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Oxford University Press, Database, 0(2014), p. bau061-bau061, 2014

DOI: 10.1093/database/bau061

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

Journal article published in 2014 by Z. W. de Beer, Z. Wilhelm De Beer, Conrad L. Schoch, Barbara Robbertse, Vincent A. Robert, Duong Vu, Gianluigi Cardinali, Csaba Vágvölgyi, Laszlo Irinyi, Wieland Meyer, R. Henrik Nilsson, Karen W. Hughes, Andrew N. Miller, Paul M. Kirk, No Value Duong Vu and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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. Reannotated 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. ; The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health. ; http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 ; am2014