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1. Ocean-wide comparisons of mesopelagic planktonic community structures

Author: Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A., Brandão, Manoela C., Pierella Karlusich, Juan J., Soviadan, Yawouvi Dodji, Gregory, Ann C., Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A., Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, Bork, Peer, Bowler, Chris, de Vargas, Colomban, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, and Jaillon, Olivier
Published: 2023
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2. Mirusviruses link herpesviruses to giant viruses

Author: Gaïa, Morgan, Meng, Lingjie, Pelletier, Eric, Forterre, Patrick, Vanni, Chiara, Fernandez-Guerra, Antonio, Jaillon, Olivier, Wincker, Patrick, Ogata, Hiroyuki, Krupovic, Mart, and Delmont, Tom O.
Published: 2023
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3. Plankton biogeography in the 21st century and impacts of climate change: advances through genomics

Author: Frémont, Paul, Gehlen, Marion, and Jaillon, Olivier
Subjects: Plankton biogeography, Genomics, Climate change, Ocean, 21st century, Biology (General), QH301-705.5
Abstract: This article summarizes recent advances in our knowledge of plankton biogeography obtained by genomic approaches and the impacts of global warming on it. Large-scale comparison of the genomic content of samples of different plankton size fractions revealed a partitioning of the oceans into genomic provinces and the impact of major oceanic currents on them. By defining ecological niches, these provinces are extrapolated to all oceans, with the exception of the Arctic Ocean. By the end of the 21st century, a major restructuring of these provinces is projected in response to a high emission greenhouse gas scenario over 50% of the surface of the studied oceans. Such a restructuring could lead to a decrease in export production by 4%. Finally, obtaining assembled sequences of a large number of plankton genomes defining this biogeography has allowed to better characterize the genomic content of the provinces and to identify the species structuring them. These genomes similarly enabled a better description of potential future changes of plankton communities under climate change.
Published: 2023
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4. Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: The class II cytokine receptors and their ligands in mammals and fish

Author: Mogensen Knud, Jaillon Olivier, Stange-thomann Nicole, Crollius Hugues, Lutfalla Georges, and Monneron Danièle
Subjects: Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background The high degree of sequence conservation between coding regions in fish and mammals can be exploited to identify genes in mammalian genomes by comparison with the sequence of similar genes in fish. Conversely, experimentally characterized mammalian genes may be used to annotate fish genomes. However, gene families that escape this principle include the rapidly diverging cytokines that regulate the immune system, and their receptors. A classic example is the class II helical cytokines (HCII) including type I, type II and lambda interferons, IL10 related cytokines (IL10, IL19, IL20, IL22, IL24 and IL26) and their receptors (HCRII). Despite the report of a near complete pufferfish (Takifugu rubripes) genome sequence, these genes remain undescribed in fish. Results We have used an original strategy based both on conserved amino acid sequence and gene structure to identify HCII and HCRII in the genome of another pufferfish, Tetraodon nigroviridis that is amenable to laboratory experiments. The 15 genes that were identified are highly divergent and include a single interferon molecule, three IL10 related cytokines and their potential receptors together with two Tissue Factor (TF). Some of these genes form tandem clusters on the Tetraodon genome. Their expression pattern was determined in different tissues. Most importantly, Tetraodon interferon was identified and we show that the recombinant protein can induce antiviral MX gene expression in Tetraodon primary kidney cells. Similar results were obtained in Zebrafish which has 7 MX genes. Conclusion We propose a scheme for the evolution of HCII and their receptors during the radiation of bony vertebrates and suggest that the diversification that played an important role in the fine-tuning of the ancestral mechanism for host defense against infections probably followed different pathways in amniotes and fish.
Published: 2003
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5. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author: Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C, Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A, Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, and Wincker, Patrick
Subjects: Genetics, Climate Action, Gene Expression Regulation, Geography, Metagenome, Microbiota, Molecular Sequence Annotation, Oceans and Seas, RNA, Messenger, Seawater, Temperature, Transcriptome, Tara Oceans Coordinators, Tara Oceans, biogeochemistry, community turnover, eco-systems biology, gene expression change, global ocean microbiome, metagenome, metatranscriptome, microbial ecology, ocean warming, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract: Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
Published: 2019

6. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author: Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon
Subjects: Genetics, Infection, Life Below Water, Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, Tara Oceans Coordinators, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract: Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
Published: 2019

7. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author: Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier
Subjects: Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract: Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.
Published: 2019

