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

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. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

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

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