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

被引:3725
|
作者
Schoch, Conrad L. [1 ]
Seifert, Keith A. [2 ]
Huhndorf, Sabine [3 ]
Robert, Vincent [4 ]
Spouge, John L. [1 ]
Levesque, C. Andre [2 ]
Chen, Wen [2 ]
Bolchacova, Elena [5 ]
Voigt, Kerstin [6 ,7 ]
Crous, Pedro W.
Miller, Andrew N. [8 ]
Wingfield, Michael J. [9 ]
Aime, M. Catherine [10 ]
An, Kwang-Deuk [11 ]
Bai, Feng-Yan [12 ]
Barreto, Robert W. [13 ]
Begerow, Dominik [14 ]
Bergeron, Marie-Josee [15 ]
Blackwell, Meredith [5 ,16 ]
Boekhout, Teun [17 ]
Bogale, Mesfin [18 ]
Boonyuen, Nattawut [19 ]
Burgaz, Ana R. [20 ]
Buyck, Bart [21 ]
Cai, Lei [12 ]
Cai, Qing [22 ]
Cardinali, G. [23 ]
Chaverri, Priscila [24 ]
Coppins, Brian J. [25 ]
Crespo, Ana [26 ]
Cubas, Paloma [26 ]
Cummings, Craig [5 ]
Damm, Ulrike
de Beer, Z. Wilhelm [9 ]
de Hoog, G. Sybren
Del-Prado, Ruth [26 ]
Dentinger, B. [27 ,58 ,59 ]
Dieguez-Uribeondo, J. [28 ]
Divakar, P. K. [26 ]
Douglas, B. [29 ]
Duenas, M. [28 ]
Duong, T. A. [30 ]
Eberhardt, U.
Edwards, J. E. [29 ]
Elshahed, M. S. [31 ]
Fliegerova, K. [32 ]
Furtado, M. [5 ]
Garcia, M. A. [28 ]
Ge, Z. W. [23 ]
Griffith, G. W. [29 ]
机构
[1] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA
[2] Agr & Agri Food Canada, Biodivers Mycol & Microbiol, Ottawa, ON K1A 0C6, Canada
[3] Field Museum, Dept Bot, Chicago, IL 60605 USA
[4] Cent Bur Schimmelcultures Fungal Biodivers Ctr CB, NL-3508 AD Utrecht, Netherlands
[5] Life Technol, 850 Lincoln Ctr Dr, Foster City, CA USA
[6] Univ Jena, Inst Microbiol, Jena Microbial Resource Collect, Beutenbergstr 11 a, D-07745 Jena, Germany
[7] Leibniz Inst Nat Prod Res & Infect Biol, Beutenbergstr 11 a, D-07745 Jena, Germany
[8] Univ Illinois, Illinois Nat Hist Survey, 1816 South Oak St, Champaign, IL 61820 USA
[9] Univ Pretoria, Forestry & Agr Biotechnol Inst FABI, Dept Microbiol & Plant Pathol, ZA-0001 Pretoria, South Africa
[10] Louisiana State Univ, Agr Ctr, Dept Plant Pathol & Crop Physiol, Baton Rouge, LA 70803 USA
[11] RIKEN, BioResource Ctr, Japan Collect Microorganisms, 2-1 Hirosawa, Wako, Saitama 3510198, Japan
[12] Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Bei Chen Xi Rd, Beijing 100101, Peoples R China
[13] Univ Fed Vicosa, Dept Fitopatol, BR-36570000 Vicosa, MG, Brazil
[14] Ruhr Univ Bochum, Geobot ND03 174, Univ Str 150, D-44801 Bochum, Germany
[15] Nat Resources Canada, Canadian Forest Serv, Laurentian Forestry Ctr, 1055 PEPS, POB 10380, Ste Foy, PQ G1V 4C7, Canada
[16] Louisiana State Univ, Dept Biol Sci, Baton Rouge, LA 70803 USA
[17] Univ Med Ctr, Dept Internal Med & Infect Dis, Utrecht, Netherlands
[18] Brandon Univ, Dept Biol, Brandon, MB R7A 6A9, Canada
[19] Natl Ctr Genet Engn & Biotechnol BIOTEC, 113 Paholyothin Rd, Pathum Thani 12120, Thailand
[20] Univ Complutense Madrid, Fac Biol, Dept Biol Vegetal 1, E-28040 Madrid, Spain