8. Niche adaptation promoted the evolutionary diversification of tiny ocean predators

Author: Latorre, Francisco, Deutschmann, Ina M., Labarre, Aurélie, Obiol, Aleix, Krabberød, Anders K., Pelletier, Eric, Sieracki, Michael E., Cruaud, Corinne, Jaillon, Olivier, Massana, Ramon, and Logares, Ramiro
Published: 2021

9. Restructuring of plankton genomic biogeography in the surface ocean under climate change

Author: Frémont, Paul, Gehlen, Marion, Vrac, Mathieu, Leconte, Jade, Delmont, Tom O., Wincker, Patrick, Iudicone, Daniele, and Jaillon, Olivier
Published: 2022
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10. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Author: Guérin, Nina, Ciccarella, Marta, Flamant, Elisa, Frémont, Paul, Mangenot, Sophie, Istace, Benjamin, Noel, Benjamin, Belser, Caroline, Bertrand, Laurie, Labadie, Karine, Cruaud, Corinne, Romac, Sarah, Bachy, Charles, Gachenot, Martin, Pelletier, Eric, Alberti, Adriana, Jaillon, Olivier, Wincker, Patrick, Aury, Jean-Marc, and Carradec, Quentin
Published: 2022
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11. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author: Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, and Pelletier, Eric
Published: 2022
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12. Publisher Correction: The DNA sequence and analysis of human chromosome 14

Author: Heilig, Roland, Eckenberg, Ralph, Petit, Jean-Louis, Fonknechten, Núria, Da Silva, Corinne, Cattolico, Laurence, Levy, Michaël, Barbe, Valérie, de Berardinis, Véronique, Ureta-Vidal, Abel, Pelletier, Eric, Vico, Virginie, Anthouard, Véronique, Rowen, Lee, Madan, Anup, Qin, Shizhen, Sun, Hui, Du, Hui, Pepin, Kymberlie, Artiguenave, François, Robert, Catherine, Cruaud, Corinne, Brüls, Thomas, Jaillon, Olivier, Friedlander, Lucie, Samson, Gaelle, Brottier, Philippe, Cure, Susan, Ségurens, Béatrice, Anière, Franck, Samain, Sylvie, Crespeau, Hervé, Abbasi, Nissa, Aiach, Nathalie, Boscus, Didier, Dickhoff, Rachel, Dors, Monica, Dubois, Ivan, Friedman, Cynthia, Gouyvenoux, Michel, James, Rose, Madan, Anuradha, Mairey–Estrada, Barbara, Mangenot, Sophie, Martins, Nathalie, Ménard, Manuela, Oztas, Sophie, Ratcliffe, Amber, Shaffer, Tristan, Trask, Barbara, Vacherie, Benoit, Bellemere, Chadia, Belser, Caroline, Besnard-Gonnet, Marielle, Bartol–Mavel, Delphine, Boutard, Magali, Briez-Silla, Stéphanie, Combette, Stephane, Dufossé-Laurent, Virginie, Ferron, Carolyne, Lechaplais, Christophe, Louesse, Claudine, Muselet, Delphine, Magdelenat, Ghislaine, Pateau, Emilie, Petit, Emmanuelle, Sirvain-Trukniewicz, Peggy, Trybou, Arnaud, Vega-Czarny, Nathalie, Bataille, Elodie, Bluet, Elodie, Bordelais, Isabelle, Dubois, Maria, Dumont, Corinne, Guérin, Thomas, Haffray, Sébastien, Hammadi, Rachid, Muanga, Jacqueline, Pellouin, Virginie, Robert, Dominique, Wunderle, Edith, Gauguet, Gilbert, Roy, Alice, Sainte-Marthe, Laurent, Verdier, Jean, Verdier-Discala, Claude, Hillier, LaDeana, Fulton, Lucinda, McPherson, John, Matsuda, Fumihiko, Wilson, Richard, Scarpelli, Claude, Gyapay, Gábor, Wincker, Patrick, Saurin, William, Quétier, Francis, Waterston, Robert, Hood, Leroy, and Weissenbach, Jean
Published: 2023
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13. Comparative genomics reveals new functional insights in uncultured MAST species

Author: Labarre, Aurelie, López-Escardó, David, Latorre, Francisco, Leonard, Guy, Bucchini, François, Obiol, Aleix, Cruaud, Corinne, Sieracki, Michael E., Jaillon, Olivier, Wincker, Patrick, Vandepoele, Klaas, Logares, Ramiro, and Massana, Ramon
Published: 2021
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14. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

