Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

Conrad L. Schoch; Barbara Robbertse; Vincent Robert; Duong Vu; Gianluigi Cardinali; Laszlo Irinyi; Wieland Meyer; R. Henrik Nilsson; Karen W. Hughes; Andrew N. Miller; Paul M.  Kirk; Kessy Abarenkov; M. Catherine Aime; Hiran A. Ariyawansa; Martin. Bidartondo; Ten Boekhout; B Buyck; Qing Cai; Jie Chen; Ana Crespo; Pedro W Crous; Ulrike Damm; Z. Wilhelm de Beer; Bryn T. M. Dentinger; Pradeep K. Divakar; Margarita Duenas; Nicolas Geau; Katerina Fliegerova; Miguel A. Garcia; Zai-Wei Ge; Gareth Wyn Griffith; Johannes Z Groenewald; Marizeth Groenewald; Martin Grube; Marieka Gryzenhout; Cécile Gueidan; Liangdong Guo; Sarah Hambleton; Richard Hamelin; Karen Hansen; Valérie Hofstetter; Seung-Beom Hong; Jos Houbraken; Kevin D. Hyde; Patrik Inderbitzin; Peter R Johnston; Samantha C. Karunarathna; Urmas Koljalg; Gabor M. Kovacs; Ekaphan Kraichak; Krisztina Krizsan; Cletus P. Kurtzman; Karl-Henrik Larsson; Steven Leavitt; Peter M. Letcher; Kare Liimatainen; Jian-Kui Liu; Jean D. Lodge; Janet J. Luangsa-Ard; H Thorsten Lumbsch; Sajeewa S. N. Maharachchikumbura; Dimuthu Manamgoda; María P. Martín; Andrew M. Minnis; Jean-Marc Moncalvo; Giuseppina Mulè; Karen K. Nakasone; Tuula Niskanen; Ibai Olariaga; Tamás Papp; Tamás Petkovits; Raquel Pino-Bodas; Martha J. Powell; Huzefa A. Raja; Dirk Redecker; J.M. Sarmiento-Ramirez; Keith A. Seifert; Bhushan Shrestha; Soili Stenroos; Benjamin Stielow; Sung-Oui Suh; Kazuaki Tanaka; Leho Tedersoo; M. Teresa Telleria; Dhanushka Udayanga; Wendy A.  Untereiner; Javier Dieguez-Uribeondo; Krishna V. Subbarao; Csaba Vágvölgyi36; Johann Visagie; Kerstin Voigt; Donald M. Walker; Bevan S. Weir; Michael Weiß; Nalin N. Wijayawardene; Michael J Wingfield; J. P. Xu; Yang Zhu L.; Ning Zhang; Wen-Ying Zhuang; Scott Federhen

doi:10.1093/database/bau061

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

Conrad L. Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, Laszlo Irinyi, Wieland Meyer, R. Henrik Nilsson, Karen W. Hughes, Andrew N. Miller, Paul M. Kirk, Kessy Abarenkov, M. Catherine Aime, Hiran A. Ariyawansa, Martin. Bidartondo, Ten Boekhout, B Buyck, Qing Cai, Jie Chen, Ana CrespoPedro W Crous, Ulrike Damm, Z. Wilhelm de Beer, Bryn T. M. Dentinger, Pradeep K. Divakar, Margarita Duenas, Nicolas Geau, Katerina Fliegerova, Miguel A. Garcia, Zai-Wei Ge, Gareth Wyn Griffith, Johannes Z Groenewald, Marizeth Groenewald, Martin Grube, Marieka Gryzenhout, Cécile Gueidan, Liangdong Guo, Sarah Hambleton, Richard Hamelin, Karen Hansen, Valérie Hofstetter, Seung-Beom Hong, Jos Houbraken, Kevin D. Hyde, Patrik Inderbitzin, Peter R Johnston, Samantha C. Karunarathna, Urmas Koljalg, Gabor M. Kovacs, Ekaphan Kraichak, Krisztina Krizsan, Cletus P. Kurtzman, Karl-Henrik Larsson, Steven Leavitt, Peter M. Letcher, Kare Liimatainen, Jian-Kui Liu, Jean D. Lodge, Janet J. Luangsa-Ard, H Thorsten Lumbsch, Sajeewa S. N. Maharachchikumbura, Dimuthu Manamgoda, María P. Martín, Andrew M. Minnis, Jean-Marc Moncalvo, Giuseppina Mulè, Karen K. Nakasone, Tuula Niskanen, Ibai Olariaga, Tamás Papp, Tamás Petkovits, Raquel Pino-Bodas, Martha J. Powell, Huzefa A. Raja, Dirk Redecker, J.M. Sarmiento-Ramirez, Keith A. Seifert, Bhushan Shrestha, Soili Stenroos, Benjamin Stielow, Sung-Oui Suh, Kazuaki Tanaka, Leho Tedersoo, M. Teresa Telleria, Dhanushka Udayanga, Wendy A. Untereiner, Javier Dieguez-Uribeondo, Krishna V. Subbarao, Csaba Vágvölgyi36, Johann Visagie, Kerstin Voigt, Donald M. Walker, Bevan S. Weir, Michael Weiß, Nalin N. Wijayawardene, Michael J Wingfield, J. P. Xu, Yang Zhu L., Ning Zhang, Wen-Ying Zhuang, Scott Federhen

