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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

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

Authors
item Robbertse, Barbara -
item Schoch, Conrad -
item Robert, Vincent -
item Duong, V -
item Cardinali, Gianluigi -
item Irinyi, Laszlo -
item Meyer, Wieland -
item Kurtzman, Cletus
item Lodge, D. Jean -
item Nakasone, Karen -

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Review Article
Publication Acceptance Date: May 28, 2014
Publication Date: July 1, 2014
Citation: Robbertse, B., Schoch, C.L., Robert, V., Duong, V., Cardinali, G., Irinyi, L., Meyer, W., Kurtzman, C.P., Lodge, D., Nakasone, K., et al. 2014. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bau061.

Technical 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 projects employing high-throughput sequencing require fast and effective methods for en masse species assignments. In this paper 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 (ITS) 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), RefSeq Targeted Loci (RTL), and will be visible during routine BLAST searches with NR prefixed accession numbers. A set of standards and protocols is proposed in order 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.

Last Modified: 12/18/2014
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