Author: Kaneko, Hiroto, Blanc-Mathieu, Romain, Endo, Hisashi, Chaffron, Samuel, Delmont, Tom O., Gaia, Morgan, Henry, Nicolas, Hernández-Velázquez, Rodrigo, Nguyen, Canh Hao, Mamitsuka, Hiroshi, Forterre, Patrick, Jaillon, Olivier, de Vargas, Colomban, Sullivan, Matthew B., Suttle, Curtis A., Guidi, Lionel, and Ogata, Hiroyuki
Published: 2021
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15. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Author: Wu, G Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Del Fabbro, Cristian, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco R, Estornell, Leandro H, Muñoz-Sanz, Juan V, Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez-Pérez, Julián, Ramón, Daniel, Brunel, Dominique, Luro, François, Chen, Chunxian, Farmerie, William G, Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astúa, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel
Subjects: Base Sequence, Breeding, Citrus, Conserved Sequence, Crops, Agricultural, Evolution, Molecular, Genetic Variation, Genome, Plant, Molecular Sequence Data, Sequence Analysis, DNA, Species Specificity
Abstract: Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
Published: 2014

16. Complex history of admixture during citrus domestication revealed by genome analysis

Author: Wu, G. Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Fabbro, Cristian Del, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco, Estornell, Leandro H., Mu?oz-Sanz, Juan V., Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez, Julián Pérez, Ramon, Daniel, Brunel, Dominique, Luro, Francois, Chen, Chunxian, Farmerie, William G., Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astua, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel
Subjects: haploid Clementine mandarin, C. maxima, C. reticulata, Mangshan, China, Huanglongbing, apomixis via nucellar polyembryony, ntrogressive hybridizations
Abstract: Although Citrus is the most globally significant tree fruit, its domestication history is poorlyunderstood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm.Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China showssubstantial sequence divergence from C. reticulata and appears to represent a distinct taxon.Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement.Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources ofvitamin C and other health-promoting compounds. Global production in 2012 exceeded 86million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly vulnerable to disease outbreaks, including citrus greening disease (also known as Huanglongbing) that is rapidly spreading throughout the world's major citrus producing regions1. Understanding the population genomics and domestication of citrus will enable strategies for improvements to citrus including resistance to greening and otherdiseases. The domestication and distribution of edible citrus types began several thousand years ago in Southeast Asia and spread globally following ancient land and sea routes. The lineages that gave rise to most modern cultivated varieties, however, are lost in undocumented antiquity, and their identities remain controversial2, 3. Several features of Citrus biology and cultivation make deciphering these origins difficult. Cultivated varieties are typically propagated clonally by grafting and through asexual seed production (apomixis via nucellar polyembryony) to maintain desirable combinations of traits (Fig. 1). Thus many important cultivar groups have characteristic basic genotypes that presumably arose through interspecific hybridization and/or successive introgressive hybridizations of wild ancestral species. These domestication events predated the global expansion of citrus cultivation by hundreds or perhaps thousands of years, with no record of the domestication process. Diversity within such groups arises through accumulated somatic mutations, generally without sexual recombination, either as limb sports on trees or variants among apomictic seedling progeny.Two wild species are believed to have contributed to domesticated pummelos, mandarins and oranges. Based on morphology and genetic markers, pummelos have generally been identified with the wild species C. maxima (Burm.) Merrill that is indigenous to Southeast Asia. Although mandarins are similarly widely identified with the species C. reticulata Blanco 4-6, wild populations of C. reticulata have not been definitively described. Various authors have taken dif
Published: 2014

17. Climate genomics—Geoscientists, ecologists, and geneticists must reinforce their collaborations to confront climate change

Author: Caccavo, Jilda Alicia, primary, Frémont, Paul, additional, Jaillon, Olivier, additional, and Gehlen, Marion, additional
Published: 2023
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18. Remarkable Compartmentalization of Transposable Elements and Pseudogenes in the Heterochromatin of the Tetraodon Nigroviridis Genome

Author: Dasilva, Corinne, Hadji, Hajer, Ozouf-Costaz, Catherine, Nicaud, Sophie, Jaillon, Olivier, Weissenbach, Jean, and Crollius, Hugues Roest
Published: 2002