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

322 Citations (Scopus)

399 Downloads (Pure)

Abstract

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

Original language	English
Pages (from-to)	1-21
Number of pages	21
Journal	Database: The Journal of Biological Databases and Curation
Issue number	2014
Early online date	28 May 2014
DOIs	https://doi.org/10.1093/database/bau061
Publication status	Published - 28 May 2014

Access to Document

10.1093/database/bau061Licence: Unclear 1

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for FungiFinal published version, 1.62 MBLicence: Unclear 1

Permanent link

Persistent link

Cite this

Schoch, C. L., Robbertse, B., Robert, V., Vu, D., Cardinali, G., Irinyi, L., Meyer, W., Nilsson, R. H., Hughes, K. W., Miller, A. N., Kirk, P. M., Abarenkov, K., Aime, M. C., Ariyawansa, H. A., Bidartondo, M., Boekhout, T., Buyck, B., Cai, Q., Chen, J., ... Federhen, S. (2014). Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi. Database: The Journal of Biological Databases and Curation, (2014), 1-21. https://doi.org/10.1093/database/bau061

@article{a6b0e69732a6428187c33d31b309d570,

title = "Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi",

abstract = "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",

author = "Schoch, {Conrad L.} and Barbara Robbertse and Vincent Robert and Duong Vu and Gianluigi Cardinali and Laszlo Irinyi and Wieland Meyer and Nilsson, {R. Henrik} and Hughes, {Karen W.} and Miller, {Andrew N.} and Kirk, {Paul M.} and Kessy Abarenkov and Aime, {M. Catherine} and Ariyawansa, {Hiran A.} and Martin. Bidartondo and Ten Boekhout and B Buyck and Qing Cai and Jie Chen and Ana Crespo and Crous, {Pedro W} and Ulrike Damm and {de Beer}, {Z. Wilhelm} and Dentinger, {Bryn T. M.} and Divakar, {Pradeep K.} and Margarita Duenas and Nicolas Geau and Katerina Fliegerova and Garcia, {Miguel A.} and Zai-Wei Ge and Griffith, {Gareth Wyn} and Groenewald, {Johannes Z} and Marizeth Groenewald and Martin Grube and Marieka Gryzenhout and C{\'e}cile Gueidan and Liangdong Guo and Sarah Hambleton and Richard Hamelin and Karen Hansen and Val{\'e}rie Hofstetter and Seung-Beom Hong and Jos Houbraken and Hyde, {Kevin D.} and Patrik Inderbitzin and Johnston, {Peter R} and Karunarathna, {Samantha C.} and Urmas Koljalg and Kovacs, {Gabor M.} and Ekaphan Kraichak and Krisztina Krizsan and Kurtzman, {Cletus P.} and Karl-Henrik Larsson and Steven Leavitt and Letcher, {Peter M.} and Kare Liimatainen and Jian-Kui Liu and Lodge, {Jean D.} and Luangsa-Ard, {Janet J.} and Lumbsch, {H Thorsten} and Maharachchikumbura, {Sajeewa S. N.} and Dimuthu Manamgoda and Mart{\'i}n, {Mar{\'i}a P.} and Minnis, {Andrew M.} and Jean-Marc Moncalvo and Giuseppina Mul{\`e} and Nakasone, {Karen K.} and Tuula Niskanen and Ibai Olariaga and Tam{\'a}s Papp and Tam{\'a}s Petkovits and Raquel Pino-Bodas and Powell, {Martha J.} and Raja, {Huzefa A.} and Dirk Redecker and J.M. Sarmiento-Ramirez and Seifert, {Keith A.} and Bhushan Shrestha and Soili Stenroos and Benjamin Stielow and Sung-Oui Suh and Kazuaki Tanaka and Leho Tedersoo and Telleria, {M. Teresa} and Dhanushka Udayanga and Untereiner, {Wendy A.} and Javier Dieguez-Uribeondo and Subbarao, {Krishna V.} and Csaba V{\'a}gv{\"o}lgyi36 and Johann Visagie and Kerstin Voigt and Walker, {Donald M.} and Weir, {Bevan S.} and Michael Wei{\ss} and Wijayawardene, {Nalin N.} and Wingfield, {Michael J} and Xu, {J. P.} and {Zhu L.}, Yang and Ning Zhang and Wen-Ying Zhuang and Scott Federhen",

