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Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Author

Listed:
  • Tobias Guldberg Frøslev

    (University of Copenhagen
    University of Copenhagen)

  • Rasmus Kjøller

    (University of Copenhagen)

  • Hans Henrik Bruun

    (University of Copenhagen)

  • Rasmus Ejrnæs

    (University of Aarhus)

  • Ane Kirstine Brunbjerg

    (University of Aarhus)

  • Carlotta Pietroni

    (University of Copenhagen)

  • Anders Johannes Hansen

    (University of Copenhagen)

Abstract

DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.

Suggested Citation

  • Tobias Guldberg Frøslev & Rasmus Kjøller & Hans Henrik Bruun & Rasmus Ejrnæs & Ane Kirstine Brunbjerg & Carlotta Pietroni & Anders Johannes Hansen, 2017. "Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01312-x
    DOI: 10.1038/s41467-017-01312-x
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    Cited by:

    1. Sarah J Vancuren & Scott J Dos Santos & Janet E Hill & the Maternal Microbiome Legacy Project Team, 2020. "Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-14, July.

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