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\n \n\n \n \n 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., Genoscope Technical Team, Batisse, J., Beluche, O., Bertrand, L., Bohers, C., Bordelais, I., Brun, E., Dubois, M., Dumont, C., Zineb, E. H., Estrada, B., Ettedgui, E., Fernandez, P., Garidi, S., Guérin, T., Gorrichon, K., Hamon, C., Kientzel, L., Lebled, S., Legrain, C., Lenoble, P., Lepretre, M., Louesse, C., Magdelenat, G., Mahieu, E., Martins, N., Milani, C., Orvain, C., Oztas, S., Payen, E., Petit, E., Rio, G., Robert, D., Ronsin, M., Vacherie, B., Voolstra, C. R., Galand, P. E., Flores, J. M., Hume, B. C. C., Perna, G., Ziegler, M., Ruscheweyh, H., Boissin, E., Romac, S., Bourdin, G., Iwankow, G., Moulin, C., Paz García, D. A., 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, O. P., Troublé, R., Thurber, R. V., Zoccola, D., Scarpelli, C., Jacoby, E. K., Oliveira, P. H., Aury, J., Allemand, D., Planes, S., & Wincker, P.\n\n\n \n \n \n \n \n Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.\n \n \n \n \n\n\n \n\n\n\n Scientific Data, 10(1): 326. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"IntegrativePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{belser_integrative_2023,\n\ttitle = {Integrative omics framework for characterization of coral reef ecosystems from the {Tara} {Pacific} expedition},\n\tvolume = {10},\n\tissn = {2052-4463},\n\turl = {https://www.nature.com/articles/s41597-023-02204-0},\n\tdoi = {10.1038/s41597-023-02204-0},\n\tabstract = {Abstract\n            \n              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,\n              i.e\n              . 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.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Scientific Data},\n\tauthor = {Belser, Caroline and Poulain, Julie and Labadie, Karine and Gavory, Frederick and Alberti, Adriana and Guy, Julie and Carradec, Quentin and Cruaud, Corinne and Da Silva, Corinne and Engelen, Stefan and Mielle, Paul and Perdereau, Aude and Samson, Gaelle and Gas, Shahinaz and {Genoscope Technical Team} and Batisse, Julie and Beluche, Odette and Bertrand, Laurie and Bohers, Chloé and Bordelais, Isabelle and Brun, Elodie and Dubois, Maria and Dumont, Corinne and Zineb, El Hajji and Estrada, Barbara and Ettedgui, Evelyne and Fernandez, Patricia and Garidi, Sonia and Guérin, Thomas and Gorrichon, Kevin and Hamon, Chadia and Kientzel, Lucille and Lebled, Sandrine and Legrain, Chloé and Lenoble, Patricia and Lepretre, Marine and Louesse, Claudine and Magdelenat, Ghislaine and Mahieu, Eric and Martins, Nathalie and Milani, Claire and Orvain, Céline and Oztas, Sophie and Payen, Emilie and Petit, Emmanuelle and Rio, Guillaume and Robert, Dominique and Ronsin, Muriel and Vacherie, Benoit and Voolstra, Christian R. and Galand, Pierre E. and Flores, J. Michel and Hume, Benjamin C. C. and Perna, Gabriela and Ziegler, Maren and Ruscheweyh, Hans-Joachim and Boissin, Emilie and Romac, Sarah and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Paz García, David A. and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Zoccola, Didier and Scarpelli, Claude and Jacoby, E’ Krame and Oliveira, Pedro H. and Aury, Jean-Marc and Allemand, Denis and Planes, Serge and Wincker, Patrick},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {326},\n}\n\n
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\n 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.\n
