Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution
Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rare...
Published in: | Molecular Ecology Resources |
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Language: | English |
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Online Access: | https://doi.org/10.1111/1755-0998.13453 |
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ftzenodo:oai:zenodo.org:5360479 2024-09-15T18:24:44+00:00 Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution Fort, Antoine McHale, Marcus Cascella, Kevin Potin, Philippe Perrineau, Marie-Mathilde Kerrison, Philip D. Da Costa, Elisabete Calado, Ricard Domingues, Maria do Rosário Azevedo, Isabel Costa Sousa-Pinto, Isabel Gachon, Claire van der Werf, Adrie De Visser, Willem Beniers, Johanna E. Jansen, Henrice Guiry, Michael D. Sulpice, Ronan 2021-06-21 https://doi.org/10.1111/1755-0998.13453 eng eng Zenodo https://zenodo.org/communities/genialgproject https://zenodo.org/communities/eu https://doi.org/10.1111/1755-0998.13453 oai:zenodo.org:5360479 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode Molecular Ecology Resources, 2021(00), 1-16, (2021-06-21) Aquaculture DNA BArcoding Phylogeny Sea lettuce Ulva info:eu-repo/semantics/article 2021 ftzenodo https://doi.org/10.1111/1755-0998.13453 2024-07-25T09:30:21Z Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce ( Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci ( rbc L, tuf A, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbc L, tuf A and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%–32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U.lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus , Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution. Article in Journal/Newspaper North East Atlantic Zenodo Molecular Ecology Resources 22 1 86 101 |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
English |
topic |
Aquaculture DNA BArcoding Phylogeny Sea lettuce Ulva |
spellingShingle |
Aquaculture DNA BArcoding Phylogeny Sea lettuce Ulva Fort, Antoine McHale, Marcus Cascella, Kevin Potin, Philippe Perrineau, Marie-Mathilde Kerrison, Philip D. Da Costa, Elisabete Calado, Ricard Domingues, Maria do Rosário Azevedo, Isabel Costa Sousa-Pinto, Isabel Gachon, Claire van der Werf, Adrie De Visser, Willem Beniers, Johanna E. Jansen, Henrice Guiry, Michael D. Sulpice, Ronan Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
topic_facet |
Aquaculture DNA BArcoding Phylogeny Sea lettuce Ulva |
description |
Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce ( Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci ( rbc L, tuf A, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbc L, tuf A and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%–32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U.lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus , Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution. |
format |
Article in Journal/Newspaper |
author |
Fort, Antoine McHale, Marcus Cascella, Kevin Potin, Philippe Perrineau, Marie-Mathilde Kerrison, Philip D. Da Costa, Elisabete Calado, Ricard Domingues, Maria do Rosário Azevedo, Isabel Costa Sousa-Pinto, Isabel Gachon, Claire van der Werf, Adrie De Visser, Willem Beniers, Johanna E. Jansen, Henrice Guiry, Michael D. Sulpice, Ronan |
author_facet |
Fort, Antoine McHale, Marcus Cascella, Kevin Potin, Philippe Perrineau, Marie-Mathilde Kerrison, Philip D. Da Costa, Elisabete Calado, Ricard Domingues, Maria do Rosário Azevedo, Isabel Costa Sousa-Pinto, Isabel Gachon, Claire van der Werf, Adrie De Visser, Willem Beniers, Johanna E. Jansen, Henrice Guiry, Michael D. Sulpice, Ronan |
author_sort |
Fort, Antoine |
title |
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
title_short |
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
title_full |
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
title_fullStr |
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
title_full_unstemmed |
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
title_sort |
exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://doi.org/10.1111/1755-0998.13453 |
genre |
North East Atlantic |
genre_facet |
North East Atlantic |
op_source |
Molecular Ecology Resources, 2021(00), 1-16, (2021-06-21) |
op_relation |
https://zenodo.org/communities/genialgproject https://zenodo.org/communities/eu https://doi.org/10.1111/1755-0998.13453 oai:zenodo.org:5360479 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.1111/1755-0998.13453 |
container_title |
Molecular Ecology Resources |
container_volume |
22 |
container_issue |
1 |
container_start_page |
86 |
op_container_end_page |
101 |
_version_ |
1810465161577758720 |