Author
ROBBERTSE, BARBARA - National Institutes Of Health (NIH) | |
SCHOCH, CONRAD - National Institutes Of Health (NIH) | |
ROBERT, VINCENT - Fungal Biodiversity | |
DUONG, V - Fungal Biodiversity | |
CARDINALI, GIANLUIGI - Universita Di Perugia | |
IRINYI, LASZLO - University Of Sydney | |
MEYER, WIELAND - University Of Sydney | |
Kurtzman, Cletus | |
LODGE, D. JEAN - Forest Service (FS) | |
NAKASONE, KAREN - Forest Service (FS) |
Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Review Article Publication Acceptance Date: 5/28/2014 Publication Date: 7/1/2014 Publication URL: http://handle.nal.usda.gov/10113/60379 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. Interpretive Summary: 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. |