Scientific Data (Jun 2023)
Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition
- Caroline Belser,
- Julie Poulain,
- Karine Labadie,
- Frederick Gavory,
- Adriana Alberti,
- Julie Guy,
- Quentin Carradec,
- Corinne Cruaud,
- Corinne Da Silva,
- Stefan Engelen,
- Paul Mielle,
- Aude Perdereau,
- Gaelle Samson,
- Shahinaz Gas,
- Genoscope Technical Team,
- Christian R. Voolstra,
- Pierre E. Galand,
- J. Michel Flores,
- Benjamin C. C. Hume,
- Gabriela Perna,
- Maren Ziegler,
- Hans-Joachim Ruscheweyh,
- Emilie Boissin,
- Sarah Romac,
- Guillaume Bourdin,
- Guillaume Iwankow,
- Clémentine Moulin,
- David A. Paz García,
- Sylvain Agostini,
- Bernard Banaigs,
- Emmanuel Boss,
- Chris Bowler,
- Colomban de Vargas,
- Eric Douville,
- Didier Forcioli,
- Paola Furla,
- Eric Gilson,
- Fabien Lombard,
- Stéphane Pesant,
- Stéphanie Reynaud,
- Shinichi Sunagawa,
- Olivier P. Thomas,
- Romain Troublé,
- Rebecca Vega Thurber,
- Didier Zoccola,
- Claude Scarpelli,
- E’ Krame Jacoby,
- Pedro H. Oliveira,
- Jean-Marc Aury,
- Denis Allemand,
- Serge Planes,
- Patrick Wincker
Affiliations
- Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Frederick Gavory
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Julie Guy
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Paul Mielle
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay
- Aude Perdereau
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Gaelle Samson
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Shahinaz Gas
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Genoscope Technical Team
- Christian R. Voolstra
- Department of Biology, University of Konstanz
- Pierre E. Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange
- J. Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science
- Benjamin C. C. Hume
- Department of Biology, University of Konstanz
- Gabriela Perna
- Department of Biology, University of Konstanz
- Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen
- Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
- Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d’Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy
- Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange
- Guillaume Bourdin
- School of Marine Sciences, University of Maine
- Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d’Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy
- Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012
- David A. Paz García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, Col. Playa Palo de Santa Rita Sur, La Paz
- Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda
- Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d’Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy
- Emmanuel Boss
- School of Marine Sciences, University of Maine
- Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange
- Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange
- Eric Douville
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay
- Didier Forcioli
- Université Côte d’Azur, CNRS, Inserm, IRCAN
- Paola Furla
- Université Côte d’Azur, CNRS, Inserm, IRCAN
- Eric Gilson
- Université Côte d’Azur, CNRS, Inserm, IRCAN
- Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange
- Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus
- Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d’Azur - Centre Scientifique de Monaco
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich
- Olivier P. Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road
- Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75 012
- Rebecca Vega Thurber
- Oregon State University, Department of Microbiology
- Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d’Azur - Centre Scientifique de Monaco
- Claude Scarpelli
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- E’ Krame Jacoby
- Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux
- Pedro H. Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d’Azur - Centre Scientifique de Monaco
- Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d’Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy
- Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay
- DOI
- https://doi.org/10.1038/s41597-023-02204-0
- Journal volume & issue
-
Vol. 10,
no. 1
pp. 1 – 19
Abstract
Abstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.