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\n \n\n \n \n Galand, P. E., Ruscheweyh, H., Salazar, G., Hochart, C., Henry, N., Hume, B. C. C., Oliveira, P. H., Perdereau, A., Labadie, K., Belser, C., Boissin, E., Romac, S., Poulain, J., Bourdin, G., Iwankow, G., Moulin, C., Armstrong, E. J., Paz-García, D. A., Ziegler, M., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, M., Forcioli, D., Furla, P., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Thomas, O. P., Troublé, R., Zoccola, D., Voolstra, C. R., Thurber, R. V., Sunagawa, S., Wincker, P., Allemand, D., & Planes, S.\n\n\n \n \n \n \n \n Diversity of the Pacific Ocean coral reef microbiome.\n \n \n \n \n\n\n \n\n\n\n Nature Communications, 14(1): 3039. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"DiversityPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 10 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{galand_diversity_2023,\n\ttitle = {Diversity of the {Pacific} {Ocean} coral reef microbiome},\n\tvolume = {14},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38500-x},\n\tdoi = {10.1038/s41467-023-38500-x},\n\tabstract = {Abstract\n            \n              Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the\n              Tara\n              Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Nature Communications},\n\tauthor = {Galand, Pierre E. and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Hochart, Corentin and Henry, Nicolas and Hume, Benjamin C. C. and Oliveira, Pedro H. and Perdereau, Aude and Labadie, Karine and Belser, Caroline and Boissin, Emilie and Romac, Sarah and Poulain, Julie and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Armstrong, Eric J. and Paz-García, David A. and Ziegler, Maren and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Voolstra, Christian R. and Thurber, Rebecca Vega and Sunagawa, Shinichi and Wincker, Patrick and Allemand, Denis and Planes, Serge},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {3039},\n}\n\n
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\n Abstract Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.\n
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\n \n\n \n \n Heitzman, J. M., Mitushasi, G., Spatafora, D., & Agostini, S.\n\n\n \n \n \n \n \n Seasonal coral-algae interactions drive White Mat Syndrome coral disease outbreaks.\n \n \n \n \n\n\n \n\n\n\n Science of The Total Environment, 900: 166379. November 2023.\n \n\n\n\n
\n\n\n\n \n \n \"SeasonalPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{heitzman_seasonal_2023,\n\ttitle = {Seasonal coral-algae interactions drive {White} {Mat} {Syndrome} coral disease outbreaks},\n\tvolume = {900},\n\tissn = {00489697},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723050040},\n\tdoi = {10.1016/j.scitotenv.2023.166379},\n\tlanguage = {en},\n\turldate = {2023-10-31},\n\tjournal = {Science of The Total Environment},\n\tauthor = {Heitzman, Joshua M. and Mitushasi, Guinther and Spatafora, Davide and Agostini, Sylvain},\n\tmonth = nov,\n\tyear = {2023},\n\tpages = {166379},\n}\n\n
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\n \n\n \n \n Hochart, C., Paoli, L., Ruscheweyh, H., Salazar, G., Boissin, E., Romac, S., Poulain, J., Bourdin, G., Iwankow, G., Moulin, C., Ziegler, M., Porro, B., Armstrong, E. J., Hume, B. C. C., Aury, J., Pogoreutz, C., Paz-García, D. A., Nugues, M. M., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, M., Forcioli, D., Furla, P., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Thomas, O. P., Troublé, R., Wincker, P., Zoccola, D., Allemand, D., Planes, S., Thurber, R. V., Voolstra, C. R., Sunagawa, S., & Galand, P. E.\n\n\n \n \n \n \n \n Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.\n \n \n \n \n\n\n \n\n\n\n Nature Communications, 14(1): 3037. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"EcologyPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{hochart_ecology_2023,\n\ttitle = {Ecology of {Endozoicomonadaceae} in three coral genera across the {Pacific} {Ocean}},\n\tvolume = {14},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38502-9},\n\tdoi = {10.1038/s41467-023-38502-9},\n\tabstract = {Abstract\n            \n              Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the\n              Endozoicomonadaceae\n              family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of\n              Endozoicomonadaceae\n              at an ocean basin-scale by sampling specimens from three coral genera (\n              Pocillopora\n              ,\n              Porites\n              ,\n              Millepora\n              ) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of\n              Endozoicomonadaceae\n              . These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in\n              Pocillopora\n              , appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in\n              Pocillopora\n              and mainly by the geographic location in\n              Porites\n              .