19. The Genome Sequence of the Malaria Mosquito Anopheles gamblae

Author: Holt, Robert A., Subramanian, G. Mani, Halpern, Aaron, Sutton, Granger G., Charlab, Rosane, Nusskern, Deborah R., Wincker, Patrick, Clark, Andrew G., Wides, Ron, Salzberg, Steven L., Loftus, Brendan, Yandell, Mark, Majoros, William H., Rusch, Douglas B., Lai, Zhongwu, Kraft, Cheryl L., Abril, Josep F., Anthouard, Veronique, Arensburger, Peter, Atkinson, Peter W., Baden, Holly, de Berardinis, Veronique, Baldwin, Danita, Benes, Vladimir, Biedler, Jim, Blass, Claudia, Bolanos, Randall, Boscus, Didier, Barnstead, Mary, Cai, Shuang, Chatuverdi, Kabir, Christophides, George K., Chrystal, Mathew A., Clamp, Michele, Cravchik, Anibal, Curwen, Val, Dana, Ali, Delcher, Art, Dew, Ian, Evans, Cheryl A., Flanigan, Michael, Grundschober-Freimoser, Anne, Friedli, Lisa, Gu, Zhiping, Guan, Ping, Guigo, Roderic, Hillenmeyer, Maureen E., Hladun, Susanne L., Hogan, James R., Hong, Young S., Hoover, Jeffrey, Jaillon, Olivier, Ke, Zhaoxi, Kodira, Chinnappa, Kokoza, Elena, Koutsos, Anastasios, Letunic, Ivica, Levitsky, Alex, Liang, Yong, Lin, Jhy-Jhu, Lobo, Neil F., Lopez, John R., Malek, Joel A., McIntosh, Tina C., Meister, Stephan, Miller, Jason, Mobarry, Clark, Mongin, Emmanuel, Murphy, Sean D., O'Brochta, David A., Pfannkoch, Cynthia, Qi, Rong, Regier, Megan A., Remington, Karin, Shao, Hongguang, Sharakhova, Maria V., Sitter, Cynthia D., Shetty, Jyoti, Smith, Thomas J., Strong, Renee, Sun, Jingtao, Thomasova, Dana, Ton, Lucas Q., Topalis, Pantelis, Tu, Zhijian, Unger, Maria F., Walenz, Brian, Wang, Aihui, Wang, Jian, Wang, Mei, Wang, Xuelan, Woodford, Kerry J., Wortman, Jennifer R., Wu, Martin, Yao, Alison, Zdobnov, Evgeny M., Zhang, Hongyu, Zhao, Qi, Zhao, Shaying, Zhu, Shiaoping C., Zhimulev, Igor, Coluzzi, Mario, della Torre, Alessandra, Roth, Charles W., Louis, Christos, Kalush, Francis, Mural, Richard J., Myers, Eugene W., Adams, Mark D., Smith, Hamilton O., Broder, Samuel, Gardner, Malcolm J., Fraser, Claire M., Birney, Ewan, Bork, Peer, Brey, Paul T., Venter, J. Craig, Weissenbach, Jean, Kafatos, Fotis C., Collins, Frank H., and Hoffman, Stephen L.
Published: 2002

20. Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Author: Sato, Shinya, Nanjappa, Deepak, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Kazamia, Elena, Tirichine, Leila, Veluchamy, Alaguraj, Heilig, Roland, Aury, Jean-Marc, Jaillon, Olivier, Wincker, Patrick, Fussy, Zoltan, Obornik, Miroslav, Muñoz-Gómez, Sergio A., Mann, David G., Bowler, Chris, and Zingone, Adriana
Published: 2020
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21. Population dynamics, interactions and evolution of marine microbes using genomic approaches

