DNA barcoding for species assignment : the case of Mediterranean marine fishes
Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to...
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ftunivmalta:oai:www.um.edu.mt:123456789/59319 2023-05-15T17:38:39+02:00 DNA barcoding for species assignment : the case of Mediterranean marine fishes Landi, Monica Dimech, Mark Arculeo, Marco Biondo, Girolama Martins, Rogelia Carneiro, Miguel Carvalho, Gary Robert Brutto, Sabrina Lo Costa, Filipe O. 2014 https://www.um.edu.mt/library/oar/handle/123456789/59319 https://doi.org/10.1371/journal.pone.0106135 en eng Public Library of Science Landi, M., Dimech, M., Arculeo, M., Biondo, G., Martins, R., Carneiro, M., . & Costa, F. O. (2014). DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One, 9(9), 1-9. https://www.um.edu.mt/library/oar/handle/123456789/59319 doi:10.1371/journal.pone.0106135 info:eu-repo/semantics/openAccess The copyright of this work belongs to the author(s)/publisher. The rights of this work are as defined by the appropriate Copyright Legislation or as modified by any successive legislation. Users may access this work and can make use of the information contained in accordance with the Copyright Legislation provided that the author must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the prior permission of the copyright holder DNA Nucleotide sequence Genes -- Research Marine species diversity Fishes -- Mediterranean Sea article 2014 ftunivmalta https://doi.org/10.1371/journal.pone.0106135 2021-10-16T18:10:11Z Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity. peer-reviewed Article in Journal/Newspaper North East Atlantic University of Malta: OAR@UM PLoS ONE 9 9 e106135 |
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Open Polar |
collection |
University of Malta: OAR@UM |
op_collection_id |
ftunivmalta |
language |
English |
topic |
DNA Nucleotide sequence Genes -- Research Marine species diversity Fishes -- Mediterranean Sea |
spellingShingle |
DNA Nucleotide sequence Genes -- Research Marine species diversity Fishes -- Mediterranean Sea Landi, Monica Dimech, Mark Arculeo, Marco Biondo, Girolama Martins, Rogelia Carneiro, Miguel Carvalho, Gary Robert Brutto, Sabrina Lo Costa, Filipe O. DNA barcoding for species assignment : the case of Mediterranean marine fishes |
topic_facet |
DNA Nucleotide sequence Genes -- Research Marine species diversity Fishes -- Mediterranean Sea |
description |
Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity. peer-reviewed |
format |
Article in Journal/Newspaper |
author |
Landi, Monica Dimech, Mark Arculeo, Marco Biondo, Girolama Martins, Rogelia Carneiro, Miguel Carvalho, Gary Robert Brutto, Sabrina Lo Costa, Filipe O. |
author_facet |
Landi, Monica Dimech, Mark Arculeo, Marco Biondo, Girolama Martins, Rogelia Carneiro, Miguel Carvalho, Gary Robert Brutto, Sabrina Lo Costa, Filipe O. |
author_sort |
Landi, Monica |
title |
DNA barcoding for species assignment : the case of Mediterranean marine fishes |
title_short |
DNA barcoding for species assignment : the case of Mediterranean marine fishes |
title_full |
DNA barcoding for species assignment : the case of Mediterranean marine fishes |
title_fullStr |
DNA barcoding for species assignment : the case of Mediterranean marine fishes |
title_full_unstemmed |
DNA barcoding for species assignment : the case of Mediterranean marine fishes |
title_sort |
dna barcoding for species assignment : the case of mediterranean marine fishes |
publisher |
Public Library of Science |
publishDate |
2014 |
url |
https://www.um.edu.mt/library/oar/handle/123456789/59319 https://doi.org/10.1371/journal.pone.0106135 |
genre |
North East Atlantic |
genre_facet |
North East Atlantic |
op_relation |
Landi, M., Dimech, M., Arculeo, M., Biondo, G., Martins, R., Carneiro, M., . & Costa, F. O. (2014). DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One, 9(9), 1-9. https://www.um.edu.mt/library/oar/handle/123456789/59319 doi:10.1371/journal.pone.0106135 |
op_rights |
info:eu-repo/semantics/openAccess The copyright of this work belongs to the author(s)/publisher. The rights of this work are as defined by the appropriate Copyright Legislation or as modified by any successive legislation. Users may access this work and can make use of the information contained in accordance with the Copyright Legislation provided that the author must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the prior permission of the copyright holder |
op_doi |
https://doi.org/10.1371/journal.pone.0106135 |
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PLoS ONE |
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9 |
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9 |
container_start_page |
e106135 |
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