\n              Millepora\n              is more rarely associated to\n              Endozoicomonadaceae\n              . Our results show that different coral genera exhibit distinct strategies of host-\n              Endozoicomonadaceae\n              associations that are defined at the bacteria lineage level.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Nature Communications},\n\tauthor = {Hochart, Corentin and Paoli, Lucas and Ruscheweyh, Hans-Joachim and Salazar, Guillem and Boissin, Emilie and Romac, Sarah and Poulain, Julie and Bourdin, Guillaume and Iwankow, Guillaume and Moulin, Clémentine and Ziegler, Maren and Porro, Barbara and Armstrong, Eric J. and Hume, Benjamin C. C. and Aury, Jean-Marc and Pogoreutz, Claudia and Paz-García, David A. and Nugues, Maggy M. and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Wincker, Patrick and Zoccola, Didier and Allemand, Denis and Planes, Serge and Thurber, Rebecca Vega and Voolstra, Christian R. and Sunagawa, Shinichi and Galand, Pierre E.},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {3037},\n}\n\n
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\n Abstract Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera ( Pocillopora , Porites , Millepora ) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae . These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora , appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites . Millepora is more rarely associated to Endozoicomonadaceae . Our results show that different coral genera exhibit distinct strategies of host- Endozoicomonadaceae associations that are defined at the bacteria lineage level.\n
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\n \n\n \n \n Hudson, C. J., Agostini, S., Wada, S., Hall-Spencer, J. M., Connell, S. D., & Harvey, B. P.\n\n\n \n \n \n \n \n Ocean acidification increases the impact of typhoons on algal communities.\n \n \n \n \n\n\n \n\n\n\n Science of The Total Environment,161269. December 2022.\n \n\n\n\n
\n\n\n\n \n \n \"OceanPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{hudson_ocean_2022,\n\ttitle = {Ocean acidification increases the impact of typhoons on algal communities},\n\tissn = {00489697},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722083735},\n\tdoi = {10.1016/j.scitotenv.2022.161269},\n\tlanguage = {en},\n\turldate = {2023-01-04},\n\tjournal = {Science of The Total Environment},\n\tauthor = {Hudson, Callum J. and Agostini, Sylvain and Wada, Shigeki and Hall-Spencer, Jason M. and Connell, Sean D. and Harvey, Ben P.},\n\tmonth = dec,\n\tyear = {2022},\n\tpages = {161269},\n}\n
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\n \n\n \n \n Lombard, F., Bourdin, G., Pesant, S., Agostini, S., Baudena, A., Boissin, E., Cassar, N., Clampitt, M., Conan, P., Da Silva, O., Dimier, C., Douville, E., Elineau, A., Fin, J., Flores, J. M., Ghiglione, J., Hume, B. C. C., Jalabert, L., John, S. G., Kelly, R. L., Koren, I., Lin, Y., Marie, D., McMinds, R., Mériguet, Z., Metzl, N., Paz-García, D. A., Pedrotti, M. L., Poulain, J., Pujo-Pay, M., Ras, J., Reverdin, G., Romac, S., Rouan, A., Röttinger, E., Vardi, A., Voolstra, C. R., Moulin, C., Iwankow, G., Banaigs, B., Bowler, C., De Vargas, C., Forcioli, D., Furla, P., Galand, P. E., Gilson, E., Reynaud, S., Sunagawa, S., Sullivan, M. B., Thomas, O. P., Troublé, R., Thurber, R. V., Wincker, P., Zoccola, D., Allemand, D., Planes, S., Boss, E., & Gorsky, G.