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Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
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  • Thomas Creedy,
  • Carmelo Andujar,
  • Emmanouil Meramveliotakis,
  • Victor Noguerales,
  • Isaac Overcast,
  • Anna Papadopoulou​,
  • Hélène Morlon,
  • Alfried Vogler,
  • Brent Emerson,
  • Paula Arribas
Thomas Creedy
Natural History Museum
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Carmelo Andujar
Instituto de Productos Naturales y Agrobiologia
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Emmanouil Meramveliotakis
University of Cyprus
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Victor Noguerales
Instituto de Productos Naturales y Agrobiologia
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Isaac Overcast
CNRS
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Anna Papadopoulou​
University of Cyprus
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Hélène Morlon
CNRS
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Alfried Vogler
Natural History Museum
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Brent Emerson
Instituto de Productos Naturales y Agrobiologia
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Paula Arribas
Instituto de Productos Naturales y Agrobiologia
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Abstract

Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the wocDNA metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.

Peer review status:ACCEPTED

20 Apr 2021Submitted to Molecular Ecology Resources
05 May 2021Submission Checks Completed
05 May 2021Assigned to Editor
19 May 2021Reviewer(s) Assigned
14 Jul 2021Review(s) Completed, Editorial Evaluation Pending
22 Jul 2021Editorial Decision: Revise Minor
28 Jul 2021Review(s) Completed, Editorial Evaluation Pending
28 Jul 20211st Revision Received
23 Aug 2021Editorial Decision: Accept