| Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi | |
Schoch, Conrad L.1; Robbertse, Barbara1; Robert, Vincent2; Duong Vu2; Cardinali, Gianluigi3; Irinyi, Laszlo4; Meyer, Wieland4; Nilsson, R. Henrik5; Hughes, Karen6; Miller, Andrew N.7; Kirk, Paul M.8; Abarenkov, Kessy9; Aime, M. Catherine10; Ariyawansa, Hiran A.11,12; Bidartondo, Martin13; Boekhout, Teun2; Buyck, Bart14; Cai, Qing15; Chen, Jie11,12; Crespo, Ana2,16; Crous, Pedro W.2; Damm, Ulrike17; De Beer, Z. Wilhelm18; Dentinger, Bryn T. M.8; Divakar, Pradeep K.16; Duenas, Margarita19; Feau, Nicolas20; Fliegerova, Katerina21; Garcia, Miguel A.22; Ge, Zai-Wei15 ; Griffith, GarethW.23; Groenewald, Johannes Z.2; Groenewald, Marizeth2; Grube, Martin24; Gryzenhout, Marieka25; Gueidan, Cecile26; Guo, Liangdong27; Hambleton, Sarah28; Hamelin, Richard20; Hansen, Karen29; Hofstetter, Valerie30; Hong, Seung-Beom31; Houbraken, Jos2; Hyde, Kevin D.11,12; Inderbitzin, Patrik32; Johnston, Peter R.33; Karunarathna, Samantha C.11,12; Koljalg, Urmas9; Kovacs, Gabor M.34,35; Kraichak, Ekaphan36; Krizsan, Krisztina37; Kurtzman, Cletus P.38; Larsson, Karl-Henrik39; Leavitt, Steven36; Letcher, Peter M.40; Liimatainen, Kare41; Liu, Jian-Kui11,12; Lodge, D. Jean42; Luangsa-ard, Janet Jennifer43; Lumbsch, H. Thorsten36; Maharachchikumbura, Sajeewa S. N.11,12; Manamgoda, Dimuthu11,12; Martin, Maria P.19; Minnis, Andrew M.44; Moncalvo, Jean-Marc45,46; Mule, Giuseppina47; Nakasone, Karen K.48; Niskanen, Tuula41; Olariaga, Ibai29; Papp, Tamas37; Petkovits, Tamas37; Pino-Bodas, Raquel49; Powell, Martha J.40; Raja, Huzefa A.50; Redecker, Dirk51; Sarmiento-Ramirez, J. M.19; Seifert, Keith A.28; Shrestha, Bhushan52; Stenroos, Soili49; Stielow, Benjamin2; Suh, Sung-Oui53; Tanaka, Kazuaki54; Tedersoo, Leho9; Teresa Telleria, M.19; Udayanga, Dhanushka11,12; Untereiner, Wendy A.55; Dieguez Uribeondo, Javier19; Subbarao, Krishna V.32; Vagvoelgyi, Csaba37; Visagie, Cobus2; Voigt, Kerstin56,57; Walker, Donald M.58; Weir, Bevan S.33; Weiss, Michael59; Wijayawardene, Nalin N.11,12; Wingfield, Michael J.18; Xu, J. P.60; Yang, Zhu L.15; Zhang, Ning61; Zhuang, Wen-Ying27; Federhen, Scott1; Yang, YP (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Menglun Township 650201, Yunnan, Peoples R China.; yangyp@mail.kib.ac.cn
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| 2014-06-30 | |
| 发表期刊 | DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
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| ISSN | 1758-0463 |
| 页码 | bau061 |
| 摘要 | DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. |
| 关键词 | Internal Transcribed Spacer Arbuscular Mycorrhizal Fungi Ribosomal Dna Interspecific Hybridization Sequence Analyses Species Complex Identification Evolution Barcode Life |
| 学科领域 | Mathematical & Computational Biology |
| DOI | 10.1093/database/bau061 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000338579600001 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.kib.ac.cn/handle/151853/18292 |
| 专题 | 中国科学院东亚植物多样性与生物地理学重点实验室 |
| 通讯作者 | Yang, YP (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Menglun Township 650201, Yunnan, Peoples R China.; yangyp@mail.kib.ac.cn |
| 作者单位 | 1.Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA 2.CBS KNAW Fungal Biodivers Ctr, NL-3508 AD Utrecht, Netherlands 3.Univ Perugia, Dept Pharmaceut Sci Microbiol, I-06100 Perugia, Italy 4.Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Mol Mycol Res Lab,Sydney Med Sch,Westmead Hosp, Westmead Millennium Inst,Ctr Infect Dis & Microbi, Westmead, NSW 2145, Australia 5.Univ Gothenburg, Dept Biol & Environm Sci, S-40530 Gothenburg, Sweden 6.Univ Tennessee, Knoxville, TN 37920 USA 7.Univ Illinois, Illinois Nat Hist Survey, Champaign, IL 61820 USA 8.Royal Bot Gardens, Jodrell Lab, Mycol Sect, Richmond TW9 3DS, Surrey, England 9.Univ Tartu, Nat Hist Museum, EE-51014 Tartu, Estonia 10.Purdue Univ, Dept Bot & Plant Pathol, W Lafayette, IN 47907 USA 11.Mae Fah Luang Univ, Inst Excellence Fungal Res, Chiang Rai 57100, Thailand 12.Mae Fah Luang Univ, Sch Sci, Chiang Rai 57100, Thailand 13.Imperial Coll London, Royal Bot Gardens, Richmond TW9 3DS, England 14.Museum Natl Hist Nat, Dept Systemat & Evolut CP39, UMR7205, F-75005 Paris, France 15.Chinese Acad Sci, Kunming Inst Bot, Kunming 650201, Yunnan, Peoples R China 16.Univ Complutense Madrid, Fac Farm, Dept Biol Vegetal 2, E-28040 Madrid, Spain 17.Senckenberg Museum Nat Hist Gorlitz, D-02806 Gorlitz, Germany 18.Univ Pretoria, Dept Microbiol & Plant Pathol, FABI, ZA-0001 Pretoria, South Africa 19.CSIC, RJB, E-28014 Madrid, Spain 20.Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1W5, Canada 21.Acad Sci Czech Republic, Inst Anim Physiol & Genet, Vvi, Prague, Czech Republic 22.Univ Toronto, Dept Biol, Mississauga, ON L5L 1C6, Canada 23.Prifysgol Aberystwyth, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DD, Ceredigion, Wales 24.Karl Franzens Univ Graz, Inst Plant Sci, A-8010 Graz, Austria 25.Univ Orange Free State, Dept Plant Sci, ZA-9300 Bloemfontein, South Africa 26.CANBR, CSIRO Plant Ind, Canberra, ACT 2601, Australia 27.Chinese Acad Sci, Inst Microbiol, State Key Lab Mycol, Beijing, Peoples R China 28.Agr & Agri Food Canada, Biodivers Mycol & Microbiol, Ottawa, ON, Canada 29.Swedish Museum Nat Hist, Dept Bot, SE-10405 Stockholm, Sweden 30.Agroscope Changins Wadenswil Res Stn ACW, Dept Rech Protect Vegetaux Grandes Cultures & Vig, CH-1260 Nyon, Switzerland 31.RDA, Korean Agr Culture Collect, Natl Acad Agr Sci, Suwon 441707, South Korea 32.Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA 33.Landcare Res, Auckland 1142, New Zealand 34.Eotvos Lorand Univ, Inst Biol, Dept Plant Anat, H-1117 Budapest, Hungary 35.Hungarian Acad Sci, Inst Plant Protect, Agr Res Ctr, H-1525 Budapest, Hungary 36.Field Museum Nat Hist, Chicago, IL 60605 USA 37.Univ Szeged, Fac Sci & Informat, Dept Microbiol, H-6726 Szeged, Hungary 38.ARS, Bacterial Foodborne Pathogens & Mycol Res Unit, USDA, Natl Ctr Agr Utilizat Res, Peoria, IL 61604 USA 39.Nat Hist Museum, N-0318 Oslo, Norway 40.Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA 41.Univ Helsinki, Dept Biosci, FIN-00014 Helsinki, Finland 42.US Forest Serv, USDA, NRS, Luquillo, PR USA 43.Natl Ctr Genet Engn & Biotechnol BIOTEC, Pathum Thani 12120, Thailand 44.Univ Wisconsin, Dept Med Microbiol & Immunol, Madison, WI 53706 USA 45.Univ Toronto, Royal Ontario Museum, Dept Nat Hist, Toronto, ON, Canada 46.Univ Toronto, Dept Ecol Evolutionary Biol, Toronto, ON, Canada 47.CNR, Inst Sci Food Prod, I-70126 Bari, Italy 48.US Forest Serv, Ctr Forest Mycol Res, No Res Stn, Madison, WI 53726 USA 49.Univ Helsinki, Finnish Museum Nat Hist, Bot Museum, FI-00014 Helsinki, Finland 50.Univ N Carolina, Dept Chem & Biochem, Greensboro, NC 27402 USA 51.Univ Bourgogne, Agroecol UMR1347, F-21000 Dijon, France 52.Sungkyunkwan Univ, Inst Life Sci & Biotechnol, Suwon 440746, South Korea 53.ATCC, Mycol & Bot Program, Manassas, VA 20110 USA 54.Hirosaki Univ, Fac Agr & Life Sci, Hirosaki, Aomori 0368561, Japan 55.Brandon Univ, Dept Biol, Brandon, MB R7A 6A9, Canada 56.Leibniz Inst Nat Prod Res & Infect Biol, Jena Microbial Resource Collect, Jena, Germany 57.Univ Jena, Jena, Germany 58.Univ Findlay, Dept Nat Sci, Findlay, OH 45840 USA 59.Univ Tubingen, Inst Evolut & Ecol, D-72076 Tubingen, Germany 60.McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada 61.Rutgers State Univ, Dept Plant Biol & Pathol, New Brunswick, NJ 08901 USA |
| 推荐引用方式 GB/T 7714 | Schoch, Conrad L.,Robbertse, Barbara,Robert, Vincent,et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,2014:bau061. |
| APA | Schoch, Conrad L..,Robbertse, Barbara.,Robert, Vincent.,Duong Vu.,Cardinali, Gianluigi.,...&yangyp@mail.kib.ac.cn.(2014).Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,bau061. |
| MLA | Schoch, Conrad L.,et al."Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi".DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2014):bau061. |
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