\n\n\n \n \n \n \n \n Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.\n \n \n \n \n\n\n \n\n\n\n Scientific Data, 10(1): 324. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"OpenPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{lombard_open_2023,\n\ttitle = {Open science resources from the {Tara} {Pacific} expedition across coral reef and surface ocean ecosystems},\n\tvolume = {10},\n\tissn = {2052-4463},\n\turl = {https://www.nature.com/articles/s41597-022-01757-w},\n\tdoi = {10.1038/s41597-022-01757-w},\n\tabstract = {Abstract\n            \n              The\n              Tara\n              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.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Scientific Data},\n\tauthor = {Lombard, Fabien and Bourdin, Guillaume and Pesant, Stéphane and Agostini, Sylvain and Baudena, Alberto and Boissin, Emilie and Cassar, Nicolas and Clampitt, Megan and Conan, Pascal and Da Silva, Ophélie and Dimier, Céline and Douville, Eric and Elineau, Amanda and Fin, Jonathan and Flores, J. Michel and Ghiglione, Jean-François and Hume, Benjamin C. C. and Jalabert, Laetitia and John, Seth G. and Kelly, Rachel L. and Koren, Ilan and Lin, Yajuan and Marie, Dominique and McMinds, Ryan and Mériguet, Zoé and Metzl, Nicolas and Paz-García, David A. and Pedrotti, Maria Luiza and Poulain, Julie and Pujo-Pay, Mireille and Ras, Joséphine and Reverdin, Gilles and Romac, Sarah and Rouan, Alice and Röttinger, Eric and Vardi, Assaf and Voolstra, Christian R. and Moulin, Clémentine and Iwankow, Guillaume and Banaigs, Bernard and Bowler, Chris and De Vargas, Colomban and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Reynaud, Stéphanie and Sunagawa, Shinichi and Sullivan, Matthew B. and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Wincker, Patrick and Zoccola, Didier and Allemand, Denis and Planes, Serge and Boss, Emmanuel and Gorsky, Gaby},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {324},\n}\n\n
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\n 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.\n
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\n \n\n \n \n Noel, B., Denoeud, F., Rouan, A., Buitrago-López, C., Capasso, L., Poulain, J., Boissin, E., Pousse, M., Da Silva, C., Couloux, A., Armstrong, E., Carradec, Q., Cruaud, C., Labadie, K., Lê-Hoang, J., Tambutté, S., Barbe, V., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, J. M., Forcioli, D., Furla, P., Galand, P. E., Lombard, F., Pesant, S., Reynaud, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Troublé, R., Thurber, R. V., Allemand, D., Planes, S., Gilson, E., Zoccola, D., Wincker, P., Voolstra, C. R., & Aury, J.\n\n\n \n \n \n \n \n Pervasive tandem duplications and convergent evolution shape coral genomes.\n \n \n \n \n\n\n \n\n\n\n Genome Biology, 24(1): 123. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"PervasivePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{noel_pervasive_2023,\n\ttitle = {Pervasive tandem duplications and convergent evolution shape coral genomes},\n\tvolume = {24},\n\tissn = {1474-760X},\n\turl = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02960-7},\n\tdoi = {10.1186/s13059-023-02960-7},\n\tabstract = {Abstract\n            \n              Background\n              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.\n            \n            \n              Results\n              \n                In the frame of the Tara Pacific expedition, we assemble two coral genomes,\n                Porites lobata\n                and\n                Pocillopora\n                cf.\n                effusa,\n                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.\n              \n            \n            \n              Conclusions\n              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.