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

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 growt...

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Autores: Creedy, Thomas, Andújar, Carmelo, Noguerales, Víctor, Overcast, Isaac, Papadopoulou, Anna, Morlon, Hélène, Vogler, Alfried P., Emerson, Brent C., Arribas, Paula
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/249758
Acceso en línea:http://hdl.handle.net/10261/249758
Access Level:acceso abierto
Palabra clave:Animal communities
Bioinformatics
Coi barcode
Community ecology
High-throughput sequencing
Metabarcoding
http://metadata.un.org/sdg/15
Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss
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spelling Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisationCreedy, ThomasAndújar, CarmeloNoguerales, VíctorOvercast, IsaacPapadopoulou, AnnaMorlon, HélèneVogler, Alfried P.Emerson, Brent C.Arribas, PaulaAnimal communitiesBioinformaticsCoi barcodeCommunity ecologyHigh-throughput sequencingMetabarcodinghttp://metadata.un.org/sdg/15Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity lossMetabarcoding 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.This research was supported by the iBioGen project, which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 810729.Peer reviewedWiley-VCHEuropean CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202120212021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/249758reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/810729.Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2497582026-05-22T06:33:51Z
dc.title.none.fl_str_mv Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
title Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
spellingShingle Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
Creedy, Thomas
Animal communities
Bioinformatics
Coi barcode
Community ecology
High-throughput sequencing
Metabarcoding
http://metadata.un.org/sdg/15
Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss
title_short Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
title_full Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
title_fullStr Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
title_full_unstemmed Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
title_sort Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation
dc.creator.none.fl_str_mv Creedy, Thomas
Andújar, Carmelo
Noguerales, Víctor
Overcast, Isaac
Papadopoulou, Anna
Morlon, Hélène
Vogler, Alfried P.
Emerson, Brent C.
Arribas, Paula
author Creedy, Thomas
author_facet Creedy, Thomas
Andújar, Carmelo
Noguerales, Víctor
Overcast, Isaac
Papadopoulou, Anna
Morlon, Hélène
Vogler, Alfried P.
Emerson, Brent C.
Arribas, Paula
author_role author
author2 Andújar, Carmelo
Noguerales, Víctor
Overcast, Isaac
Papadopoulou, Anna
Morlon, Hélène
Vogler, Alfried P.
Emerson, Brent C.
Arribas, Paula
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Animal communities
Bioinformatics
Coi barcode
Community ecology
High-throughput sequencing
Metabarcoding
http://metadata.un.org/sdg/15
Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss
topic Animal communities
Bioinformatics
Coi barcode
Community ecology
High-throughput sequencing
Metabarcoding
http://metadata.un.org/sdg/15
Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss
description 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.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/249758
url http://hdl.handle.net/10261/249758
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/810729.
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Wiley-VCH
publisher.none.fl_str_mv Wiley-VCH
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.811543

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