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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ftdoajarticles:oai:doaj.org/article:127c4296a66742c69e66970e616b099e 2023-05-15T17:38:35+02:00 DNA barcoding for species assignment: the case of Mediterranean marine fishes. Monica Landi Mark Dimech Marco Arculeo Girolama Biondo Rogelia Martins Miguel Carneiro Gary Robert Carvalho Sabrina Lo Brutto Filipe O Costa 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0106135 https://doaj.org/article/127c4296a66742c69e66970e616b099e EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4164363?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0106135 https://doaj.org/article/127c4296a66742c69e66970e616b099e PLoS ONE, Vol 9, Iss 9, p e106135 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0106135 2022-12-31T02:09:49Z 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 ... Article in Journal/Newspaper North East Atlantic Directory of Open Access Journals: DOAJ Articles PLoS ONE 9 9 e106135 |
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Medicine R Science Q Monica Landi Mark Dimech Marco Arculeo Girolama Biondo Rogelia Martins Miguel Carneiro Gary Robert Carvalho Sabrina Lo Brutto Filipe O Costa DNA barcoding for species assignment: the case of Mediterranean marine fishes. |
topic_facet |
Medicine R Science Q |
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 ... |
format |
Article in Journal/Newspaper |
author |
Monica Landi Mark Dimech Marco Arculeo Girolama Biondo Rogelia Martins Miguel Carneiro Gary Robert Carvalho Sabrina Lo Brutto Filipe O Costa |
author_facet |
Monica Landi Mark Dimech Marco Arculeo Girolama Biondo Rogelia Martins Miguel Carneiro Gary Robert Carvalho Sabrina Lo Brutto Filipe O Costa |
author_sort |
Monica Landi |
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 (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0106135 https://doaj.org/article/127c4296a66742c69e66970e616b099e |
genre |
North East Atlantic |
genre_facet |
North East Atlantic |
op_source |
PLoS ONE, Vol 9, Iss 9, p e106135 (2014) |
op_relation |
http://europepmc.org/articles/PMC4164363?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0106135 https://doaj.org/article/127c4296a66742c69e66970e616b099e |
op_doi |
https://doi.org/10.1371/journal.pone.0106135 |
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PLoS ONE |
container_volume |
9 |
container_issue |
9 |
container_start_page |
e106135 |
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