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Genome Biology},\n\tauthor = {Noel, Benjamin and Denoeud, France and Rouan, Alice and Buitrago-López, Carol and Capasso, Laura and Poulain, Julie and Boissin, Emilie and Pousse, Mélanie and Da Silva, Corinne and Couloux, Arnaud and Armstrong, Eric and Carradec, Quentin and Cruaud, Corinne and Labadie, Karine and Lê-Hoang, Julie and Tambutté, Sylvie and Barbe, Valérie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, J. Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sullivan, Matthew B. and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Allemand, Denis and Planes, Serge and Gilson, Eric and Zoccola, Didier and Wincker, Patrick and Voolstra, Christian R. and Aury, Jean-Marc},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {123},\n}\n\n
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\n 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.\n
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\n \n\n \n \n Reimer, J. D., Agostini, S., Golbuu, Y., Harvey, B. P., Izumiyama, M., Jamodiong, E. A., Kawai, E., Kayanne, H., Kurihara, H., Ravasi, T., Wada, S., & Rodolfo-Metalpa, R.\n\n\n \n \n \n \n \n High abundances of zooxanthellate zoantharians (Palythoa and Zoanthus) at multiple natural analogues: potential model anthozoans?.\n \n \n \n \n\n\n \n\n\n\n Coral Reefs. April 2023.\n \n\n\n\n
\n\n\n\n \n \n \"HighPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{reimer_high_2023,\n\ttitle = {High abundances of zooxanthellate zoantharians ({Palythoa} and {Zoanthus}) at multiple natural analogues: potential model anthozoans?},\n\tissn = {1432-0975},\n\turl = {https://doi.org/10.1007/s00338-023-02381-9},\n\tdoi = {10.1007/s00338-023-02381-9},\n\tabstract = {Whilst natural analogues for future ocean conditions such as CO2 seeps and enclosed lagoons in coral reef regions have received much recent research attention, most efforts in such locations have focused on the effects of prolonged high CO2 levels on scleractinian corals and fishes. Here, we demonstrate that the three species of zooxanthellate zoantharians, hexacorallian non-calcifying “cousins” of scleractinians, are common across five coral reef natural analogue sites with high CO2 levels in the western Pacific Ocean, in Japan (n = 2), Palau, Papua New Guinea, and New Caledonia (n = 1 each). These current observations support previously reported cases of high Palythoa and Zoanthus abundance and dominance on various impacted coral reefs worldwide. The results demonstrate the need for more research on the ecological roles of zooxanthellate zoantharians in coral reef systems, as well as examining other “understudied” taxa that may become increasingly important in the near future under climate change scenarios. Given their abundance in these sites combined with ease in sampling and non-CITES status, some zoantharian species should make excellent hexacoral models for examining potential resilience or resistance mechanisms of anthozoans to future high pCO2 conditions.},\n\tjournal = {Coral Reefs},\n\tauthor = {Reimer, James Davis and Agostini, Sylvain and Golbuu, Yimnang and Harvey, Ben P. and Izumiyama, Michael and Jamodiong, Emmeline A. and Kawai, Erina and Kayanne, Hajime and Kurihara, Haruko and Ravasi, Timothy and Wada, Shigeki and Rodolfo-Metalpa, Riccardo},\n\tmonth = apr,\n\tyear = {2023},\n}\n\n
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\n Whilst natural analogues for future ocean conditions such as CO2 seeps and enclosed lagoons in coral reef regions have received much recent research attention, most efforts in such locations have focused on the effects of prolonged high CO2 levels on scleractinian corals and fishes. Here, we demonstrate that the three species of zooxanthellate zoantharians, hexacorallian non-calcifying “cousins” of scleractinians, are common across five coral reef natural analogue sites with high CO2 levels in the western Pacific Ocean, in Japan (n = 2), Palau, Papua New Guinea, and New Caledonia (n = 1 each). These current observations support previously reported cases of high Palythoa and Zoanthus abundance and dominance on various impacted coral reefs worldwide. The results demonstrate the need for more research on the ecological roles of zooxanthellate zoantharians in coral reef systems, as well as examining other “understudied” taxa that may become increasingly important in the near future under climate change scenarios. Given their abundance in these sites combined with ease in sampling and non-CITES status, some zoantharian species should make excellent hexacoral models for examining potential resilience or resistance mechanisms of anthozoans to future high pCO2 conditions.\n
