Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions

Detalhes bibliográficos
Autor(a) principal: Lavrador, Ana Sofia Castro
Data de Publicação: 2023
Outros Autores: Fontes, João T., Vieira, Pedro Emanuel Ferreira Reis, Costa, Filipe O., Duarte, Sofia Alexandra Ferreira
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: https://hdl.handle.net/1822/82756
Resumo: The script developed to create the DNA sequence reference library is available at https://github.com/tadeu95/Curated-BINs-Reference-Library (accessed on 25 January 2023). Metabarcoding datasets will be made available upon request since they belong to a study that is not published yet.
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spelling Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regionsEuropean coastal ecosystemsDNA reference librariesCOI barcode sequencesCiências Naturais::Ciências BiológicasScience & TechnologyProteger a vida marinhaThe script developed to create the DNA sequence reference library is available at https://github.com/tadeu95/Curated-BINs-Reference-Library (accessed on 25 January 2023). Metabarcoding datasets will be made available upon request since they belong to a study that is not published yet.The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.This research was funded by national funds through the Foundation for Science and Technology (FCT I.P.), grant number PTDC/BIA-BMA/29754/2017 (NIS-DNA: Early detection and monitoring of non-indigenous species (NIS) in coastal ecosystems based on high-throughput sequencing tools) and by the “Contrato-Programa” UIDB/04050/2020. Financial support granted by the FCT I.P. to S.D. (CEECIND/00667/2017) is also acknowledged. A.S.L. (UI/BD/150871/2021) and J.T.F. (UI/BD/150910/2021) are supported by the Collaboration Protocol for Financing the Multiannual Research Grants Plan for Doctoral Students with financial support from FCT I.P. and the European Social Fund under the Northern Regional Operational Program—Norte2020.MDPIUniversidade do MinhoLavrador, Ana Sofia CastroFontes, João T.Vieira, Pedro Emanuel Ferreira ReisCosta, Filipe O.Duarte, Sofia Alexandra Ferreira20232023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/82756engLavrador, A.S.; Fontes, J.T.; Vieira, P.E.; Costa, F.O.; Duarte, S. Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity 2023, 15, 174. https://doi.org/10.3390/d150201741424-281810.3390/d15020174https://www.mdpi.com/1424-2818/15/2/174info: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:RCAAP2023-07-21T12:20:53Zoai:repositorium.sdum.uminho.pt:1822/82756Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:14:02.400562Repositório 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 Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
title Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
spellingShingle Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
Lavrador, Ana Sofia Castro
European coastal ecosystems
DNA reference libraries
COI barcode sequences
Ciências Naturais::Ciências Biológicas
Science & Technology
Proteger a vida marinha
title_short Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
title_full Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
title_fullStr Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
title_full_unstemmed Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
title_sort Compilation, revision, and annotation of DNA barcodes of marine invertebrate Non-Indigenous Species (NIS) occurring in european coastal regions
author Lavrador, Ana Sofia Castro
author_facet Lavrador, Ana Sofia Castro
Fontes, João T.
Vieira, Pedro Emanuel Ferreira Reis
Costa, Filipe O.
Duarte, Sofia Alexandra Ferreira
author_role author
author2 Fontes, João T.
Vieira, Pedro Emanuel Ferreira Reis
Costa, Filipe O.
Duarte, Sofia Alexandra Ferreira
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Lavrador, Ana Sofia Castro
Fontes, João T.
Vieira, Pedro Emanuel Ferreira Reis
Costa, Filipe O.
Duarte, Sofia Alexandra Ferreira
dc.subject.por.fl_str_mv European coastal ecosystems
DNA reference libraries
COI barcode sequences
Ciências Naturais::Ciências Biológicas
Science & Technology
Proteger a vida marinha
topic European coastal ecosystems
DNA reference libraries
COI barcode sequences
Ciências Naturais::Ciências Biológicas
Science & Technology
Proteger a vida marinha
description The script developed to create the DNA sequence reference library is available at https://github.com/tadeu95/Curated-BINs-Reference-Library (accessed on 25 January 2023). Metabarcoding datasets will be made available upon request since they belong to a study that is not published yet.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-01-01T00:00:00Z
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 https://hdl.handle.net/1822/82756
url https://hdl.handle.net/1822/82756
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Lavrador, A.S.; Fontes, J.T.; Vieira, P.E.; Costa, F.O.; Duarte, S. Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity 2023, 15, 174. https://doi.org/10.3390/d15020174
1424-2818
10.3390/d15020174
https://www.mdpi.com/1424-2818/15/2/174
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 MDPI
publisher.none.fl_str_mv MDPI
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
instname_str 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
repository.mail.fl_str_mv
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