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Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples

2024-08-26Journal article Open access
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dc.contributor.authorFerreira, André O.
dc.contributor.authorBarroso, Cristina
dc.contributor.authorMouteira Azevedo, Olga
dc.contributor.authorDuarte, Sofia
dc.contributor.authorEgas, Conceição
dc.contributor.authorFontes, João T.
dc.contributor.authorRé, Pedro
dc.contributor.authorSantos, A. Miguel P.
dc.contributor.authorCosta, Filipe O.
dc.date.accessioned2024-11-08T10:26:46Z
dc.date.available2024-11-08T10:26:46Z
dc.date.issued2024-08-26
dc.description.abstractIchthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.eng
dc.description.sponsorshipCIRCNA/BRB/0156/2019; DFA/BD/6653/2020; UI/BD/150910/2021; LA/P/0058/2020
dc.identifier.doi10.1038/s41598-024-69963-7
dc.identifier.issn2045-2322
dc.identifier.urihttp://hdl.handle.net/10400.1/26233
dc.language.isoeng
dc.peerreviewedyes
dc.publisherNature Research
dc.relationCENTRE OF MOLECULAR AND ENVIRONMENTAL BIOLOGY
dc.relationAquatic Research Infrastructure Network
dc.relationCenter for Innovative Biomedicine and Biotechnology
dc.relationCenter for Innovative Biomedicine and Biotechnology
dc.relationAlgarve Centre for Marine Sciences
dc.relationAlgarve Centre for Marine Sciences
dc.relationCentre for Marine and Environmental Research
dc.relation.ispartofScientific Reports
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.titleMulti-marker DNA metabarcoding for precise species identification in ichthyoplankton sampleseng
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleCENTRE OF MOLECULAR AND ENVIRONMENTAL BIOLOGY
oaire.awardTitleAquatic Research Infrastructure Network
oaire.awardTitleCenter for Innovative Biomedicine and Biotechnology
oaire.awardTitleCenter for Innovative Biomedicine and Biotechnology
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitleAlgarve Centre for Marine Sciences
oaire.awardTitleCentre for Marine and Environmental Research
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04050%2F2020/PT
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oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/LA%2FP%2F0101%2F2020/PT
oaire.citation.issue1
oaire.citation.startPage19772
oaire.citation.titleScientific Reports
oaire.citation.volume14
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oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameMouteira Azevedo
person.familyNameSantos
person.givenNameOlga
person.givenNameA. Miguel P.
person.identifier290283
person.identifier.ciencia-id541E-93D0-BFC3
person.identifier.orcid0000-0002-2133-7791
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