CA, Chen, W, Bolchacova, E, Voigt, K, Crous, PW, Miller, AN, Wingfield, MJ, Aime, MC, An, KD, Bai, FY, Barreto, RW, Begerow, D, Bergeron, MJ, Blackwell, M, Boekhout, T, Bogale, M, Boonyuen, N, Burgaz, AR, Buyck, B, Cai, L, Cai, Q, Cardinali, G, Chaverri, P, Coppins, BJ, Crespo, A, Cubas, P, Cummings, C, Damm, U, de Beer, ZW, de Hoog, GS, Del-Prado, R, Dentinger, B, Diéguez-Uribeondo, J, Divakar, PK, Douglas, B, Dueñas, M, Duong, TA, Eberhardt, U, Edwards, JE, Elshahed, MS, Fliegerova, K, Furtado, M, García, MA, Ge, ZW, Griffith, GW, Griffiths, K, Groenewald, JZ, Groenewald, M, Grube, M, Gryzenhout, M, Guo, LD, Hagen, F, Hambleton, S, Hamelin, RC, Hansen, K, Harrold, P, Heller, G, Herrera, C, Hirayama, K, Hirooka, Y, Ho, HM, Hoffmann, K, Hofstetter, V, Högnabba, F, Hollingsworth, PM, Hong, SB, Hosaka, K, Houbraken, J, Hughes, K, Huhtinen, S, Hyde, KD, James, T, Johnson, EM, Johnson, JE, Johnston, PR, Jones, EBG, Kelly, LJ, Kirk, PM, Knapp, DG, Kõljalg, U, Kovács, G, Kurtzman, CP, Landvik, S, Leavitt, SD, Liggenstoffer, AS, Liimatainen, K, Lombard, L, Luangsa-ard, JJ, Lumbsch, HT, Maganti, H, Maharachchikumbura, SSN, Martin, MP, May, TW, McTaggart, AR, Methven, AS, Meyer, W, Moncalvo, JM, Mongkolsamrit, S, Nagy, LG, Nilsson, RH, Niskanen, T, Nyilasi, I, Okada, G, Okane, I, Olariaga, I, Otte, J, Papp, T, Park, D, Petkovits, T, Pino-Bodas, R, Quaedvlieg, W, Raja, HA, Redecker, D, Rintoul, TL, Ruibal, C, Sarmiento-Ramírez, JM, Schmitt, I, Schüßler, A, Shearer, C, Sotome, K, Stefani, FOP, Stenroos, S, Stielow, B, Stockinger, H, Suetrong, S, Suh, SO, Sung, GH, Suzuki, M, Tanaka, K, Tedersoo, L, Telleria, MT, Tretter, E, Untereiner, WA, Urbina, H, Vágvölgyi, C, Vialle, A, Vu, TD, Walther, G, Wang, QM, Wang, Y, Weir, BS, Weiß, M, White, MM, Xu, J, Yahr, R, Yang, ZL, Yurkov, A, Zamora, JC, Zhang, N, Zhuang, WY & Schindel, D 2012, 'Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi', Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 16, pp. 6241-6246. https://doi.org/10.1073/pnas.1117018109
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 ; 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. ; Kirk, Paul M. ; Knapp, Dániel G. ; Kõljalg, Urmas ; Kovács, G. ; Kurtzman, Cletus P. ; Landvik, Sara ; Leavitt, Steven D. ; Liggenstoffer, Audra S. ; Liimatainen, Kare ; 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, Wiel ; Moncalvo, Jean Marc ; Mongkolsamrit, Suchada ; Nagy, László G. ; Nilsson, R. Henrik ; Niskanen, Tuula ; Nyilasi, Ildikó ; Okada, Gen ; Okane, Izumi ; Olariaga, Ibai ; Otte, Jürgen ; Papp, T. ; Park, Duckchul ; Petkovits, Tamás ; Pino-Bodas, Raquel ; 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, C. ; 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. / Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. In: Proceedings of the National Academy of Sciences of the United States of America. 2012 ; Vol. 109, No. 16. pp. 6241-6246.
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title = "Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi",
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.",
keywords = "DNA barcoding, Fungal biodiversity",
