Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions
Autor(a) principal: | |
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Data de Publicação: | 2020 |
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/1822/72848 |
Resumo: | DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications. |
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Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regionsBOLDDNA barcode markersGap-analysisGenBankMarine and coastal ecosystemsNon-indigenous speciesEngenharia e Tecnologia::Biotecnologia AmbientalDNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.FCT - Fundação para a Ciência e a Tecnologia(PTDC/BIA-BMA/29754/2017)Pensoft PublishersUniversidade do MinhoDuarte, Sofia Alexandra FerreiraVieira, Pedro Emanuel Ferreira ReisCosta, Filipe O.20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/72848engDuarte, S., Vieira, P. E., Costa, F. O. (2020). Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics, 4, e551622534-970810.3897/mbmg.4.55162https://mbmg.pensoft.net/article/55162/info: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:RCAAP2023-07-21T12:28:27Zoai:repositorium.sdum.uminho.pt:1822/72848Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:23:17.477796Repositório 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 |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
title |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
spellingShingle |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions Duarte, Sofia Alexandra Ferreira BOLD DNA barcode markers Gap-analysis GenBank Marine and coastal ecosystems Non-indigenous species Engenharia e Tecnologia::Biotecnologia Ambiental |
title_short |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
title_full |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
title_fullStr |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
title_full_unstemmed |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
title_sort |
Assessment of species gaps in DNA barcode libraries of nonindigenous species (NIS) occurring in European coastal regions |
author |
Duarte, Sofia Alexandra Ferreira |
author_facet |
Duarte, Sofia Alexandra Ferreira Vieira, Pedro Emanuel Ferreira Reis Costa, Filipe O. |
author_role |
author |
author2 |
Vieira, Pedro Emanuel Ferreira Reis Costa, Filipe O. |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Duarte, Sofia Alexandra Ferreira Vieira, Pedro Emanuel Ferreira Reis Costa, Filipe O. |
dc.subject.por.fl_str_mv |
BOLD DNA barcode markers Gap-analysis GenBank Marine and coastal ecosystems Non-indigenous species Engenharia e Tecnologia::Biotecnologia Ambiental |
topic |
BOLD DNA barcode markers Gap-analysis GenBank Marine and coastal ecosystems Non-indigenous species Engenharia e Tecnologia::Biotecnologia Ambiental |
description |
DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020 2020-01-01T00:00:00Z |
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 |
http://hdl.handle.net/1822/72848 |
url |
http://hdl.handle.net/1822/72848 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Duarte, S., Vieira, P. E., Costa, F. O. (2020). Assessment of species gaps in DNA barcode libraries of non-indigenous species (NIS) occurring in European coastal regions. Metabarcoding and Metagenomics, 4, e55162 2534-9708 10.3897/mbmg.4.55162 https://mbmg.pensoft.net/article/55162/ |
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 |
Pensoft Publishers |
publisher.none.fl_str_mv |
Pensoft Publishers |
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 |
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1799132706681913344 |