The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

By R. Henrik Nilsson, Karl-Henrik Larsson, Andy F. S. Taylor, Johan Bengtsson-Palme, T. Jeppesen, D. Schigel, P. Kennedy, Kathryn T Picard, Frank Oliver Glöckner, Leho Tedersoo and 3 more. Nucleic Acids Res., 2018

3,023 citations recorded by the source corpus.

Abstract UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer (ITS) region—and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

Subfields: Cell Biology, Pharmacology, Plant Science

View Paper: https://www.semanticscholar.org/paper/a29d8e790a7d87b08c0dc94ffc12ad9a7d4d40f1

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In Cell Biology

1. Ji‐Zheng He
2. L. Mommer

In Pharmacology

1. Qing‐Lin Chen
2. Yong-guan Zhu

In Plant Science

1. L. Mommer
2. J. van Ruijven
3. Yong-guan Zhu
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5. Hangwei Hu

Citations in the corpus

• Do soil‐borne fungal pathogens mediate plant diversity–productivity relationships? Evidence and future opportunities (2020, methodology): “Therefore, a two-step approach, which combines tools like FUNGuild to identify potential fungal pathogens with a literature survey to check the pathogen status for the fungi identified to species level, is recommended to increase the reliability of the functional assignment (Nilsson et al., 2018).”
• Deterministic selection dominates microbial community assembly in termite mounds (2020, methodology): “Representative sequences were assigned to taxonomic lineages using the RDP classi er against the SILVA database for bacteria [50] and UNITE database for fungi [51].”
• The European Nucleotide Archive in 2019 (2019, background): “ee/) (5-7) that consume ENA, add value through such curation processes and make their data available to tool and service providers.”
• A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project (2024, methodology): “For protists, where the V4 or V9 region of 18S rRNA gene is sequenced, we have chosen to query the databases at SILVA (Quast et al. , 2012) or PR2 (Guillou et al. , 2013), while for fungi, we additionally use UNITE (Nilsson et al. , 2019) given the reduced amount of fungal sequences in BOLD.”