Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/50410 |
Resumo: | In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only. |
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Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communitiesAnimalsAnnelidaArthropodsBiomassChordataCnidariaComputer SimulationDNA Barcoding, TaxonomicDNA PrimersEchinodermataEcosystemElectron Transport Complex IVGene LibraryHigh-Throughput Nucleotide SequencingMolluscaPhylogenyPolymerase Chain ReactionSequence Analysis, DNABiodiversityDNA barcodinghigh-throughput sequencingbioassessmentmarine macrobenthosScience & TechnologyIn marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only.This work was supported by FEDER through POFCCOMPETE by national funds from 'Fundacao para a Ciencia e a Tecnologia (FCT)' in the scope of the grant FCOMP-01-0124-FEDER-015429 and also by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER007569). This work was also funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI). J.L. was supported by a PhD fellowship (SFRH/BD/69750/2010) from FCT and C.H. by a CAPES Post-doctoral fellowship, under Science Without Borders Program (Ministry of Education, Brazil)info:eu-repo/semantics/publishedVersionCanadian Science PublishingUniversidade do MinhoHollatz, ClaudiaLeite, Bárbara Daniela RochaLobo, JorgeFroufe, HugoEgas, ConceiçãoCosta, Filipe O.2017-032017-03-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/50410engHollatz C, Leite BR, Lobo J, Froufe H, Egas C, Costa FO (2017). Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities. Genome 60: 260-271 doi: 10.1139/gen-2015-0220.0831-279610.1139/gen-2015-022028145743info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:53:10Zoai:repositorium.sdum.uminho.pt:1822/50410Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:52:29.570175Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
title |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
spellingShingle |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities Hollatz, Claudia Animals Annelida Arthropods Biomass Chordata Cnidaria Computer Simulation DNA Barcoding, Taxonomic DNA Primers Echinodermata Ecosystem Electron Transport Complex IV Gene Library High-Throughput Nucleotide Sequencing Mollusca Phylogeny Polymerase Chain Reaction Sequence Analysis, DNA Biodiversity DNA barcoding high-throughput sequencing bioassessment marine macrobenthos Science & Technology |
title_short |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
title_full |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
title_fullStr |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
title_full_unstemmed |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
title_sort |
Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities |
author |
Hollatz, Claudia |
author_facet |
Hollatz, Claudia Leite, Bárbara Daniela Rocha Lobo, Jorge Froufe, Hugo Egas, Conceição Costa, Filipe O. |
author_role |
author |
author2 |
Leite, Bárbara Daniela Rocha Lobo, Jorge Froufe, Hugo Egas, Conceição Costa, Filipe O. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Hollatz, Claudia Leite, Bárbara Daniela Rocha Lobo, Jorge Froufe, Hugo Egas, Conceição Costa, Filipe O. |
dc.subject.por.fl_str_mv |
Animals Annelida Arthropods Biomass Chordata Cnidaria Computer Simulation DNA Barcoding, Taxonomic DNA Primers Echinodermata Ecosystem Electron Transport Complex IV Gene Library High-Throughput Nucleotide Sequencing Mollusca Phylogeny Polymerase Chain Reaction Sequence Analysis, DNA Biodiversity DNA barcoding high-throughput sequencing bioassessment marine macrobenthos Science & Technology |
topic |
Animals Annelida Arthropods Biomass Chordata Cnidaria Computer Simulation DNA Barcoding, Taxonomic DNA Primers Echinodermata Ecosystem Electron Transport Complex IV Gene Library High-Throughput Nucleotide Sequencing Mollusca Phylogeny Polymerase Chain Reaction Sequence Analysis, DNA Biodiversity DNA barcoding high-throughput sequencing bioassessment marine macrobenthos Science & Technology |
description |
In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-03 2017-03-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/50410 |
url |
http://hdl.handle.net/1822/50410 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Hollatz C, Leite BR, Lobo J, Froufe H, Egas C, Costa FO (2017). Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities. Genome 60: 260-271 doi: 10.1139/gen-2015-0220. 0831-2796 10.1139/gen-2015-0220 28145743 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Canadian Science Publishing |
publisher.none.fl_str_mv |
Canadian Science Publishing |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799133116750626816 |