Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
Journal article, 2017

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.

database curation

molecular ecology

Molecular identification

Sanger sequencing

DNA barcoding

high-throughput sequencing

Author

R. Henrik Nilsson

Gothenburg Global Biodiversity Centre

University of Gothenburg

Marisol Sánchez-García

Clark University

M. Ryberg

Uppsala University

Kessy Abarenkov

University of Tartu

Christian Wurzbacher

University of Gothenburg

Gothenburg Global Biodiversity Centre

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

MycoKeys

1314-4057 (ISSN) 1314-4049 (eISSN)

26 13-24

Subject Categories

Biological Systematics

DOI

10.3897/mycokeys.26.14591

More information

Latest update

5/17/2018