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Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory

Journal article
Authors R. Henrik Nilsson
Marisol Sánchez-García,
Martin Ryberg
Kessy Abarenkov
Christian Wurzbacher
Erik Kristiansson
Published in MycoKeys
Volume 26
Pages 13-24
ISSN 1314-4057
Publication year 2017
Published at Department of Mathematical Sciences
Department of Biological and Environmental Sciences
Pages 13-24
Language en
Links https://doi.org/10.3897/mycokeys.26...
https://mycokeys.pensoft.net/articl...
Keywords Molecular identification, DNA barcoding, database curation, Sanger sequencing, high-throughput sequencing, molecular ecology
Subject categories Bioinformatics (Computational Biology), Microbiology in the medical area, Botany, Microbiology, Bioinformatics and Systems Biology, Biological Systematics

Abstract

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.

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