To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested t...

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Autores: Antich, Adrià, Palacín Cabañas, Cruz, Wangensteen Fuentes, Owen S. (Simon), Turon, Xavier
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/177185
Acceso en línea:https://hdl.handle.net/2445/177185
Access Level:acceso abierto
Palabra clave:Biodiversitat
Anàlisi de conglomerats
Seqüència de nucleòtids
Biodiversity
Cluster analysis
Nucleotide sequence
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spelling To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeographyAntich, AdriàPalacín Cabañas, CruzWangensteen Fuentes, Owen S. (Simon)Turon, XavierBiodiversitatAnàlisi de conglomeratsSeqüència de nucleòtidsBiodiversityCluster analysisNucleotide sequenceBackground: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Results: Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in diferent orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little infuence on the fnal outcome. Conclusions: We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.BioMed Central2021202120212021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion24 p.application/pdfhttps://hdl.handle.net/2445/177185Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1186/s12859-021-04115-6BMC Bioinformatics, 2021, vol. 22, p. 177https://doi.org/10.1186/s12859-021-04115-6cc-by (c) Antich, Adrià et al., 2021https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1771852026-05-29T05:05:01Z
dc.title.none.fl_str_mv To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
title To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
spellingShingle To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
Antich, Adrià
Biodiversitat
Anàlisi de conglomerats
Seqüència de nucleòtids
Biodiversity
Cluster analysis
Nucleotide sequence
title_short To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
title_full To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
title_fullStr To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
title_full_unstemmed To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
title_sort To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
dc.creator.none.fl_str_mv Antich, Adrià
Palacín Cabañas, Cruz
Wangensteen Fuentes, Owen S. (Simon)
Turon, Xavier
author Antich, Adrià
author_facet Antich, Adrià
Palacín Cabañas, Cruz
Wangensteen Fuentes, Owen S. (Simon)
Turon, Xavier
author_role author
author2 Palacín Cabañas, Cruz
Wangensteen Fuentes, Owen S. (Simon)
Turon, Xavier
author2_role author
author
author
dc.subject.none.fl_str_mv Biodiversitat
Anàlisi de conglomerats
Seqüència de nucleòtids
Biodiversity
Cluster analysis
Nucleotide sequence
topic Biodiversitat
Anàlisi de conglomerats
Seqüència de nucleòtids
Biodiversity
Cluster analysis
Nucleotide sequence
description Background: The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. Results: Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in diferent orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little infuence on the fnal outcome. Conclusions: We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/177185
url https://hdl.handle.net/2445/177185
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1186/s12859-021-04115-6
BMC Bioinformatics, 2021, vol. 22, p. 177
https://doi.org/10.1186/s12859-021-04115-6
dc.rights.none.fl_str_mv cc-by (c) Antich, Adrià et al., 2021
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Antich, Adrià et al., 2021
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 24 p.
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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