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

Author

Belser, Caroline, Poulain, Julie, Labadie, Karine, Gavory, Frederick, Alberti, Adriana, Guy, Julie, Carradec, Quentin, Cruaud, Corinne, da Silva, Corinne, Engelen, Stefan, Mielle, Paul, Perdereau, Aude, Samson, Gaelle, Gaz, Shahinaz, Team, Genoscope Technical, Voolstra, Christian R, Galand, Pierre E, Flores, J. Michel, Hume, Benjamin Cc, Perna, Gabriela, Ziegler, Maren, Ruscheweyh, Hans-Joachim, Boissin, Emilie, Romac, Sarah, Bourdin, Guillaume, Iwankow, Guillaume, Moulin, Clémentine, García, David A Paz, Coordinators, Tara Pacific Consortium, Scarpelli, Claude, Jacoby, E Krame, Oliveira, Pedro H, Aury, Jean-Marc, Allemand, Denis, Planes, Serge, and Wincker, Patrick

Subjects
Quantitative Biology - Quantitative Methods
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 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.

Published
2022

4. Different environmental response strategies in sympatric corals from Pacific Islands

Author

Porro, Barbara, Zamoum, Thamilla, Forcioli, Didier, Gilson, Eric, Poquet, Adrien, Di Franco, Eugenio, Barnay-Verdier, Stéphanie, Lombard, Fabien, Voolstra, Christian R., Hume, Benjamin C. C., Galand, Pierre E., Moulin, Clémentine, Boissin, Emilie, Bourdin, Guillaume, Iwankow, Guillaume, Poulain, Julie, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Planes, Serge, Allemand, Denis, Röttinger, Eric, and Furla, Paola

Published
2023
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5. Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Author

Canesi, Marine, Douville, Eric, Montagna, Paolo, Taviani, Marco, Stolarski, Jarosław, Bordier, Louise, Dapoigny, Arnaud, Coulibaly, Gninwoyo Eric Hermann, Simon, Anne-Catherine, Agelou, Mathieu, Fin, Jonathan, Metzl, Nicolas, Iwankow, Guillaume, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie

Published
2023
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6. Same calls, different meanings: Acoustic communication of Holocentridae.

Author

Banse, Marine, Hanssen, Noémie, Sabbe, Justine, Lecchini, David, Donaldson, Terry J., Iwankow, Guillaume, Lagant, Anthony, and Parmentier, Eric

Subjects
SOUND recordings, VISUAL communication, SOCIAL types, WRASSES, EELS
Abstract

The literature on sound production behaviours in fish in the wild is quite sparse. In several taxa, associations between different sound types and given behaviours have been reported. In the Holocentridae, past nomenclature of the different sound types (knocks, growls, grunts, staccatos and thumps) has been confusing because it relies on the use of several terms that are not always based on fine descriptions. Our study aims to ascertain whether holocentrids can produce a variety of sounds in the wild and if these sounds are associated with specific behaviours. Additionally, we aim to determine whether sounds produced by hand-held specimens, a common methodology to record sounds in standardised conditions in fishes, could correspond to some sounds produced by free-swimming individuals in natural conditions. Our study shows that all holocentrid species are able to produce sounds in 6 behavioural contexts of both agonistic (conspecific and heterospecific chases, competition) and social signalling types (acceleration, broadcasting, body quivering), in addition to previously described mobbing towards moray eels and symbiotic interactions with cleaner wrasses. In holocentrids, acoustic communication is not only based on single calls but can also involve series of sounds of different types that are arranged randomly. The large amount of combinations within acoustical events for each behaviour, resulting from both the quantity of sounds and their diversity, supports the absence of stereotypy. This suggests that sounds are produced to reinforce visual communication during the day in this family. Our results also suggest that sounds recorded by hand-held fishes are produced naturally in the wild. Our study challenges past nomenclatures and demonstrates sound critical function in augmenting visual communication, advancing our comprehension of acoustic ecology in teleost species. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Author

Voolstra, Christian R., primary, Hume, Benjamin C. C., additional, Armstrong, Eric J., additional, Mitushasi, Guinther, additional, Porro, Barbara, additional, Oury, Nicolas, additional, Agostini, Sylvain, additional, Boissin, Emilie, additional, Poulain, Julie, additional, Carradec, Quentin, additional, Paz-García, David A., additional, Zoccola, Didier, additional, Magalon, Hélène, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Planes, Serge, additional, Allemand, Denis, additional, and Forcioli, Didier, additional

Published
2023
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9. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals

