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Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
University of Gothenburg, Department of Biological and Environmental Sciences; Gothenburg Global Biodiversity Centre.
Clark University, Department of Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. University of Tennessee.ORCID iD: 0000-0002-6795-4349
University of Tartu, Natural History Museum.
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2017 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, Vol. 26, p. 13-24Article in journal (Refereed) Published
Abstract [en]

DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

Place, publisher, year, edition, pages
2017. Vol. 26, p. 13-24
Keyword [en]
Molecular identification, DNA barcoding, database curation, Sanger sequencing, high-throughput sequencing, molecular ecology
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:uu:diva-334539DOI: 10.3897/mycokeys.26.14591ISI: 000408265600002OAI: oai:DiVA.org:uu-334539DiVA, id: diva2:1159815
Funder
Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 215-2011-498Swedish Research Council FormasSwedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 226-2014-1109Knut and Alice Wallenberg FoundationStiftelsen Olle Engkvist ByggmästareLars Hierta Memorial Foundation
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2017-11-24Bibliographically approved

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