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Journal articles
Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life
Frédéric Rimet
1, *
Eva Aylagas
2
Ángel Borja
3, 4
Agnes Bouchez
1
Alexis Canino
1
Christian Chauvin
5
Teofana Chonova
1
Fedor Ciampor Jr
6
Filipe Costa
7
Benoit Ferrari
8
Romain Gastineau
9
Chloé Goulon
1
Muriel Gugger
10
Maria Holzmann
11
Regine Jahn
12
Maria Kahlert
13
Wolf-Henning Kusber
12
Christophe Laplace-Treyture
5
Florian Leese
14
Frederik Leliaert
15
David Mann
16, 17
Frédéric Marchand
18
Vona Méléder
19
Jan Pawlowski
11, 20, 21
Serena Rasconi
1
Sinziana Rivera
1
Rodolphe Rougerie
22
Magali Schweizer
23
Rosa Trobajo
16
Valentin Vasselon
24
Régis Vivien
8
Alexander Weigand
25
Andrzej Witkowski
9
Jonas Zimmermann
12
Torbjørn Ekrem
26
*
Corresponding author
Frédéric Rimet 1
Correspondent author
Eva Aylagas 2
Author
Ángel Borja 3, 4
Author
Agnes Bouchez 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : agnes-bouchez ORCID : https://orcid.org/0000-0001-8802-6966
Alexis Canino 1
Author
Christian Chauvin 5
Author
Teofana Chonova 1
Author
Fedor Ciampor Jr 6
Author
Filipe O. Costa 7
Author
Benoit J.D. Ferrari 8
Author
Romain Gastineau 9
Author
Chloé Goulon 1
Author
Wolf-Henning Kusber 12
Author
Christophe Laplace-Treyture 5
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : christophe-laplace-treyture ORCID : https://orcid.org/0000-0002-0833-473X
Florian Leese 14
Author
Frederik Leliaert 15
Author
David G. Mann 16, 17
Author
Frédéric Marchand 18
Author IdHAL : frederic-marchand ORCID : https://orcid.org/0000-0002-8380-579X
Vona Méléder 19
Author
Jan Pawlowski 11, 20, 21
Author
Serena Rasconi 1
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : serena-rasconi ORCID : https://orcid.org/0000-0001-6667-8904
Sinziana Rivera 1
Author
Rodolphe Rougerie 22
Author IdHAL : rodolphe-rougerie ORCID : https://orcid.org/0000-0003-0937-2815
Magali Schweizer 23
Author
Rosa Trobajo 16
Author
Valentin Vasselon 24
Author IdHAL : valentin-vasselon ORCID : https://orcid.org/0000-0001-5038-7918
Régis Vivien 8
Author
Alexander Weigand 25
Author
1
CARRTEL - Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (74200 Thonon-les-Bains, France - 73376 Le Bourget du Lac, France - France)
- USMB [Université de Savoie] [Université de Chambéry] - Université Savoie Mont Blanc (27, rue Marcoz - 73000 Chambéry - France)
- INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement : UMR0042 (France)
2
KAUST - King Abdullah University of Science and Technology (King Abdullah University of Science and Technology P.O.Box 55455 Jeddah 21534, Saudi Arabia - Saudi Arabia)
4
King Abdulaziz University ( Djeddah 21589 - Saudi Arabia)
5
UR EABX - Ecosystèmes aquatiques et changements globaux (50 avenue de Verdun - Gazinet, F-33612 Cestas - France)
6
SAS - Slovak Academy of Science [Bratislava] (Štefánikova 898/49, 811 04 Staré Mesto - Bratislava - Slovakia)
7
Universidade do Minho (Largo do Paço, 4704-553 Braga - Portugal)
8
Swiss Centre for Applied Ecotoxicology (Ecotox Center) (Swiss Centre for Applied Ecotoxicology (Ecotox Center), EPFL ENAC IIE-GE, Station 2, CH-1015, Lausanne, Switzerland - Switzerland)
- EPFL - Ecole Polytechnique Fédérale de Lausanne (CH-1015 Lausanne, Switzerland - Switzerland)
9
Technical university of Szczecin (France)
10
Collection des Cyanobactéries (Département Microbiologie - 25-28 rue du Docteur Roux, 75724 Paris Cedex 15 - )
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
11
University of Geneva [Switzerland] (Bd du Pont-d'Arve 40, CH-1211 Geneva 4 - Switzerland)
12
Freie Universität Berlin (Kaiserswerther Str. 16-18, 14195 Berlin - Germany)
13
SLU - Swedish University of Agricultural Sciences (S-750 07 Uppsala - Sweden)
14
Universitat Duisberg-Essen (Forsthausweg 2, 47057 Duisburg - Germany)
