Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
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 ma...
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doaj-5afb866d3f5e4f3fb40e241c637e5a302020-11-24T23:14:26ZengPensoft PublishersMycoKeys1314-40571314-40492017-08-0126132410.3897/mycokeys.26.1459114591Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactoryR. Henrik Nilsson0Marisol Sánchez-García1Martin K. Ryberg2Kessy Abarenkov3Christian Wurzbacher4Erik Kristiansson5University of GothenburgClark UniversityUppsala UniversityUniversity of Tartu, Natural History MuseumUniversity of GothenburgChalmers University of Technology 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. https://mycokeys.pensoft.net/articles.php?id=14591 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
R. Henrik Nilsson Marisol Sánchez-García Martin K. Ryberg Kessy Abarenkov Christian Wurzbacher Erik Kristiansson |
spellingShingle |
R. Henrik Nilsson Marisol Sánchez-García Martin K. Ryberg Kessy Abarenkov Christian Wurzbacher Erik Kristiansson Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory MycoKeys |
author_facet |
R. Henrik Nilsson Marisol Sánchez-García Martin K. Ryberg Kessy Abarenkov Christian Wurzbacher Erik Kristiansson |
author_sort |
R. Henrik Nilsson |
title |
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory |
title_short |
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory |
title_full |
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory |
title_fullStr |
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory |
title_full_unstemmed |
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory |
title_sort |
read quality-based trimming of the distal ends of public fungal dna sequences is nowhere near satisfactory |
publisher |
Pensoft Publishers |
series |
MycoKeys |
issn |
1314-4057 1314-4049 |
publishDate |
2017-08-01 |
description |
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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url |
https://mycokeys.pensoft.net/articles.php?id=14591 |
work_keys_str_mv |
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