4.4 Article

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

期刊

MYCOKEYS
卷 -, 期 26, 页码 13-24

出版社

PENSOFT PUBL
DOI: 10.3897/mycokeys.26.14591

关键词

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

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资金

  1. Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning (FORMAS) [215-2011-498]
  2. same agency (FORMAS) [226-2014-1109]
  3. Alfred P. Sloan Foundation
  4. FORMAS
  5. Wallenberg
  6. Stiftelsen Olle Engkvist
  7. Stiftelsen Lars Hiertas Minne
  8. Stiftelsen Birgit och Birger Wahlstroms minnesfond for den bohuslanska havs-och insjomiljon
  9. Kapten Carl Stenholms donationsfond
  10. Marie Sklodowska-Curie postdoctoral grant (CRYPTRANS)

向作者/读者索取更多资源

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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