Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accom...

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Autores: Andújar, Carmelo, Creedy, Thomas J., Arribas, Paula, López, Heriberto, Salces-Castellano, Antonia, Pérez‐Delgado, Antonio José, Vogler, Alfried P., Emerson, Brent C.
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:dnet:digitalcsic_::262c8b210cbdc32e1b46359c8d7b6863
Acceso en línea:http://hdl.handle.net/10261/237534
Access Level:acceso abierto
Palabra clave:Denoising
Pseudogene
Taxonomic inflation
HTS
Intraspecific variation
NUMT
Spurious sequences
NGS
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spelling Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode dataAndújar, CarmeloCreedy, Thomas J.Arribas, PaulaLópez, HeribertoSalces-Castellano, AntoniaPérez‐Delgado, Antonio JoséVogler, Alfried P.Emerson, Brent C.DenoisingPseudogeneTaxonomic inflationHTSIntraspecific variationNUMTSpurious sequencesNGSMetabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at ).C. A. was supported by the Spanish Ministry of Economy and Competitiveness (MINECO, Spain) (CGL2015‐74178‐JIN) and Fundación CajaCanarias/Obra social “la Caixa.” B. C. E. was supported by the project CGL2017‐85718‐P (AEI, Spain/FEDER, EU). P. A., T. J. C., B. C. E. and A. P. V. were supported by the iBioGen project funded by the H2020 European Research Council, Grant/Award Number: 810729. We extend our gratitude to the regional governments of Andalucía and Canarias (Spain) for facilitating collecting of samples, to Jesús Arribas for assistance with field sampling, and Carlos Martínez for the mathematical advice.Peer reviewedWiley-VCHMinisterio de Economía y Competitividad (España)Fundación CajaCanariasFundación la CaixaConsejo 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/10261/237534reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/810729MICINN/CGL2017/85718‐Phttps://doi.org/10.1111/1755-0998.13337Síinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::262c8b210cbdc32e1b46359c8d7b68632026-05-22T06:33:51Z
dc.title.none.fl_str_mv Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
title Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
spellingShingle Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
Andújar, Carmelo
Denoising
Pseudogene
Taxonomic inflation
HTS
Intraspecific variation
NUMT
Spurious sequences
NGS
title_short Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
title_full Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
title_fullStr Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
title_full_unstemmed Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
title_sort Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
dc.creator.none.fl_str_mv Andújar, Carmelo
Creedy, Thomas J.
Arribas, Paula
López, Heriberto
Salces-Castellano, Antonia
Pérez‐Delgado, Antonio José
Vogler, Alfried P.
Emerson, Brent C.
author Andújar, Carmelo
author_facet Andújar, Carmelo
Creedy, Thomas J.
Arribas, Paula
López, Heriberto
Salces-Castellano, Antonia
Pérez‐Delgado, Antonio José
Vogler, Alfried P.
Emerson, Brent C.
author_role author
author2 Creedy, Thomas J.
Arribas, Paula
López, Heriberto
Salces-Castellano, Antonia
Pérez‐Delgado, Antonio José
Vogler, Alfried P.
Emerson, Brent C.
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
Fundación CajaCanarias
Fundación la Caixa
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Denoising
Pseudogene
Taxonomic inflation
HTS
Intraspecific variation
NUMT
Spurious sequences
NGS
topic Denoising
Pseudogene
Taxonomic inflation
HTS
Intraspecific variation
NUMT
Spurious sequences
NGS
description Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at ).
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/10261/237534
url http://hdl.handle.net/10261/237534
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/810729
MICINN/CGL2017/85718‐P
https://doi.org/10.1111/1755-0998.13337
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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