Author: Universitat Politècnica de Catalunya. Departament d'Enginyeria Civil i Ambiental, Logares Haurie, Ramiro Ernesto, Jaillon, Olivier, Mösso Aranda, César, Latorre Pérez, Francisco, Universitat Politècnica de Catalunya. Departament d'Enginyeria Civil i Ambiental, Logares Haurie, Ramiro Ernesto, Jaillon, Olivier, Mösso Aranda, César, and Latorre Pérez, Francisco
Abstract: A la portada: Institut de Ciències del Mar, (English) There is a myriad of microorganisms on Earth contributing to global biogeochemical cycles. In the surface ocean, the smallest microbes (picoplankton) are responsible for an important fraction of the total atmospheric carbon and nitrogen fixation. The ocean picoplankton encompasses both prokaryotes (bacteria and archaea) and tiny unicellular eukaryotes (protists). Despite their overall importance for the functioning of the biosphere, many questions remain unanswered on their biogeography, population dynamics, interactions, and evolution. Answering these questions is essential in the context of global change, as alterations of the ocean microbiome could impact the function of multiple ecosystems. In this thesis, we aim at reducing the knowledge gap on the above topics through the application of High-Throughput Sequencing (HTS) and genomic approaches, using data collected during the circumglobal Tara Oceans and Malaspina-2010 expeditions, as well as at the Gulf of Maine (North Atlantic), and two Northwestern Mediterranean coastal microbial observatories (BBMO and SOLA stations). Chapters 1 and 2 are dedicated to a small protistan group of heterotrophic flagellates (HF): the Marine Stramenopiles (MAST)-4, relevant during picoplankton grazing and nutrient remineralization. Due to its widespread distribution and relatively high abundance, MAST-4 has become a target group of microbes to study HF. Unfortunately, MAST-4 remains uncultured. We investigated four evolutionary-related species of MAST-4 (species A, B, C, and E) by reconstructing their genomes with Single-Cell genomics data. In chapter 1, co-occurrence and biogeographic analyses in the surface global ocean indicated contrasting patterns driven by temperature. Although MAST-4 species were similar in terms of broad metabolic functions, they differed in the set of genes related to the food degradation machinery. We proposed that differential niche adaptation to temperature and prey type has promoted the evo, (Español) Existen un sinfín de microorganismos que contribuyen a los ciclos biogeoquímicos globales. En la superficie oceánica, los microbios más pequeños (picoplancton) son responsables de fijar una gran parte del total de carbono y nitrógeno terrestre. El picoplancton agrupa tanto a procariotas (bacterias y arqueas) como a pequeños eucariotas unicelulares (protistas). A pesar de su importancia en el funcionamiento de la biosfera, existen aún muchas preguntas sin respuesta relacionadas con su biogeografía, dinámica poblacional, interacciones, y evolución. Responder dichas preguntas es esencial en el contexto del cambio climático, ya que alteraciones en la microbiota marina podría impactar en el funcionamiento de múltiples ecosistemas. El principal objetivo de la tesis es llenar el vacío existente sobre los temas mencionados a través de la aplicación de técnicas de secuenciación de alto rendimiento (HTS) y de métodos genómicos, usando datos recolectados durante las expediciones globales de Tara Oceans y Malaspina-2010, el Golfo de Maine (Océano Atlántico Norte), y dos observatorios situados en la costa noroeste del mar Mediterráneo (BBMO y SOLA). Los capítulos 1 y 2 están dedicados a un grupo de pequeños protistas flagelados heterótrofos (HF): los Stramenopilos Marinos (MAST)-4, relevantes en el consumo de picoplancton y la re-mineralización de nutrientes. Debido a su distribución generalizada y su abundancia relativa elevada, MAST-4 se ha convertido en un grupo microbiano modelo para estudiar a los HF. Hemos reconstruido los genomas de cuatro especies relacionadas evolutivamente de MAST-4 (A, B, C, y E) usando datos de genómica de célula única (SCG). En el capítulo 1, los análisis de coocurrencia y biogeografía en la superficie oceánica global indicaron patrones contrastantes relacionados con la temperatura. Aunque las especies de MAST-4 compartían funciones metabólicas, su contenido genético relacionado con la degradación de comida era diferente. Por lo tanto, pro, Postprint (published version)
Published: 2023

22. Computing marine plankton connectivity under thermal constraints

Author: Manral, Darshika, Iovino, Doroteaciro, Jaillon, Olivier, Masina, Simona, Sarmento, Hugo, Iudicone, Daniele, Amaral-Zettler, Linda, van Sebille, Erik, Manral, Darshika, Iovino, Doroteaciro, Jaillon, Olivier, Masina, Simona, Sarmento, Hugo, Iudicone, Daniele, Amaral-Zettler, Linda, and van Sebille, Erik
Abstract: Ocean currents are a key driver of plankton dispersal across the oceanic basins. However, species specific temperature constraints may limit the plankton dispersal. We propose a methodology to estimate the connectivity pathways and timescales for plankton species with given constraints on temperature tolerances, by combining Lagrangian modeling with network theory. We demonstrate application of two types of temperature constraints: thermal niche and adaptation potential and compare it to the surface water connectivity between sample stations in the Atlantic Ocean. We find that non-constrained passive particles representative of a plankton species can connect all the stations within three years at the surface with pathways mostly along the major ocean currents. However, under thermal constraints, only a subset of stations can establish connectivity. Connectivity time increases marginally under these constraints, suggesting that plankton can keep within their favorable thermal conditions by advecting via slightly longer paths. Effect of advection depth on connectivity is observed to be sensitive to the width of the thermal constraints, along with decreasing flow speeds with depth and possible changes in pathways.
Published: 2023