Author

Rouan, Alice, primary, Pousse, Melanie, additional, Djerbi, Nadir, additional, Porro, Barbara, additional, Bourdin, Guillaume, additional, Carradec, Quentin, additional, Hume, Benjamin CC., additional, Poulain, Julie, additional, Lê-Hoang, Julie, additional, Armstrong, Eric, additional, Agostini, Sylvain, additional, Salazar, Guillem, additional, Ruscheweyh, Hans-Joachim, additional, Aury, Jean-Marc, additional, Paz-García, David A., additional, McMinds, Ryan, additional, Giraud-Panis, Marie-Josèphe, additional, Deshuraud, Romane, additional, Ottaviani, Alexandre, additional, Morini, Lycia Die, additional, Leone, Camille, additional, Wurzer, Lia, additional, Tran, Jessica, additional, Zoccola, Didier, additional, Pey, Alexis, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, de Vargas, Colomban, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, Douville, Eric, additional, Flores, Michel, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Planes, Serge, additional, Allemand, Denis, additional, Pesant, Stephane, additional, Galand, Pierre E., additional, Wincker, Patrick, additional, Sunagawa, Shinichi, additional, Röttinger, Eric, additional, Furla, Paola, additional, Voolstra, Christian R., additional, Forcioli, Didier, additional, Lombard, Fabien, additional, and Gilson, Eric, additional

Published
2023
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10. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Author

Veglia, Alex J., primary, Bistolas, Kalia S. I., additional, Voolstra, Christian R., additional, Hume, Benjamin C. C., additional, Ruscheweyh, Hans-Joachim, additional, Planes, Serge, additional, Allemand, Denis, additional, Boissin, Emilie, additional, Wincker, Patrick, additional, Poulain, Julie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Correa, Adrienne M. S., additional, and Vega Thurber, Rebecca L., additional

Published
2023
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11. Pervasive tandem duplications and convergent evolution shape coral genomes

Author

Noel, Benjamin, primary, Denoeud, France, additional, Rouan, Alice, additional, Buitrago-López, Carol, additional, Capasso, Laura, additional, Poulain, Julie, additional, Boissin, Emilie, additional, Pousse, Mélanie, additional, Da Silva, Corinne, additional, Couloux, Arnaud, additional, Armstrong, Eric, additional, Carradec, Quentin, additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Lê-Hoang, Julie, additional, Tambutté, Sylvie, additional, Barbe, Valérie, additional, Moulin, Clémentine, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, J. Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Allemand, Denis, additional, Planes, Serge, additional, Gilson, Eric, additional, Zoccola, Didier, additional, Wincker, Patrick, additional, Voolstra, Christian R., additional, and Aury, Jean-Marc, additional

Published
2023
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12. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean

Author

Armstrong, Eric J., primary, Lê-Hoang, Julie, additional, Carradec, Quentin, additional, Aury, Jean-Marc, additional, Noel, Benjamin, additional, Hume, Benjamin C. C., additional, Voolstra, Christian R., additional, Poulain, Julie, additional, Belser, Caroline, additional, Paz-García, David A., additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Da Silva, Corinne, additional, Moulin, Clémentine, additional, Boissin, Emilie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Romac, Sarah, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Sullivan, Matthew B., additional, Sunagawa, Shinichi, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Zoccola, Didier, additional, Planes, Serge, additional, Allemand, Denis, additional, and Wincker, Patrick, additional

Published
2023
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13. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author

Lombard, Fabien, primary, Bourdin, Guillaume, additional, Pesant, Stéphane, additional, Agostini, Sylvain, additional, Baudena, Alberto, additional, Boissin, Emilie, additional, Cassar, Nicolas, additional, Clampitt, Megan, additional, Conan, Pascal, additional, Da Silva, Ophélie, additional, Dimier, Céline, additional, Douville, Eric, additional, Elineau, Amanda, additional, Fin, Jonathan, additional, Flores, J. Michel, additional, Ghiglione, Jean-François, additional, Hume, Benjamin C. C., additional, Jalabert, Laetitia, additional, John, Seth G., additional, Kelly, Rachel L., additional, Koren, Ilan, additional, Lin, Yajuan, additional, Marie, Dominique, additional, McMinds, Ryan, additional, Mériguet, Zoé, additional, Metzl, Nicolas, additional, Paz-García, David A., additional, Pedrotti, Maria Luiza, additional, Poulain, Julie, additional, Pujo-Pay, Mireille, additional, Ras, Joséphine, additional, Reverdin, Gilles, additional, Romac, Sarah, additional, Rouan, Alice, additional, Röttinger, Eric, additional, Vardi, Assaf, additional, Voolstra, Christian R., additional, Moulin, Clémentine, additional, Iwankow, Guillaume, additional, Banaigs, Bernard, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Forcioli, Didier, additional, Furla, Paola, additional, Galand, Pierre E., additional, Gilson, Eric, additional, Reynaud, Stéphanie, additional, Sunagawa, Shinichi, additional, Sullivan, Matthew B., additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Thurber, Rebecca Vega, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Boss, Emmanuel, additional, and Gorsky, Gaby, additional

Published
2023
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14. Diversity of the Pacific Ocean coral reef microbiome

Author

Galand, Pierre E., primary, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Hochart, Corentin, additional, Henry, Nicolas, additional, Hume, Benjamin C. C., additional, Oliveira, Pedro H., additional, Perdereau, Aude, additional, Labadie, Karine, additional, Belser, Caroline, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Armstrong, Eric J., additional, Paz-García, David A., additional, Ziegler, Maren, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Voolstra, Christian R., additional, Thurber, Rebecca Vega, additional, Sunagawa, Shinichi, additional, Wincker, Patrick, additional, Allemand, Denis, additional, and Planes, Serge, additional

