A DNA mini‐barcode for marine macrophytes

Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we...

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Detalhes bibliográficos
Autores: Ortega, Alejandra, Geraldi, Nathan R., Díaz‐Rúa, Rubén, Ørberg, Sarah B., Krause-Jensen, Dorte, Duarte, Carlos M.
Formato: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2020
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/226519
Acesso em linha:http://hdl.handle.net/10261/226519
Access Level:acceso abierto
Palavra-chave:DNA barcoding
eDNA
Environmental DNA
Macroalgae
Marine macrophytes
Mini‐barcode
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spelling A DNA mini‐barcode for marine macrophytesOrtega, AlejandraGeraldi, Nathan R.Díaz‐Rúa, RubénØrberg, Sarah B.Krause-Jensen, DorteDuarte, Carlos M.DNA barcodingeDNAEnvironmental DNAMacroalgaeMarine macrophytesMini‐barcodeStudies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%–100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny‐based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini‐barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.This research was supported by King Abdullah University of Science and Technology through baseline support to CMD. DKJ and SBØ received support from the Independent Research Fund Denmark (8021‐00222 B, ‘CARMA').John Wiley & SonsKing Abdullah University of Science and TechnologyIndependent Research Fund DenmarkConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2021202120202021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/226519reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://doi.org/10.1111/1755-0998.13164Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2265192026-05-22T06:33:51Z
dc.title.none.fl_str_mv A DNA mini‐barcode for marine macrophytes
title A DNA mini‐barcode for marine macrophytes
spellingShingle A DNA mini‐barcode for marine macrophytes
Ortega, Alejandra
DNA barcoding
eDNA
Environmental DNA
Macroalgae
Marine macrophytes
Mini‐barcode
title_short A DNA mini‐barcode for marine macrophytes
title_full A DNA mini‐barcode for marine macrophytes
title_fullStr A DNA mini‐barcode for marine macrophytes
title_full_unstemmed A DNA mini‐barcode for marine macrophytes
title_sort A DNA mini‐barcode for marine macrophytes
dc.creator.none.fl_str_mv Ortega, Alejandra
Geraldi, Nathan R.
Díaz‐Rúa, Rubén
Ørberg, Sarah B.
Krause-Jensen, Dorte
Duarte, Carlos M.
author Ortega, Alejandra
author_facet Ortega, Alejandra
Geraldi, Nathan R.
Díaz‐Rúa, Rubén
Ørberg, Sarah B.
Krause-Jensen, Dorte
Duarte, Carlos M.
author_role author
author2 Geraldi, Nathan R.
Díaz‐Rúa, Rubén
Ørberg, Sarah B.
Krause-Jensen, Dorte
Duarte, Carlos M.
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv King Abdullah University of Science and Technology
Independent Research Fund Denmark
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv DNA barcoding
eDNA
Environmental DNA
Macroalgae
Marine macrophytes
Mini‐barcode
topic DNA barcoding
eDNA
Environmental DNA
Macroalgae
Marine macrophytes
Mini‐barcode
description Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%–100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny‐based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini‐barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.
publishDate 2020
dc.date.none.fl_str_mv 2020
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/10261/226519
url http://hdl.handle.net/10261/226519
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://doi.org/10.1111/1755-0998.13164
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
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 15.198674

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