[21] Museum Natl Hist Nat, Dept Systemat & Evolut CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France
[22] Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Yunnan, Peoples R China
[23] Univ Perugia, Dipartimento Biol Applicata Microbiol, Perugia, Italy
[24] Univ Maryland, Dept Plant Sci & Landscape Architecture, 2112 Plant Sci Bldg, College Pk, MD 20742 USA
[25] Royal Bot Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Midlothian, Scotland
[26] Univ Complutense Madrid, Fac Farm, Dept Biol Vegetal 2, Madrid 28040, Spain
[27] Royal Bot Gardens, Jodrell Lab, Richmond TW9 3DS, Surrey, England
[28] RJB CSIC, Real Jardin Bot, Plaza Murillo 2, Madrid 28014, Spain
[29] Prifysgol Aberystwyth, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DD, Ceredigion, Wales
[30] Univ Pretoria, Dept Genet, Forestry & Agr Biotechnol Inst FABI, ZA-0001 Pretoria, South Africa
[31] Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA
[32] Czech Acad Sci, Inst Anim Physiol & Genet, VVI, Prague, Czech Republic
[33] Royal Bot Gardens Melbourne, Birdwood Ave, South Yarra, Vic 3141, Australia
[34] Karl Franzens Univ Graz, Inst Pflanzenwissensch, Holteigasse 6, A-8010 Graz, Austria
[35] Univ Free State, Dept Plant Sci, POB 339, ZA-9300 Bloemfontein, South Africa
[36] Swedish Museum Nat Hist, Dept Cryptogam Bot, POB 50007, SE-10405 Stockholm, Sweden
[37] Hirosaki Univ, Fac Agr & Life Sci, 3 Bunkyo Cho, Hirosaki, Aomori 0368561, Japan
[38] Natl Taipei Univ Educ, Dept Sci Educ, Taipei 10642, Taiwan
[39] Agroscope Changins Wadenswil Res Stn ACW, Dept Rech Protect Vegetaux Grandes Cultures & Vi, CP 1012, CH-1260 Nyon, Switzerland
[40] Univ Helsinki, Finnish Museum Nat Hist, Bot Museum, FI-00014 Helsinki, Finland
[41] RDA, Natl Acad Agr Sci, Korean Agr Culture Collect, Suwon 441707, South Korea
[42] Natl Museum Nat & Sci, Tsukuba, Ibaraki, Japan
[43] Univ Tennessee, Ecol & Evolutionary Biol, Knoxville, TN 37920 USA
[44] Univ Turku, Herbarium, FI-20014 Turku, Finland
[45] Mae Fah Luang Univ, Chiang Rai 57100, Thailand
[46] King Saud Univ, Coll Sci, Bot & Microbiol Dept, POB 2455, Riyadh 1145, Saudi Arabia
[47] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA
[48] Landcare Res, Private Bag 92170, Auckland 1142, New Zealand
[49] CABI UK, Bakeham Lane, Egham TW20 9TY, Surrey, England
[50] Eotvos Lorand Univ, Inst Biol, Dept Plant Anat, Pazmany Peter Setany 1-c, H-1117 Budapest, Hungary
基金
英国生物技术与生命科学研究理事会; 美国国家卫生研究院; 美国国家科学基金会;
关键词
DNA barcoding; fungal biodiversity; PHYLOGENETIC-RELATIONSHIPS; BASIDIOMYCETOUS YEASTS; INTRAGENOMIC VARIATION; RPB1; SEQUENCES; SUBUNIT; EVOLUTION; SYSTEMATICS; DIVERSITY; INFERENCE; PHYLUM;
D O I
10.1073/pnas.1117018109
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页码:6241 / 6246
页数:6
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