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Pré-Publication, Document De Travail Année : 2021

Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

Thomas Creedy
Carmelo Andujar
  • Fonction : Auteur
Emmanouil Meramveliotakis
  • Fonction : Auteur
Victor Noguerales
  • Fonction : Auteur
Isaac Overcast
  • Fonction : Auteur
Anna Papadopoulou​
  • Fonction : Auteur
Hélène Morlon
Alfried Vogler
Brent Emerson
Paula Arribas

Résumé

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.

Dates et versions

hal-03358533 , version 1 (29-09-2021)

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Thomas Creedy, Carmelo Andujar, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, et al.. Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation. 2021. ⟨hal-03358533⟩
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