The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms

Caroline Vernette, Nicolas Henry, Julien Lecubin, Colomban de Vargas, Pascal Hingamp, Magali Lescot

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA miTags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables.
Original languageEnglish (US)
Pages (from-to)1347-1358
Number of pages12
JournalMolecular Ecology Resources
Volume21
Issue number4
DOIs
StatePublished - Jan 12 2021
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-15
Acknowledgements: This article is contribution number 111 of Tara Oceans. The authors would like to thank Guillem Salazar for providing us with the Malaspina-2010 16S-V4V5 OTU tables. We are grateful for the contribution of the ECOMAP team at Roscoff Marine Station, and in particular Miguel Méndez Sandin and Fabrice Not, for testing the web server and suggesting functionalities. Thanks also to Noan Le Bescot for the plankton drawing used on the interfaces. The web server is hosted by the OSU Pythéas cluster with the help of Cyrille Blanpain and the SIP members. Adrien Malgoyre from the SIP is thanked for the development of the OSU Pythéas gitlab. We are grateful to the Institut Français de Bioinformatique for providing help and computing resources. Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (http://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, The French Ministry of Research, and the French Government ‘Investissements d’Avenir’ programmes, FRANCE GENOMIQUE, MEMO LIFE and PSL* Research University. We also thank the support and commitment of agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST. The global sampling effort was enabled by countless scientists and crew who sampled aboard the Tara from 2009–2013, and we thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. We are also grateful to the countries who graciously granted sampling permissions. The authors declare that all data reported herein are fully and freely available from the date of publication, with no restrictions, and that all of the analyses, publications, and ownership of data are free from legal entanglement or restriction by the various nations whose waters the Tara Oceans expeditions. This work was supported by the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), the Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02) and SeqDigger (ANR-19-CE45-0008).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Biotechnology

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