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

By C. Schoch, B. Robbertse, V. Robert, D. Vu, G. Cardinali, L. Irinyi, W. Meyer, R. Henrik Nilsson, K. Hughes, A. Miller and 91 more. Database J. Biol. Databases Curation, 2014

432 citations recorded by the source corpus.

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

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f94aaed417769920b162cb95feba944a3e91922c

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Citations in the corpus

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015, methodology): “Sequences were selected, mostly from type specimens of valid descriptions, and then current correct species names were associated with the sequences with the aim to represent most of the accepted fun-Nucleic gal orders (8).”
Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces (2015, background): “Following revision of the taxonomy of kingdom Fungi, the anaerobic fungi are now assinged to phylum Neocallimastigomycota (Hibbett et al. 2007).”
Identification and nomenclature of the genus Penicillium (2014, methodology): “For ITS the RefSeq data set, accessible from the NCBI homepage (http://www.ncbi.nlm.nih.gov/refseq/), is now available and can be used to query ITS sequences against a verified ITS database (Schoch et al. 2014).”
Top 50 most wanted fungi (2016, neutral): “Common rules of thumb for ITS sequence similarity thresholds (Schoch et al. 2012, 2014; Irinyi et al. 2014) suggest that these lineages each represent at least a new (or previously unsequenced) genus, and in some cases an order or potentially even higher.”
Phylogeny, identification and nomenclature of the genus Aspergillus (2014, methodology): “In a step towards cleaning up misidenti ﬁ ed GenBank sequences, the RefSeq initiative was launched (http://www.ncbi.nlm.nih.gov/refseq/), which contains only veri ﬁ ed ITS sequences (Schoch et al. 2014).”
Improving ITS sequence data for identification of plant pathogenic fungi (2014, background): “Another 38 sequences were annotated as ITS sequences by their submitters but were found to represent other genes and markers (notably the ribosomal small and large subunits) and were re-annotated accordingly.”
NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, positive): “The annotation of type material in NCBI Taxonomy (7) has greatly enhanced the NCBI curated database Ref-seq (11), specifically focusing on certain targeted loci (set up as a separate BioProject; 64).”
New scientific discoveries: Plants and fungi (2020, background): “The debate is also still ongoing as to whether a short DNA sequence is sufficiently robust evidence to justify the publication of a new species name (Zamora et al., 2018), especially as thousands of well-known names still lack DNA barcodes (Schoch et al., 2014).”