year = "2014",

month = may,

day = "28",

doi = "10.1093/database/bau061",

language = "English",

pages = "1--21",

journal = "Database: The Journal of Biological Databases and Curation",

issn = "1758-0463",

publisher = "Oxford University Press",

number = "2014",

}

Schoch, CL, Robbertse, B, Robert, V, Vu, D, Cardinali, G, Irinyi, L, Meyer, W, Nilsson, RH, Hughes, KW, Miller, AN, Kirk, PM, Abarenkov, K, Aime, MC, Ariyawansa, HA, Bidartondo, M, Boekhout, T, Buyck, B, Cai, Q, Chen, J, Crespo, A, Crous, PW, Damm, U, de Beer, ZW, Dentinger, BTM, Divakar, PK, Duenas, M, Geau, N, Fliegerova, K, Garcia, MA, Ge, Z-W, Griffith, GW, Groenewald, JZ, Groenewald, M, Grube, M, Gryzenhout, M, Gueidan, C, Guo, L, Hambleton, S, Hamelin, R, Hansen, K, Hofstetter, V, Hong, S-B, Houbraken, J, Hyde, KD, Inderbitzin, P, Johnston, PR, Karunarathna, SC, Koljalg, U, Kovacs, GM, Kraichak, E, Krizsan, K, Kurtzman, CP, Larsson, K-H, Leavitt, S, Letcher, PM, Liimatainen, K, Liu, J-K, Lodge, JD, Luangsa-Ard, JJ, Lumbsch, HT, Maharachchikumbura, SSN, Manamgoda, D, Martín, MP, Minnis, AM, Moncalvo, J-M, Mulè, G, Nakasone, KK, Niskanen, T, Olariaga, I, Papp, T, Petkovits, T, Pino-Bodas, R, Powell, MJ, Raja, HA, Redecker, D, Sarmiento-Ramirez, JM, Seifert, KA, Shrestha, B, Stenroos, S, Stielow, B, Suh, S-O, Tanaka, K, Tedersoo, L, Telleria, MT, Udayanga, D, Untereiner, WA, Dieguez-Uribeondo, J, Subbarao, KV, Vágvölgyi36, C, Visagie, J, Voigt, K, Walker, DM, Weir, BS, Weiß, M, Wijayawardene, NN, Wingfield, MJ, Xu, JP, Zhu L., Y, Zhang, N, Zhuang, W-Y & Federhen, S 2014, 'Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi', Database: The Journal of Biological Databases and Curation, no. 2014, pp. 1-21. https://doi.org/10.1093/database/bau061

TY - JOUR

T1 - Finding needles in haystacks

T2 - Linking scientific names, reference specimens and molecular data for Fungi

AU - Schoch, Conrad L.