author = "Schoch, {Conrad L.} and Seifert, {Keith A.} and Sabine Huhndorf and Vincent Robert and Spouge, {John L.} and Levesque, {C. Andr{\'e}} and Wen Chen and Elena Bolchacova and Kerstin Voigt and Crous, {Pedro W.} and Miller, {Andrew N.} and Wingfield, {Michael J.} and Aime, {M. Catherine} and An, {Kwang Deuk} and Bai, {Feng Yan} and Barreto, {Robert W.} and Dominik Begerow and Bergeron, {Marie Jos{\'e}e} and Meredith Blackwell and Teun Boekhout and Mesfin Bogale and Nattawut Boonyuen and Burgaz, {Ana R.} and Bart Buyck and Lei Cai and Qing Cai and G. Cardinali and Priscila Chaverri and Coppins, {Brian J.} and Ana Crespo and Paloma Cubas and Craig Cummings and Ulrike Damm and {de Beer}, {Z. Wilhelm} and {de Hoog}, {G. Sybren} and Ruth Del-Prado and Bryn Dentinger and Javier Di{\'e}guez-Uribeondo and Divakar, {Pradeep K.} and Brian Douglas and Margarita Due{\~n}as and Duong, {Tuan A.} and Ursula Eberhardt and Edwards, {Joan E.} and Elshahed, {Mostafa S.} and Katerina Fliegerova and Manohar Furtado and Garc{\'i}a, {Miguel A.} and Ge, {Zai Wei} and Griffith, {Gareth W.} and K. Griffiths and Groenewald, {Johannes Z.} and Marizeth Groenewald and Martin Grube and Marieka Gryzenhout and Guo, {Liang Dong} and Ferry Hagen and Sarah Hambleton and Hamelin, {Richard C.} and Karen Hansen and Paul Harrold and Gregory Heller and Cesar Herrera and Kazuyuki Hirayama and Yuuri Hirooka and Ho, {Hsiao Man} and Kerstin Hoffmann and Val{\'e}rie Hofstetter and Filip H{\"o}gnabba and Hollingsworth, {Peter M.} and Hong, {Seung Beom} and Kentaro Hosaka and Jos Houbraken and Karen Hughes and Seppo Huhtinen and Hyde, {Kevin D.} and Timothy James and Johnson, {Eric M.} and Johnson, {Joan E.} and Johnston, {Peter R.} and Jones, {E. B Gareth} and Kelly, {Laura J.} and Kirk, {Paul M.} and Knapp, {D{\'a}niel G.} and Urmas K{\~o}ljalg and G. Kov{\'a}cs and Kurtzman, {Cletus P.} and Sara Landvik and Leavitt, {Steven D.} and Liggenstoffer, {Audra S.} and Kare Liimatainen and Lorenzo Lombard and Luangsa-ard, {J. Jennifer} and Lumbsch, {H. Thorsten} and Harinad Maganti and Maharachchikumbura, {Sajeewa S N} and Martin, {Mar{\'i}a P.} and May, {Tom W.} and McTaggart, {Alistair R.} and Methven, {Andrew S.} and Wiel Meyer and Moncalvo, {Jean Marc} and Suchada Mongkolsamrit and Nagy, {L{\'a}szl{\'o} G.} and Nilsson, {R. Henrik} and Tuula Niskanen and Ildik{\'o} Nyilasi and Gen Okada and Izumi Okane and Ibai Olariaga and J{\"u}rgen Otte and T. Papp and Duckchul Park and Tam{\'a}s Petkovits and Raquel Pino-Bodas and William Quaedvlieg and Raja, {Huzefa A.} and Dirk Redecker and Rintoul, {Tara L.} and Constantino Ruibal and Sarmiento-Ram{\'i}rez, {Jullie M.} and Imke Schmitt and Arthur Sch{\"u}{\ss}ler and Carol Shearer and Kozue Sotome and Stefani, {Franck O P} and Soili Stenroos and Benjamin Stielow and Herbert Stockinger and Satinee Suetrong and Suh, {Sung Oui} and Sung, {Gi Ho} and Motofumi Suzuki and Kazuaki Tanaka and Leho Tedersoo and Telleria, {M. Teresa} and Eric Tretter and Untereiner, {Wendy A.} and Hector Urbina and C. V{\'a}gv{\"o}lgyi and Agathe Vialle and Vu, {Thuy Duong} and Grit Walther and Wang, {Qi Ming} and Yan Wang and Weir, {Bevan S.} and Michael Wei{\ss} and White, {Merlin M.} and Jianping Xu and Rebecca Yahr and Yang, {Zhu L.} and Andrey Yurkov and Zamora, {Juan Carlos} and Ning Zhang and Zhuang, {Wen Ying} and David Schindel",
year = "2012",
month = "4",
day = "17",
doi = "10.1073/pnas.1117018109",
language = "English",
volume = "109",
pages = "6241--6246",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "16",