23. Predicting global distributions of eukaryotic plankton communities from satellite data

Author: Kaneko, Hiroto, Endo, Hisashi, Henry, Nicolas, Berney, Cédric, Mahe, Frédéric, Poulain, Julie, Labadie, Karine, Beluche, Odette, El Hourany, Roy, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Pesant, Stéphane, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Chaffron, Samuel, Wincker, Patrick, Nakamura, Ryosuke, Karp-Boss, Lee, Boss, Emmanuel, Tomii, Kentaro, Ogata, Hiroshi Y., Kaneko, Hiroto, Endo, Hisashi, Henry, Nicolas, Berney, Cédric, Mahe, Frédéric, Poulain, Julie, Labadie, Karine, Beluche, Odette, El Hourany, Roy, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Pesant, Stéphane, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Chaffron, Samuel, Wincker, Patrick, Nakamura, Ryosuke, Karp-Boss, Lee, Boss, Emmanuel, Tomii, Kentaro, and Ogata, Hiroshi Y.
Abstract: Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.
Published: 2023

24. Computing marine plankton connectivity under thermal constraints

Author: Sub Physical Oceanography, Marine and Atmospheric Research, Manral, Darshika, Iovino, Doroteaciro, Jaillon, Olivier, Masina, Simona, Sarmento, Hugo, Iudicone, Daniele, Amaral-Zettler, Linda, van Sebille, Erik, Sub Physical Oceanography, Marine and Atmospheric Research, Manral, Darshika, Iovino, Doroteaciro, Jaillon, Olivier, Masina, Simona, Sarmento, Hugo, Iudicone, Daniele, Amaral-Zettler, Linda, and van Sebille, Erik
Published: 2023

25. Pan-Arctic plankton community structure and its global connectivity

Author: Ibarbalz, Federico M., Henry, Nicolas, Mahe, Frédéric, Ardyna, Mathieu, Zingone, Adriana, Scalco, Eleonora, Lovejoy, Thomas E., Lombard, Fabien, Jaillon, Olivier, Iudicone, Daniele, Malviya, Shruti, Sullivan, Matthew B., Chaffron, Samuel, Karsenti, Eric, Babin, Marcel, Boss, Emmanuel, Wincker, Patrick, Zinger, Lucie, de Vargas, Colomban, Bowler, Chris, Karp-Boss, Lee, Ibarbalz, Federico M., Henry, Nicolas, Mahe, Frédéric, Ardyna, Mathieu, Zingone, Adriana, Scalco, Eleonora, Lovejoy, Thomas E., Lombard, Fabien, Jaillon, Olivier, Iudicone, Daniele, Malviya, Shruti, Sullivan, Matthew B., Chaffron, Samuel, Karsenti, Eric, Babin, Marcel, Boss, Emmanuel, Wincker, Patrick, Zinger, Lucie, de Vargas, Colomban, Bowler, Chris, and Karp-Boss, Lee
Abstract: The Arctic Ocean (AO) is being rapidly transformed by global warming, but its biodiversity remains understudied for many planktonic organisms, in particular for unicellular eukaryotes that play pivotal roles in marine food webs and biogeochemical cycles. The aim of this study was to characterize the biogeographic ranges of species that comprise the contemporary pool of unicellular eukaryotes in the AO as a first step toward understanding mechanisms that structure these communities and identifying potential target species for monitoring. Leveraging the Tara Oceans DNA metabarcoding data, we mapped the global distributions of operational taxonomic units (OTUs) found on Arctic shelves into five biogeographic categories, identified biogeographic indicators, and inferred the degree to which AO communities of unicellular eukaryotes share members with assemblages from lower latitudes. Arctic/Polar indicator OTUs, as well as some globally ubiquitous OTUs, dominated the detection and abundance of DNA reads in the Arctic samples. OTUs detected only in Arctic samples (Arctic-exclusives) showed restricted distribution with relatively low abundances, accounting for 10–16% of the total Arctic OTU pool. OTUs with high abundances in tropical and/or temperate latitudes (non-Polar indicators) were also found in the AO but mainly at its periphery. We observed a large change in community taxonomic composition across the Atlantic-Arctic continuum, supporting the idea that advection and environmental filtering are important processes that shape plankton assemblages in the AO. Altogether, this study highlights the connectivity between the AO and other oceans, and provides a framework for monitoring and assessing future changes in this vulnerable ecosystem.
Published: 2023