AU - Robbertse, Barbara

AU - Robert, Vincent

AU - Vu, Duong

AU - Cardinali, Gianluigi

AU - Irinyi, Laszlo

AU - Meyer, Wieland

AU - Nilsson, R. Henrik

AU - Hughes, Karen W.

AU - Miller, Andrew N.

AU - Kirk, Paul M.

AU - Abarenkov, Kessy

AU - Aime, M. Catherine

AU - Ariyawansa, Hiran A.

AU - Bidartondo, Martin.

AU - Boekhout, Ten

AU - Buyck, B

AU - Cai, Qing

AU - Chen, Jie

AU - Crespo, Ana

AU - Crous, Pedro W

AU - Damm, Ulrike

AU - de Beer, Z. Wilhelm

AU - Dentinger, Bryn T. M.

AU - Divakar, Pradeep K.

AU - Duenas, Margarita

AU - Geau, Nicolas

AU - Fliegerova, Katerina

AU - Garcia, Miguel A.

AU - Ge, Zai-Wei

AU - Griffith, Gareth Wyn

AU - Groenewald, Johannes Z

AU - Groenewald, Marizeth

AU - Grube, Martin

AU - Gryzenhout, Marieka

AU - Gueidan, Cécile

AU - Guo, Liangdong

AU - Hambleton, Sarah

AU - Hamelin, Richard

AU - Hansen, Karen

AU - Hofstetter, Valérie

AU - Hong, Seung-Beom

AU - Houbraken, Jos

AU - Hyde, Kevin D.

AU - Inderbitzin, Patrik

AU - Johnston, Peter R

AU - Karunarathna, Samantha C.

AU - Koljalg, Urmas

AU - Kovacs, Gabor M.

AU - Kraichak, Ekaphan

AU - Krizsan, Krisztina

AU - Kurtzman, Cletus P.

AU - Larsson, Karl-Henrik

AU - Leavitt, Steven

AU - Letcher, Peter M.

AU - Liimatainen, Kare

AU - Liu, Jian-Kui

AU - Lodge, Jean D.

AU - Luangsa-Ard, Janet J.

AU - Lumbsch, H Thorsten

AU - Maharachchikumbura, Sajeewa S. N.

AU - Manamgoda, Dimuthu

AU - Martín, María P.

AU - Minnis, Andrew M.

AU - Moncalvo, Jean-Marc

AU - Mulè, Giuseppina

AU - Nakasone, Karen K.

AU - Niskanen, Tuula

AU - Olariaga, Ibai

AU - Papp, Tamás

AU - Petkovits, Tamás

AU - Pino-Bodas, Raquel

AU - Powell, Martha J.

AU - Raja, Huzefa A.

AU - Redecker, Dirk

AU - Sarmiento-Ramirez, J.M.

AU - Seifert, Keith A.

AU - Shrestha, Bhushan

AU - Stenroos, Soili

AU - Stielow, Benjamin

AU - Suh, Sung-Oui

AU - Tanaka, Kazuaki

AU - Tedersoo, Leho

AU - Telleria, M. Teresa

AU - Udayanga, Dhanushka

AU - Untereiner, Wendy A.

AU - Dieguez-Uribeondo, Javier

AU - Subbarao, Krishna V.

AU - Vágvölgyi36, Csaba

AU - Visagie, Johann

AU - Voigt, Kerstin

AU - Walker, Donald M.

AU - Weir, Bevan S.

AU - Weiß, Michael

AU - Wijayawardene, Nalin N.

AU - Wingfield, Michael J

AU - Xu, J. P.

AU - Zhu L., Yang

AU - Zhang, Ning

AU - Zhuang, Wen-Ying

AU - Federhen, Scott

PY - 2014/5/28

Y1 - 2014/5/28

N2 - 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

AB - 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

UR - http://hdl.handle.net/2160/26360

U2 - 10.1093/database/bau061

DO - 10.1093/database/bau061

M3 - Article

C2 - 24980130

SN - 1758-0463

SP - 1

EP - 21

JO - Database: The Journal of Biological Databases and Curation

JF - Database: The Journal of Biological Databases and Curation

IS - 2014

ER -

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

Abstract

Access to Document

Permanent link

Other files and links

Fingerprint

Cite this