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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Main Authors: | , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2021
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Online Access: | https://pure.uhi.ac.uk/en/publications/6cc429fe-2be6-438f-a988-83f43e1c72da https://doi.org/10.1111/1755-0998.13453 https://pureadmin.uhi.ac.uk/ws/files/16183285/1755_0998.13453.pdf https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13453 |
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ftuhipublicatio:oai:pure.atira.dk:publications/6cc429fe-2be6-438f-a988-83f43e1c72da 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. Costa, Elisabete Calado, Ricardo Domingues, Maria Do Rosário Costa Azevedo, Isabel Sousa‐pinto, Isabel Gachon, Claire Werf, Adrie Visser, Willem Beniers, Johanna E. Jansen, Henrice Guiry, Michael D. Sulpice, Ronan 2021-07-05 application/pdf https://pure.uhi.ac.uk/en/publications/6cc429fe-2be6-438f-a988-83f43e1c72da https://doi.org/10.1111/1755-0998.13453 https://pureadmin.uhi.ac.uk/ws/files/16183285/1755_0998.13453.pdf https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13453 eng eng https://pure.uhi.ac.uk/en/publications/6cc429fe-2be6-438f-a988-83f43e1c72da info:eu-repo/semantics/openAccess Fort , A , Mchale , M , Cascella , K , Potin , P , Perrineau , M , Kerrison , P D , Costa , E , Calado , R , Domingues , M D R , Costa Azevedo , I , Sousa‐pinto , I , Gachon , C , Werf , A , Visser , W , Beniers , J E , Jansen , H , Guiry , M D & Sulpice , R 2021 , ' Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution ' , Molecular Ecology Resources . https://doi.org/10.1111/1755-0998.13453 aquaculture DNA barcoding phylogeny sea lettuce ulva article 2021 ftuhipublicatio https://doi.org/10.1111/1755-0998.13453 2024-07-15T23:38:41Z 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 (rbcL, tufA, 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 rbcL, tufA 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 University of the Highlands and Islands: Research Database of UHI Molecular Ecology Resources |
institution |
Open Polar |
collection |
University of the Highlands and Islands: Research Database of UHI |
op_collection_id |
ftuhipublicatio |
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. Costa, Elisabete Calado, Ricardo Domingues, Maria Do Rosário Costa Azevedo, Isabel Sousa‐pinto, Isabel Gachon, Claire Werf, Adrie 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 (rbcL, tufA, 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 rbcL, tufA 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. Costa, Elisabete Calado, Ricardo Domingues, Maria Do Rosário Costa Azevedo, Isabel Sousa‐pinto, Isabel Gachon, Claire Werf, Adrie 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. Costa, Elisabete Calado, Ricardo Domingues, Maria Do Rosário Costa Azevedo, Isabel Sousa‐pinto, Isabel Gachon, Claire Werf, Adrie 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 |
publishDate |
2021 |
url |
https://pure.uhi.ac.uk/en/publications/6cc429fe-2be6-438f-a988-83f43e1c72da https://doi.org/10.1111/1755-0998.13453 https://pureadmin.uhi.ac.uk/ws/files/16183285/1755_0998.13453.pdf https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13453 |
genre |
North East Atlantic |
genre_facet |
North East Atlantic |
op_source |
Fort , A , Mchale , M , Cascella , K , Potin , P , Perrineau , M , Kerrison , P D , Costa , E , Calado , R , Domingues , M D R , Costa Azevedo , I , Sousa‐pinto , I , Gachon , C , Werf , A , Visser , W , Beniers , J E , Jansen , H , Guiry , M D & Sulpice , R 2021 , ' Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution ' , Molecular Ecology Resources . https://doi.org/10.1111/1755-0998.13453 |
op_relation |
https://pure.uhi.ac.uk/en/publications/6cc429fe-2be6-438f-a988-83f43e1c72da |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1111/1755-0998.13453 |
container_title |
Molecular Ecology Resources |
_version_ |
1810465151907790848 |