Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition
Caroline Belser, Julie Poulain, Karine Labadie, Frédérick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne Da Silva, Stéfan Engelen, Paul Mielle, Aude Perdereau, Gaëlle Samson, Shahinaz Gas, Genoscope Technical Team, Julie Batisse, Odette Beluche, Laurie Bertrand, Chloé Bohers, Isabelle Bordelais, Élodie Brun, Maria Dubois, Corinne Dumont, El Hajji Zineb, Barbara D. Estrada, Evelyne Ettedgui, Patricia Carina Fernández, Sonia Garidi, Thomas Guérin, Kévin Gorrichon, Chadia Hamon, Lucille Kientzel, Sandrine Lebled, Chloé Legrain, Patricia Lenoble, Marine Leprêtre, Claudine Louesse, Ghislaine Magdelenat, Eric Mahieu, Nathalie Martins, Claire Milani, Céline Orvain, Sophie Oztas, Emilie Payen, Emmanuelle Petit, Guillaume Rio, Dominique Robert, Muriel Ronsin, Benoît Vacherie, Christian R. Voolstra, Pierre E. Galand, J. Michel Flores, Benjamin C. C. Hume, Gabriela Perna, Maren Ziegler, Hans‐Joachim Ruscheweyh, Émilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, David A. Paz‐García, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Éric Douville, Didier Forcioli, Paola Furla, Éric 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
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.