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\n \n\n \n \n Rouan, A., Pousse, M., Djerbi, N., Porro, B., Bourdin, G., Carradec, Q., Hume, B. C., Poulain, J., Lê-Hoang, J., Armstrong, E., Agostini, S., Salazar, G., Ruscheweyh, H., Aury, J., Paz-García, D. A., McMinds, R., Giraud-Panis, M., Deshuraud, R., Ottaviani, A., Morini, L. D., Leone, C., Wurzer, L., Tran, J., Zoccola, D., Pey, A., Moulin, C., Boissin, E., Iwankow, G., Romac, S., De Vargas, C., Banaigs, B., Boss, E., Bowler, C., Douville, E., Flores, M., Reynaud, S., Thomas, O. P., Troublé, R., Thurber, R. V., Planes, S., Allemand, D., Pesant, S., Galand, P. E., Wincker, P., Sunagawa, S., Röttinger, E., Furla, P., Voolstra, C. R., Forcioli, D., Lombard, F., & Gilson, E.\n\n\n \n \n \n \n \n Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals.\n \n \n \n \n\n\n \n\n\n\n Nature Communications, 14(1): 3038. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"TelomerePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 5 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{rouan_telomere_2023,\n\ttitle = {Telomere {DNA} length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals},\n\tvolume = {14},\n\tissn = {2041-1723},\n\turl = {https://www.nature.com/articles/s41467-023-38499-1},\n\tdoi = {10.1038/s41467-023-38499-1},\n\tabstract = {Abstract\n            \n              Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive\n              Pocillopora\n              spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant\n              Porites\n              spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Nature Communications},\n\tauthor = {Rouan, Alice and Pousse, Melanie and Djerbi, Nadir and Porro, Barbara and Bourdin, Guillaume and Carradec, Quentin and Hume, Benjamin Cc. and Poulain, Julie and Lê-Hoang, Julie and Armstrong, Eric and Agostini, Sylvain and Salazar, Guillem and Ruscheweyh, Hans-Joachim and Aury, Jean-Marc and Paz-García, David A. and McMinds, Ryan and Giraud-Panis, Marie-Josèphe and Deshuraud, Romane and Ottaviani, Alexandre and Morini, Lycia Die and Leone, Camille and Wurzer, Lia and Tran, Jessica and Zoccola, Didier and Pey, Alexis and Moulin, Clémentine and Boissin, Emilie and Iwankow, Guillaume and Romac, Sarah and De Vargas, Colomban and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and Douville, Eric and Flores, Michel and Reynaud, Stéphanie and Thomas, Olivier P. and Troublé, Romain and Thurber, Rebecca Vega and Planes, Serge and Allemand, Denis and Pesant, Stephane and Galand, Pierre E. and Wincker, Patrick and Sunagawa, Shinichi and Röttinger, Eric and Furla, Paola and Voolstra, Christian R. and Forcioli, Didier and Lombard, Fabien and Gilson, Eric},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {3038},\n}\n\n
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\n Abstract Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health.\n
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\n \n\n \n \n Seto, M., Harvey, B. P., Wada, S., & Agostini, S.\n\n\n \n \n \n \n \n Potential ecosystem regime shift resulting from elevated CO$_{\\textrm{2}}$ and inhibition of macroalgal recruitment by turf algae.\n \n \n \n \n\n\n \n\n\n\n Theoretical Ecology, 16: 1–12. January 2023.\n \n\n\n\n
