Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Frédéric Rimet; Eva Aylagas; Ángel Borja; Agnès Bouchez; Alexis Canino; Christian Chauvin; Teofana Chonova; Fedor Ciampor Jr; Filipe O. Costa; Benoit J. D. Ferrari; Romain Gastineau; Chloé Goulon; Muriel Gugger; Maria Holzmann; Regine Jahn; Maria Kahlert; Wolf-Henning Kusber; Christophe Laplace-Treyture; Florian Leese; Frederik Leliaert; David G. Mann; Frédéric Marchand; Vona Méléder; Jan Pawlowski; Serena Rasconi; Sinziana Rivera; Rodolphe Rougerie; Magali Schweizer; Rosa Trobajo; Valentin Vasselon; Régis Vivien; Alexander Weigand; Andrzej Witkowski; Jonas Zimmermann; Torbjørn Ekrem

doi:10.3897/mbmg.5.58056

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Frédéric Rimet, Eva Aylagas, Ángel Borja, Agnès Bouchez, Alexis Canino, Christian Chauvin, Teofana Chonova, Fedor Ciampor Jr, Filipe O. Costa, Benoit J. D. Ferrari, Romain Gastineau, Chloé Goulon, Muriel Gugger, Maria Holzmann, Regine Jahn, Maria Kahlert, Wolf-Henning Kusber, Christophe Laplace-Treyture, Florian Leese, Frederik LeliaertDavid G. Mann, Frédéric Marchand, Vona Méléder, Jan Pawlowski, Serena Rasconi, Sinziana Rivera, Rodolphe Rougerie, Magali Schweizer, Rosa Trobajo, Valentin Vasselon, Régis Vivien, Alexander Weigand, Andrzej Witkowski, Jonas Zimmermann, Torbjørn Ekrem

King Abdullah University of Science and Technology

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

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.

Original language	English (US)
Journal	Metabarcoding and Metagenomics
Volume	5
DOIs	https://doi.org/10.3897/mbmg.5.58056
State	Published - Feb 26 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-03-03
Acknowledgements: Patricia Mergen (Botanical Garden of Meise, Belgium) is thanked for introducing experts who co-authored this paper. We thank Charlotte Duval and Claude Yéprémian of the MNHN (Muséum National d’Histoire Naturelle, Paris, France) for their comments. We acknowledge Axel Hausmann, Matthias F. Geiger and two additional anonymous reviewers for their constructive comments.
This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 https://dnaqua.net/) is a collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016). Reference libraries, together with their feasibility and quality, are one of the most important subjects of DNAqua-Net and several meetings highlighted the need to improve the reference data and maintain their quality and reliability. This has been formalised in the discussion of Weigand et al. (2019).

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10.3897/mbmg.5.58056

https://repository.kaust.edu.sa/bitstream/10754/667795/1/MBMG_article_58056_en_1.pdf

Cite this

Rimet, F., Aylagas, E., Borja, Á., Bouchez, A., Canino, A., Chauvin, C., Chonova, T., Ciampor Jr, F., Costa, F. O., Ferrari, B. J. D., Gastineau, R., Goulon, C., Gugger, M., Holzmann, M., Jahn, R., Kahlert, M., Kusber, W.-H., Laplace-Treyture, C., Leese, F., ... Ekrem, T. (2021). Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. Metabarcoding and Metagenomics, 5. https://doi.org/10.3897/mbmg.5.58056

@article{7abe1dffe1f04688a60ee1de1694c53b,

title = "Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life",

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.",

author = "Fr{\'e}d{\'e}ric Rimet and Eva Aylagas and {\'A}ngel Borja and Agn{\`e}s Bouchez and Alexis Canino and Christian Chauvin and Teofana Chonova and {Ciampor Jr}, Fedor and Costa, {Filipe O.} and Ferrari, {Benoit J. D.} and Romain Gastineau and Chlo{\'e} Goulon and Muriel Gugger and Maria Holzmann and Regine Jahn and Maria Kahlert and Wolf-Henning Kusber and Christophe Laplace-Treyture and Florian Leese and Frederik Leliaert and Mann, {David G.} and Fr{\'e}d{\'e}ric Marchand and Vona M{\'e}l{\'e}der and Jan Pawlowski and Serena Rasconi and Sinziana Rivera and Rodolphe Rougerie and Magali Schweizer and Rosa Trobajo and Valentin Vasselon and R{\'e}gis Vivien and Alexander Weigand and Andrzej Witkowski and Jonas Zimmermann and Torbj{\o}rn Ekrem",

