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

By

Nilsson, R. Henrik
Sánchez-García, Marisol
Ryberg, Martin K.
Abarenkov, Kessy
Wurzbacher, Christian
Kristiansson, Erik

Type

Article

Date of Publication

2017

Original Publication

Journal of orthoptera research : JOR

Volume

26

Pages

13-24

Subjects

database curation , DNA barcoding , high-throughput sequencing , Molecular ecology , molecular identification , Sanger sequencing

Contributed by

Pensoft Publishers

Language

English

Published by

Philadelphia, Penn Orthopterists' Society 1992-

Identifiers

DOI: https://doi.org/10.3897/mycokeys.26.14591

 

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.