\n\n\n\n \n \n \"PotentialPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{seto_potential_2023,\n\ttitle = {Potential ecosystem regime shift resulting from elevated {CO}$_{\\textrm{2}}$ and inhibition of macroalgal recruitment by turf algae},\n\tvolume = {16},\n\tissn = {1874-1738, 1874-1746},\n\turl = {https://link.springer.com/10.1007/s12080-022-00550-0},\n\tdoi = {10.1007/s12080-022-00550-0},\n\tlanguage = {en},\n\turldate = {2023-01-04},\n\tjournal = {Theoretical Ecology},\n\tauthor = {Seto, Mayumi and Harvey, Ben P. and Wada, Shigeki and Agostini, Sylvain},\n\tmonth = jan,\n\tyear = {2023},\n\tpages = {1--12},\n}\n\n
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\n \n\n \n \n Veglia, A. J., Bistolas, K. S. I., Voolstra, C. R., Hume, B. C. C., Ruscheweyh, H., Planes, S., Allemand, D., Boissin, E., Wincker, P., Poulain, J., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., De Vargas, C., Douville, E., Flores, M., Forcioli, D., Furla, P., Galand, P. E., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sunagawa, S., Thomas, O. P., Troublé, R., Zoccola, D., Correa, A. M. S., & Vega Thurber, R. L.\n\n\n \n \n \n \n \n Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.\n \n \n \n \n\n\n \n\n\n\n Communications Biology, 6(1): 566. June 2023.\n \n\n\n\n
\n\n\n\n \n \n \"EndogenousPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{veglia_endogenous_2023,\n\ttitle = {Endogenous viral elements reveal associations between a non-retroviral {RNA} virus and symbiotic dinoflagellate genomes},\n\tvolume = {6},\n\tissn = {2399-3642},\n\turl = {https://www.nature.com/articles/s42003-023-04917-9},\n\tdoi = {10.1038/s42003-023-04917-9},\n\tabstract = {Abstract\n            \n              Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially\n              Symbiodinium\n              ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2023-06-12},\n\tjournal = {Communications Biology},\n\tauthor = {Veglia, Alex J. and Bistolas, Kalia S. I. and Voolstra, Christian R. and Hume, Benjamin C. C. and Ruscheweyh, Hans-Joachim and Planes, Serge and Allemand, Denis and Boissin, Emilie and Wincker, Patrick and Poulain, Julie and Moulin, Clémentine and Bourdin, Guillaume and Iwankow, Guillaume and Romac, Sarah and Agostini, Sylvain and Banaigs, Bernard and Boss, Emmanuel and Bowler, Chris and De Vargas, Colomban and Douville, Eric and Flores, Michel and Forcioli, Didier and Furla, Paola and Galand, Pierre E. and Gilson, Eric and Lombard, Fabien and Pesant, Stéphane and Reynaud, Stéphanie and Sunagawa, Shinichi and Thomas, Olivier P. and Troublé, Romain and Zoccola, Didier and Correa, Adrienne M. S. and Vega Thurber, Rebecca L.},\n\tmonth = jun,\n\tyear = {2023},\n\tpages = {566},\n}\n\n
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\n Abstract Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium ), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.\n
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\n \n\n \n \n Zhao, L., Harvey, B. P., Higuchi, T., Agostini, S., Tanaka, K., Murakami-Sugihara, N., Morgan, H., Baker, P., Hall-Spencer, J. M., & Shirai, K.\n\n\n \n \n \n \n \n Ocean acidification stunts molluscan growth at CO2 seeps.\n \n \n \n \n\n\n \n\n\n\n Science of The Total Environment, 873: 162293. May 2023.\n \n\n\n\n
\n\n\n\n \n \n \"OceanPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n  \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{zhao_ocean_2023,\n\ttitle = {Ocean acidification stunts molluscan growth at {CO2} seeps},\n\tvolume = {873},\n\tissn = {00489697},\n\turl = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723009099},\n\tdoi = {10.1016/j.scitotenv.2023.162293},\n\tlanguage = {en},\n\turldate = {2023-02-24},\n\tjournal = {Science of The Total Environment},\n\tauthor = {Zhao, Liqiang and Harvey, Ben P. and Higuchi, Tomihiko and Agostini, Sylvain and Tanaka, Kentaro and Murakami-Sugihara, Naoko and Morgan, Holly and Baker, Phoebe and Hall-Spencer, Jason M. and Shirai, Kotaro},\n\tmonth = may,\n\tyear = {2023},\n\tpages = {162293},\n}\n\n
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