26. Population dynamics, interactions and evolution of marine microbes using genomic approaches

Author: Logares, Ramiro, Jaillon, Olivier, Ministerio de Ciencia e Innovación (España), Latorre, Fran, Logares, Ramiro, Jaillon, Olivier, Ministerio de Ciencia e Innovación (España), and Latorre, Fran
Abstract: [EN] There is a myriad of microorganisms on Earth contributing to global biogeochemical cycles. In the surface ocean, the smallest microbes (picoplankton) are responsible for an important fraction of the total atmospheric carbon and nitrogen fixation. The ocean picoplankton encompasses both prokaryotes (bacteria and archaea) and tiny unicellular eukaryotes (protists). Despite their overall importance for the functioning of the biosphere, many questions remain unanswered on their biogeography, population dynamics, interactions, and evolution. Answering these questions is essential in the context of global change, as alterations of the ocean microbiome could impact the function of multiple ecosystems. In this thesis, we aim at reducing the knowledge gap on the above topics through the application of High-Throughput Sequencing (HTS) and genomic approaches, using data collected during the circumglobal Tara Oceans and Malaspina-2010 expeditions, as well as at the Gulf of Maine (North Atlantic), and two Northwestern Mediterranean coastal microbial observatories (BBMO and SOLA stations). [...], [ES] Existen un sinfín de microorganismos que contribuyen a los ciclos biogeoquímicos globales. En la superficie oceánica, los microbios más pequeños (picoplancton) son responsables de fijar una gran parte del total de carbono y nitrógeno terrestre. El picoplancton agrupa tanto a procariotas (bacterias y arqueas) como a pequeños eucariotas unicelulares (protistas). A pesar de su importancia en el funcionamiento de la biosfera, existen aún muchas preguntas sin respuesta relacionadas con su biogeografía, dinámica poblacional, interacciones y evolución. Responder dichas preguntas es esencial en el contexto del cambio climático, ya que alteraciones en la microbiota marina podría impactar en el funcionamiento de múltiples ecosistemas. El principal objetivo de la tesis es llenar el vacío existente sobre los temas mencionados a través de la aplicación de técnicas de secuenciación de alto rendimiento (HTS) y de métodos genómicos, usando datos recolectados durante las expediciones globales de Tara Oceans y Malaspina-2010, el Golfo de Maine (Océano Atlántico Norte), y dos observatorios situados en la costa noroeste del mar Mediterráneo (BBMO y SOLA). [...]
Published: 2023

27. Ocean-wide comparisons of mesopelagic planktonic community structures

Author: Fonds Français pour l'Environnement Mondial, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), European Commission, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Ministère de la Recherche et des Technologies (France), Agencia Estatal de Investigación (España), Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A., Brandão, Manoela C., Pierella Karlusich, Juan J., Soviadan, Yawouvi Dodji, Gregory, Ann C., Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A., Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels‐Lewis, Stefanie, Pesant, Stéphane, Karsenti, Eric, Tara Oceans Coordinators, Acinas, Silvia G., Bork, Peer, Bowler, Chris, Vargas, Colomban de, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, Jaillon, Olivier, Fonds Français pour l'Environnement Mondial, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), European Commission, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Ministère de la Recherche et des Technologies (France), Agencia Estatal de Investigación (España), Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A., Brandão, Manoela C., Pierella Karlusich, Juan J., Soviadan, Yawouvi Dodji, Gregory, Ann C., Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A., Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels‐Lewis, Stefanie, Pesant, Stéphane, Karsenti, Eric, Tara Oceans Coordinators, Acinas, Silvia G., Bork, Peer, Bowler, Chris, Vargas, Colomban de, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, and Jaillon, Olivier
Abstract: For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3− and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities
Published: 2023

