@article{Schoch:2014:database/bau061,
author = {Schoch, CL and Robbertse, B and Robert, V and Duong, V and Cardinali, G and Irinyi, L and Meyer, W and Nilsson, RH and Hughes, K and Miller, AN and Kirk, PM and Abarenkov, K and Aime, MC and Ariyawansa, HA and Bidartondo, M and Boekhout, T and Buyck, B and Cai, Q and Chen, J and Crespo, A and Crous, PW and Damm, U and De, Beer ZW and Dentinger, BTM and Divakar, PK and Duenas, M and Feau, N and Fliegerova, K and Garcia, MA and Ge, Z-W and Griffith, G and Groenewald, JZ and Groenewald, M and Grube, M and Gryzenhout, M and Gueidan, C and Guo, L and Hambleton, S and Hamelin, R and Hansen, K and Hofstetter, V and Hong, S-B and Houbraken, J and Hyde, KD and Inderbitzin, P and Johnston, PR and Karunarathna, SC and Koljalg, U and Kovacs, GM and Kraichak, E and Krizsan, K and Kurtzman, CP and Larsson, K-H and Leavitt, S and Letcher, PM and Liimatainen, K and Liu, J-K and Lodge, DJ and Luangsa-ard, JJ and Lumbsch, HT and Maharachchikumbura, SSN and Manamgoda, D and Martin, MP and Minnis, AM and },
doi = {database/bau061},
journal = {Database},
title = {Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi},
url = {http://dx.doi.org/10.1093/database/bau061},
volume = {2014},
year = {2014}
}

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TY  - JOUR
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.
AU  - Schoch,CL
AU  - Robbertse,B
AU  - Robert,V
AU  - Duong,V
AU  - Cardinali,G
AU  - Irinyi,L
AU  - Meyer,W
AU  - Nilsson,RH
AU  - Hughes,K
AU  - Miller,AN
AU  - Kirk,PM
AU  - Abarenkov,K
AU  - Aime,MC
AU  - Ariyawansa,HA
AU  - Bidartondo,M
AU  - Boekhout,T
AU  - Buyck,B
AU  - Cai,Q
AU  - Chen,J
AU  - Crespo,A
AU  - Crous,PW
AU  - Damm,U
AU  - De,Beer ZW
AU  - Dentinger,BTM
AU  - Divakar,PK
AU  - Duenas,M
AU  - Feau,N
AU  - Fliegerova,K
AU  - Garcia,MA
AU  - Ge,Z-W
AU  - Griffith,G
AU  - Groenewald,JZ
AU  - Groenewald,M
AU  - Grube,M
AU  - Gryzenhout,M
AU  - Gueidan,C
AU  - Guo,L
AU  - Hambleton,S
AU  - Hamelin,R
AU  - Hansen,K
AU  - Hofstetter,V
AU  - Hong,S-B
AU  - Houbraken,J
AU  - Hyde,KD
AU  - Inderbitzin,P
AU  - Johnston,PR
AU  - Karunarathna,SC
AU  - Koljalg,U
AU  - Kovacs,GM
AU  - Kraichak,E
AU  - Krizsan,K
AU  - Kurtzman,CP
AU  - Larsson,K-H
AU  - Leavitt,S
AU  - Letcher,PM
AU  - Liimatainen,K
AU  - Liu,J-K
AU  - Lodge,DJ
AU  - Luangsa-ard,JJ
AU  - Lumbsch,HT
AU  - Maharachchikumbura,SSN
AU  - Manamgoda,D
AU  - Martin,MP
AU  - Minnis,AM
AU  - Moncalvo,J-M
AU  - Mule,G
AU  - Nakasone,KK
AU  - Niskanen,T
AU  - Olariaga,I
AU  - Papp,T
AU  - Petkovits,T
AU  - Pino-Bodas,R
AU  - Powell,MJ
AU  - Raja,HA
AU  - Redecker,D
AU  - Sarmiento-Ramirez,JM
AU  - Seifert,KA
AU  - Shrestha,B
AU  - Stenroos,S
AU  - Stielow,B
AU  - Suh,S-O
AU  - Tanaka,K
AU  - Tedersoo,L
AU  - Teresa,Telleria M
AU  - Udayanga,D
AU  - Untereiner,WA
AU  - Dieguez,Uribeondo J
AU  - Subbarao,KV
AU  - Vagvoelgyi,C
AU  - Visagie,C
AU  - Voigt,K
AU  - Walker,DM
AU  - Weir,BS
AU  - Weiss,M
AU  - Wijayawardene,NN
AU  - Wingfield,MJ
AU  - Xu,JP
AU  - Yang,ZL
AU  - Zhang,N
AU  - Zhuang,W-Y
AU  - Federhen,S
DO  - database/bau061
PY  - 2014///
SN  - 0162-4105
TI  - Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
T2  - Database
UR  - http://dx.doi.org/10.1093/database/bau061
UR  - http://hdl.handle.net/10044/1/40960
VL  - 2014
ER  - 

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