Published
2023
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15. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Author

Hochart, Corentin, primary, Paoli, Lucas, additional, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Ziegler, Maren, additional, Porro, Barbara, additional, Armstrong, Eric J., additional, Hume, Benjamin C. C., additional, Aury, Jean-Marc, additional, Pogoreutz, Claudia, additional, Paz-García, David A., additional, Nugues, Maggy M., additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Wincker, Patrick, additional, Zoccola, Didier, additional, Allemand, Denis, additional, Planes, Serge, additional, Thurber, Rebecca Vega, additional, Voolstra, Christian R., additional, Sunagawa, Shinichi, additional, and Galand, Pierre E., additional

Published
2023
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16. Pervasive tandem duplications and convergent evolution shape coral genomes

Author

Noel, Benjamin, Denoeud, France, Rouan, Alice, Buitrago-López, Carol, Capasso, Laura, Poulain, Julie, Boissin, Emilie, Pousse, Mélanie, da Silva, Corinne, Couloux, Arnaud, Armstrong, Eric, Carradec, Quentin, Cruaud, Corinne, Labadie, Karine, Lê-Hoang, Julie, Tambutté, Sylvie, Barbe, Valérie, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew, Sunagawa, Shinichi, Thomas, Olivier, Troublé, Romain, Thurber, Rebecca, Allemand, Denis, Planes, Serge, Gilson, Eric, Zoccola, Didier, Wincker, Patrick, Voolstra, Christian, Aury, Jean-Marc, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU]Sciences of the Universe [physics]
Abstract

Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience. † Benjamin Noel and France Denoeud have equal contribution.

Published
2023
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17. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems

Author

Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, Gorsky, Gaby, Lombard, Fabien, Bourdin, Guillaume, Pesant, Stéphane, Agostini, Sylvain, Baudena, Alberto, Boissin, Emilie, Cassar, Nicolas, Clampitt, Megan, Conan, Pascal, Da Silva, Ophélie, Dimier, Céline, Douville, Eric, Elineau, Amanda, Fin, Jonathan, Flores, J. Michel, Ghiglione, Jean-françois, Hume, Benjamin C. C., Jalabert, Laetitia, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Mcminds, Ryan, Mériguet, Zoé, Metzl, Nicolas, Paz-garcía, David A., Pedrotti, Maria Luiza, Poulain, Julie, Pujo-pay, Mireille, Ras, Joséphine, Reverdin, Gilles, Romac, Sarah, Rouan, Alice, Röttinger, Eric, Vardi, Assaf, Voolstra, Christian R., Moulin, Clémentine, Iwankow, Guillaume, Banaigs, Bernard, Bowler, Chris, De Vargas, Colomban, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stéphanie, Sunagawa, Shinichi, Sullivan, Matthew B., Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Allemand, Denis, Planes, Serge, Boss, Emmanuel, and Gorsky, Gaby

Abstract

The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Published
2023
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18. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Author

Voolstra, Christian R., Hume, Benjamin C. C., Armstrong, Eric J., Mitushasi, Guinther, Porro, Barbara, Oury, Nicolas, Agostini, Sylvain, Boissin, Emilie, Poulain, Julie, Carradec, Quentin, Paz-garcía, David A., Zoccola, Didier, Magalon, Hélène, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Vega Thurber, Rebecca, Wincker, Patrick, Planes, Serge, Allemand, Denis, Forcioli, Didier, Voolstra, Christian R., Hume, Benjamin C. C., Armstrong, Eric J., Mitushasi, Guinther, Porro, Barbara, Oury, Nicolas, Agostini, Sylvain, Boissin, Emilie, Poulain, Julie, Carradec, Quentin, Paz-garcía, David A., Zoccola, Didier, Magalon, Hélène, Moulin, Clémentine, Bourdin, Guillaume, Iwankow, Guillaume, Romac, Sarah, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Vega Thurber, Rebecca, Wincker, Patrick, Planes, Serge, Allemand, Denis, and Forcioli, Didier

Abstract

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla—across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

Published
2023
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20. Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis

Author

Peyran, Claire, Boissin, Emilie, Morage, Titouan, Nebot-Colomer, E (Elisabet), Iwankow, Guillaume, Planes, Serge, Peyran, Claire, Boissin, Emilie, Morage, Titouan, Nebot-Colomer, E (Elisabet), Iwankow, Guillaume, and Planes, Serge

Abstract

Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, Pinna nobilis, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, Haplosporidium pinnae. In this context, we focused on a single population (Peyrefite, Banyuls-sur- mer, France) where 640 individuals were sampled in 2011, 2015, and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (Ho) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011–2015 and 2015–2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9% of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that P. nobilis exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by H. pinnae, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.

Published
2021

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

Author

Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, and Wincker P

Subjects
Animals, Biodiversity, Ecosystem, Anthozoa, Coral Reefs
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., (© 2023. The Author(s).)

Published
2023
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