15
Botanic Garden Meise (Bouchout Domain, Nieuwelaan 38 1860 Meise - Belgium)
16
IRTA - Institute of Agrifood Research and Technology [Sant Carles de la Ràpita] (Poble Nou, Km 5,5, 43540 Sant Carles de la Ràpita - Spain)
- IRTA - Institute of Agrifood Research and Technology (Torre Marimon 08140 Caldes de Montbui (Barcelona) - Spain)
17
Royal Botanic Garden Edinburgh (Arboretum Pl, Edinburgh EH3 5NZ, Royaume-Uni - United Kingdom)
18
U3E - Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique - U3E (Rennes, France) (France)
19
UN - Université de Nantes (1, quai de Tourville - BP 13522 - 44035 Nantes cedex 1 - France)
20
PAN - Polish Academy of Sciences (00-901 Warszawa - Poland)
21
ID-Gene ecodiagnostics [Geneva] (Campus Biotech Innovation Park, 1202, Geneva - Switzerland)
22
ISYEB - Institut de Systématique, Evolution, Biodiversité (57 rue Cuvier - CP 50 - 75005 Paris - France)
- MNHN - Muséum national d'Histoire naturelle (57, rue Cuvier - 75231 Paris Cedex 05 - France)
- EPHE - École pratique des hautes études (4-14 Rue Ferrus, 75014 Paris - France)
- PSL - Université Paris sciences et lettres (60 rue Mazarine 75006 Paris - France)
- SU - Sorbonne Université (21 rue de l’École de médecine - 75006 Paris - France)
- CNRS - Centre National de la Recherche Scientifique : UMR7205 (France)
- UA - Université des Antilles (Université des Antilles | Fouillole - BP 250 - 97157 Pointe-à-Pitre - France)
23
LPG - Laboratoire de Planétologie et Géodynamique [UMR 6112] (2 Rue de la Houssinière - BP 92208 44322 NANTES CEDEX 3 - France)
- UA - Université d'Angers : UMR6112 (Université d'Angers - 40 Rue de Rennes, BP 73532 - 49035 Angers CEDEX 01 - France)
- UN UFR ST - Université de Nantes - UFR des Sciences et des Techniques : UMR6112 (2, rue de la Houssinière - BP 92208 - 44322 Nantes cedex 3 - France)
- UN - Université de Nantes (1, quai de Tourville - BP 13522 - 44035 Nantes cedex 1 - France)
- INSU - CNRS - Institut national des sciences de l'Univers : UMR6112 (INSU-CNRS 3 rue Michel-Ange, 75794 Paris Cedex 16 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6112 (France)
24
SCIMABIO Interface SAS (5 rue des Quatre Vents, 74200 Thonon-les-Bains - France)
25
MNHN - Musée National d'Histoire Naturelle de Luxembourg (Luxembourg)
26
NTNU - Norwegian University of Science and Technology [Trondheim] (NO-7491 Trondheim - Norway)
Abstract : DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
Document type :
Journal articles
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03159791
Contributor : Bénédicte Benedic <>
Submitted on : Thursday, March 4, 2021 - 5:01:51 PM
Last modification on : Tuesday, September 21, 2021 - 4:06:05 PM
Long-term archiving on: : Saturday, June 5, 2021 - 7:16:12 PM
Contributor : Bénédicte Benedic <>
Submitted on : Thursday, March 4, 2021 - 5:01:51 PM
Last modification on : Tuesday, September 21, 2021 - 4:06:05 PM
Long-term archiving on: : Saturday, June 5, 2021 - 7:16:12 PM
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MBMG_article_58056_en_1.pdf
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Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-03159791, version 1
- DOI : 10.3897/mbmg.5.58056
Collections
PASTEUR | COLISA | LIFE | POLE_MIGRATEURS_AMPHIHALINS | U3E | LPG | UNIV-NANTES | PSL | UNIV-AG | UNIV-SAVOIE | MNHN | ISYEB | EPHE | UNIV-ANGERS | CNRS | INRAE | INSU | SU-SCIENCES | INRAE-AQUA | CARRTEL | SORBONNE-UNIVERSITE | SU-TI
Citation
Frédéric Rimet, Eva Aylagas, Ángel Borja, Agnes Bouchez, Alexis Canino, et al.. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. Metabarcoding and Metagenomics, Pensoft Publishers 2021, 5, pp.e58056. ⟨10.3897/mbmg.5.58056⟩. ⟨pasteur-03159791⟩
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