}

TY - JOUR

T1 - Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

AU - Schoch, Conrad L.

AU - Seifert, Keith A.

AU - Huhndorf, Sabine

AU - Robert, Vincent

AU - Spouge, John L.

AU - Levesque, C. André

AU - Chen, Wen

AU - Bolchacova, Elena

AU - Voigt, Kerstin

AU - Crous, Pedro W.

AU - Miller, Andrew N.

AU - Wingfield, Michael J.

AU - Aime, M. Catherine

AU - An, Kwang Deuk

AU - Bai, Feng Yan

AU - Barreto, Robert W.

AU - Begerow, Dominik

AU - Bergeron, Marie Josée

AU - Blackwell, Meredith

AU - Boekhout, Teun

AU - Bogale, Mesfin

AU - Boonyuen, Nattawut

AU - Burgaz, Ana R.

AU - Buyck, Bart

AU - Cai, Lei

AU - Cai, Qing

AU - Cardinali, G.

AU - Chaverri, Priscila

AU - Coppins, Brian J.

AU - Crespo, Ana

AU - Cubas, Paloma

AU - Cummings, Craig

AU - Damm, Ulrike

AU - de Beer, Z. Wilhelm

AU - de Hoog, G. Sybren

AU - Del-Prado, Ruth

AU - Dentinger, Bryn

AU - Diéguez-Uribeondo, Javier

AU - Divakar, Pradeep K.

AU - Douglas, Brian

AU - Dueñas, Margarita

AU - Duong, Tuan A.

AU - Eberhardt, Ursula

AU - Edwards, Joan E.

AU - Elshahed, Mostafa S.

AU - Fliegerova, Katerina

AU - Furtado, Manohar

AU - García, Miguel A.

AU - Ge, Zai Wei

AU - Griffith, Gareth W.

AU - Griffiths, K.

AU - Groenewald, Johannes Z.

AU - Groenewald, Marizeth

AU - Grube, Martin

AU - Gryzenhout, Marieka

AU - Guo, Liang Dong

AU - Hagen, Ferry

AU - Hambleton, Sarah

AU - Hamelin, Richard C.

AU - Hansen, Karen

AU - Harrold, Paul

AU - Heller, Gregory

AU - Herrera, Cesar

AU - Hirayama, Kazuyuki

AU - Hirooka, Yuuri

AU - Ho, Hsiao Man

AU - Hoffmann, Kerstin

AU - Hofstetter, Valérie

AU - Högnabba, Filip

AU - Hollingsworth, Peter M.

AU - Hong, Seung Beom

AU - Hosaka, Kentaro

AU - Houbraken, Jos

AU - Hughes, Karen

AU - Huhtinen, Seppo

AU - Hyde, Kevin D.

AU - James, Timothy

AU - Johnson, Eric M.

AU - Johnson, Joan E.

AU - Johnston, Peter R.

AU - Jones, E. B Gareth

AU - Kelly, Laura J.

AU - Kirk, Paul M.

AU - Knapp, Dániel G.

AU - Kõljalg, Urmas

AU - Kovács, G.

AU - Kurtzman, Cletus P.

AU - Landvik, Sara

AU - Leavitt, Steven D.

AU - Liggenstoffer, Audra S.

AU - Liimatainen, Kare

AU - Lombard, Lorenzo

AU - Luangsa-ard, J. Jennifer

AU - Lumbsch, H. Thorsten

AU - Maganti, Harinad

AU - Maharachchikumbura, Sajeewa S N

AU - Martin, María P.

AU - May, Tom W.

AU - McTaggart, Alistair R.

AU - Methven, Andrew S.

AU - Meyer, Wiel

AU - Moncalvo, Jean Marc

AU - Mongkolsamrit, Suchada

AU - Nagy, László G.

AU - Nilsson, R. Henrik

AU - Niskanen, Tuula

AU - Nyilasi, Ildikó

AU - Okada, Gen

AU - Okane, Izumi

AU - Olariaga, Ibai

AU - Otte, Jürgen

AU - Papp, T.

AU - Park, Duckchul

AU - Petkovits, Tamás

AU - Pino-Bodas, Raquel

AU - Quaedvlieg, William

AU - Raja, Huzefa A.

AU - Redecker, Dirk

AU - Rintoul, Tara L.

AU - Ruibal, Constantino

AU - Sarmiento-Ramírez, Jullie M.

AU - Schmitt, Imke

AU - Schüßler, Arthur

AU - Shearer, Carol

AU - Sotome, Kozue

AU - Stefani, Franck O P

AU - Stenroos, Soili

AU - Stielow, Benjamin

AU - Stockinger, Herbert

AU - Suetrong, Satinee

AU - Suh, Sung Oui

AU - Sung, Gi Ho

AU - Suzuki, Motofumi

AU - Tanaka, Kazuaki

AU - Tedersoo, Leho

AU - Telleria, M. Teresa

AU - Tretter, Eric

AU - Untereiner, Wendy A.

AU - Urbina, Hector

AU - Vágvölgyi, C.

AU - Vialle, Agathe

AU - Vu, Thuy Duong

AU - Walther, Grit

AU - Wang, Qi Ming

AU - Wang, Yan

AU - Weir, Bevan S.

AU - Weiß, Michael

AU - White, Merlin M.

AU - Xu, Jianping

AU - Yahr, Rebecca

AU - Yang, Zhu L.

AU - Yurkov, Andrey

AU - Zamora, Juan Carlos

AU - Zhang, Ning

AU - Zhuang, Wen Ying

AU - Schindel, David

PY - 2012/4/17

Y1 - 2012/4/17

N2 - 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.

AB - 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.

KW - DNA barcoding

KW - Fungal biodiversity

UR - http://www.scopus.com/inward/record.url?scp=84859972408&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84859972408&partnerID=8YFLogxK

U2 - 10.1073/pnas.1117018109

DO - 10.1073/pnas.1117018109

M3 - Article

C2 - 22454494

AN - SCOPUS:84859972408

VL - 109

SP - 6241

EP - 6246

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 16

ER -