note = "KAUST Repository Item: Exported on 2021-03-03 Acknowledgements: Patricia Mergen (Botanical Garden of Meise, Belgium) is thanked for introducing experts who co-authored this paper. We thank Charlotte Duval and Claude Y{\'e}pr{\'e}mian of the MNHN (Mus{\'e}um National d{\textquoteright}Histoire Naturelle, Paris, France) for their comments. We acknowledge Axel Hausmann, Matthias F. Geiger and two additional anonymous reviewers for their constructive comments. This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 https://dnaqua.net/) is a collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016). Reference libraries, together with their feasibility and quality, are one of the most important subjects of DNAqua-Net and several meetings highlighted the need to improve the reference data and maintain their quality and reliability. This has been formalised in the discussion of Weigand et al. (2019).",

year = "2021",

month = feb,

day = "26",

doi = "10.3897/mbmg.5.58056",

language = "English (US)",

volume = "5",

journal = "Metabarcoding and Metagenomics",

issn = "2534-9708",

publisher = "Pensoft Publishers",

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Rimet, F, Aylagas, E, Borja, Á, Bouchez, A, Canino, A, Chauvin, C, Chonova, T, Ciampor Jr, F, Costa, FO, Ferrari, BJD, Gastineau, R, Goulon, C, Gugger, M, Holzmann, M, Jahn, R, Kahlert, M, Kusber, W-H, Laplace-Treyture, C, Leese, F, Leliaert, F, Mann, DG, Marchand, F, Méléder, V, Pawlowski, J, Rasconi, S, Rivera, S, Rougerie, R, Schweizer, M, Trobajo, R, Vasselon, V, Vivien, R, Weigand, A, Witkowski, A, Zimmermann, J & Ekrem, T 2021, 'Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life', Metabarcoding and Metagenomics, vol. 5. https://doi.org/10.3897/mbmg.5.58056

TY - JOUR

T1 - Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

AU - Rimet, Frédéric

AU - Aylagas, Eva

AU - Borja, Ángel

AU - Bouchez, Agnès

AU - Canino, Alexis

AU - Chauvin, Christian

AU - Chonova, Teofana

AU - Ciampor Jr, Fedor

AU - Costa, Filipe O.

AU - Ferrari, Benoit J. D.

AU - Gastineau, Romain

AU - Goulon, Chloé

AU - Gugger, Muriel

AU - Holzmann, Maria

AU - Jahn, Regine

AU - Kahlert, Maria

AU - Kusber, Wolf-Henning

AU - Laplace-Treyture, Christophe

AU - Leese, Florian

AU - Leliaert, Frederik

AU - Mann, David G.

AU - Marchand, Frédéric

AU - Méléder, Vona

AU - Pawlowski, Jan

AU - Rasconi, Serena

AU - Rivera, Sinziana

AU - Rougerie, Rodolphe

AU - Schweizer, Magali

AU - Trobajo, Rosa

AU - Vasselon, Valentin

AU - Vivien, Régis

AU - Weigand, Alexander

AU - Witkowski, Andrzej

AU - Zimmermann, Jonas

AU - Ekrem, Torbjørn

N1 - KAUST Repository Item: Exported on 2021-03-03 Acknowledgements: Patricia Mergen (Botanical Garden of Meise, Belgium) is thanked for introducing experts who co-authored this paper. We thank Charlotte Duval and Claude Yéprémian of the MNHN (Muséum National d’Histoire Naturelle, Paris, France) for their comments. We acknowledge Axel Hausmann, Matthias F. Geiger and two additional anonymous reviewers for their constructive comments. This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 https://dnaqua.net/) is a collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016). Reference libraries, together with their feasibility and quality, are one of the most important subjects of DNAqua-Net and several meetings highlighted the need to improve the reference data and maintain their quality and reliability. This has been formalised in the discussion of Weigand et al. (2019).

PY - 2021/2/26

Y1 - 2021/2/26

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/667795

UR - https://mbmg.pensoft.net/article/58056/

U2 - 10.3897/mbmg.5.58056

DO - 10.3897/mbmg.5.58056

M3 - Article

SN - 2534-9708

VL - 5

JO - Metabarcoding and Metagenomics

JF - Metabarcoding and Metagenomics

ER -

Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Abstract

Bibliographical note

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