Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Caroline Belser (1) , Julie Poulain (1) , Karine Labadie (2) , Frederick Gavory (1) , Adriana Alberti (3, 1) , Julie Guy (2) , Quentin Carradec (1) , Corinne Cruaud (2) , Corinne da Silva (1) , Stefan Engelen (1) , Paul Mielle (4) , Aude Perdereau (2) , Gaelle Samson (2) , Shahinaz Gas (2) , Genoscope Technical Team (2) , Christian R Voolstra (5) , Pierre E Galand (6) , J. Michel Flores (7) , Benjamin Cc Hume (5) , Gabriela Perna (5) , Maren Ziegler (8) , Hans-Joachim Ruscheweyh (9) , Emilie Boissin (10) , Sarah Romac (11) , Guillaume Bourdin (12) , Guillaume Iwankow (10) , Clémentine Moulin (13) , David A Paz García (14) , Sylvain Agostini (15) , Bernard Banaigs (10, 16) , Emmanuel Boss (12) , Chris Bowler (17) , Colomban de Vargas (11) , Éric Douville (18, 19) , Didier Forcioli (20, 21) , Paola Furla (20, 21) , Éric Gilson (20, 21) , Fabien Lombard (22) , Stephane Pesant (23) , Stéphanie Reynaud (24) , Shinichi Sunagawa (9) , Olivier Thomas (25) , Romain Troublé (13) , Rebecca Vega Thurber (26) , Didier Zoccola (24) , Claude Scarpelli (2) , E Krame Jacoby (2) , Pedro H Oliveira (2) , Jean-Marc Aury (1) , Denis Allemand (24) , Serge Planes (10) , Patrick Wincker (1)

1 UMR 8030 - Génomique métabolique
2 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
3 I2BC - Institut de Biologie Intégrative de la Cellule
4 CNRGH - Centre National de Recherche en Génomique Humaine
5 Universität Konstanz
6 LECOB - Laboratoire d'Ecogéochimie des environnements benthiques
7 Weizmann Institute of Science [Rehovot, Israël]
8 JLU - Justus-Liebig-Universität Gießen = Justus Liebig University
9 D-BIOL - Department of Biology [ETH Zürich]
10 CRIOBE - Centre de recherches insulaires et observatoire de l'environnement
11 SBR - Station biologique de Roscoff
12 University of Maine
13 Tara Expéditions
14 CONACYT-CIBNOR - Centro de Investigaciones Biologicas del Noroeste [Mexico]
15 Université de Tsukuba = University of Tsukuba
16 LabEX CORAIL - Laboratoire d'Excellence CORAIL
17 IBENS - Institut de biologie de l'ENS Paris
18 LSCE - Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette]
19 GEOTRAC - Géochrononologie Traceurs Archéométrie
20 IRCAN - Institut de Recherche sur le Cancer et le Vieillissement
21 UCA - Université Côte d'Azur
22 LOV - Laboratoire d'océanographie de Villefranche
23 EMBL - European Molecular Biology Laboratory
24 CSM - Centre Scientifique de Monaco
25 NUI Galway - National University of Ireland [Galway]
26 OSU - Oregon State University

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 host coral 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.

Domains: Bioinformatics [q-bio.QM]

Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, et al.. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. 2022. ⟨cea-03713370v2⟩