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

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. 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

Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review

“…Ideally, DNA barcode regions should be the same for all kingdoms (Schoch et al, 2012). In animals and algae, the variation between species (interspecific) in COX1 fragment is higher than within a species (intraspecific).…”

“…Ideally, the interspecific variation of barcode locus should exceed the intraspecific variation (barcode gap) (Schoch et al, 2012). The barcoding locus will be optimal when the sequence is constant within species and is unique for each species (Hebert et al, 2003) to enable differentiation, even in closely related species.…”

“…All of the curated sequences have associated specimen data to ensure correct species identification and name change tracking. The re-annotated and verified fungi sequences are deposited in the RefSeq Targeted Loci (RTL) database, which can be accessed and searched using specialized BLAST (Schoch et al, 2014). Currently, several ITS fungal databases are also available, i.e.…”

“…However, the ITS will remain as the key choice for fungal identification. The search for alternative regions as DNA marker to improve fungal identification, especially in specific heredities, has already started (Schoch et al, 2014).…”

Spelling out Jaapia species

“…On the other hand, the automatic Jaapia PlutoF multiple sequence alignment (UCL7_001618) obtained through UNITE has six sequences distributed in two SH clusters. The sequence GU187524 (J. argillacea) published in Binder et al (2010) is the reference sequence of the species hypothesis SH235459.06FU cluster; recently this sequence (GU187524) was also selected as the reference sequence of the species J. argillacea, and it appears in the INSD database with the number NR_119766 (Schoch et al 2014). The SH235459.06FU cluster also includes the sequences EU118636 (J. argillacea) and EU118637 (J. ochroleuca) from Larsson (2007), and the sequence KC514904 (J. argillacea) from an unpublished paper.…”