28. AtlantECO Deliverable 2.1: AtlantECO-BASE1

Author: Vogt, Meike, Sarmento, Hugo, Benedetti, Fabio, Huber, Paula, Arboleda-Baena, Clara, Bader, Ruby Rose, Eriksson, Dominic, Knecht, Nielja, Chénier, Noémy, Jaillon, Olivier, Frémont, Paul, Lombard, Fabien, Guidi, Lionel, Ricour, Florian, Van Sebille, Erik, Schmiz, Sophie, Manral, Darshika, Clerc, Corentin, Santos, Gleice, Maiorano, Luigi, De Angelis, Daniele, Chaffron, Samuel, Eveillard, Damien, Amaral-Zettler, Linda, Gehlen, Marion, Benard, Germain, and Frölicher, Thomas
Subjects: marine plankton data, plastisphere observations, microplastics observations, optical imaging observations, omics observations, traditional microscopy observations, carbon flux data observations
Abstract: This deliverable reports on Task 2.2 ‘Assembly of observations about microbiomes, plastics, the plastisphere and carbon fluxes’. It used protocols established in task 2.1 ‘Definition of common standards for the assembly of spatially explicit data’ to compile, quality-control and grid existing high-quality observations into a knowledge base of observations (D2.1). Data included into AtlantECO-BASE1 consisted of contributions from the five following data sources and tasks: Task 2.2.1 ‘Microbiome data from traditional microscopy (presence-absence, abundance and biomass)’, Task 2.2.2 ‘Microbiome data from state-of-the-art optical/imaging analysis’, Task 2.2.3 ‘Microbiome and plastisphere data from state-of-the-art genetic analyses’, Task 2.2.4 ‘Nano-, micro and macroplastics data from state-of-the-art sampling methods’, and Task 2.2.5 ‘Carbon flux data from estimated from high resolution bio-optical sensors’. Additional data contributions and mapping efforts from other partners and work packages (Task 2.3) are also included. A comprehensive list and description of all data sets collected can be found in the Appendix Tables to this document.
Published: 2023
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29. Computing marine plankton connectivity under thermal constraints

Author: Manral, Darshika, primary, Iovino, Doroteaciro, additional, Jaillon, Olivier, additional, Masina, Simona, additional, Sarmento, Hugo, additional, Iudicone, Daniele, additional, Amaral-Zettler, Linda, additional, and van Sebille, Erik, additional
Published: 2023
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30. Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front

Author: Frémont, Paul, primary, Da Silva, Corinne, additional, Campese, Lucia, additional, Villar, Émilie, additional, Rastogi, Achal, additional, Aury, Jean-Marc, additional, Bowler, Chris, additional, Boss, Lee Karp, additional, Wincker, Patrick, additional, Pelletier, Eric, additional, Gehlen, Marion, additional, Iudicone, Daniele, additional, and Jaillon, Olivier, additional
Published: 2022
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31. The Intangible Age : How insurers are building a better world

Author: Jaillon, Olivier, Jaillon, Olivier, Jaillon, Olivier, and Jaillon, Olivier
Abstract: The intangible age has dawned. Welcome to a world buoyed by asset sharing, as ownership slips ever further into the background. Particularly visible in millennials’ lifestyles, this groundswell is gradually taking over all aspects of everyday life, as everything around us becomes available to hire – from phones, computers, and clothes, to free-floating scooters and bikes. The new generation is no longer prioritizing ownership and possession of consumerist status symbols, preferring instead to experiment with new ways of achieving success and fulfillment. More than just a technological shift linked to an explosion in digital devices, the changes now underway reflect a radical transformation of mindsets. In this context, insurance companies are serving as social and economic stabilizers, equipping societies with the tools needed to withstand shock and develop over the long term. Olivier Jaillon’s essay delivers enlightening insight into the anthropological and technological breakthroughs currently afoot. In a book that readily shatters the si- lence surrounding inheritance and wealth accumulation, the author offers up a defense of one of his deepest convictions: by facilitating this shift from tangible assets to the intangible age, insurance companies will be playing a direct role in fulfilling our individual and collective aspirations. Fewer constraints, less inequality, more freedom, and greater solidarity – terms destined to become the cornerstones and guiding values of the insurance of the future.
Published: 2021

32. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean-Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), University of British Columbia (UBC), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Dipartimento di Fisica e Astronomia 'Galileo Galilei', Università degli Studi di Padova = University of Padua (Unipd), Consorzio Nazionale Interuniversitario per le Scienze FIsiche della Materia (CNISM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), 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), Institut de Biologie François JACOB (JACOB), Ohio State University [Columbus] (OSU), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Maine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), French National Research Agency (ANR)HYDROGEN/ANR-14CE23-0001, National Science Foundation (NSF)OCE-1536989, OCE-1829831, Commissariat a l'Energie Atomique et aux Energies Alternatives, Graphene Flagship, European Project: 634486,H2020,H2020-BG-2014-2,INMARE(2015), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Universita degli Studi di Padova, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Infectiologie Santé Publique (ISP-311), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Institut Pprime (PPRIME), Université de Poitiers-ENSMA-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)
Subjects: 010504 meteorology & atmospheric sciences, Biogeography, Oceans and Seas, Context (language use), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, plankton biogeography, genomics, Ecosystem, genetics, 14. Life underwater, microbial oceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Seascape, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, metagenomics, General Immunology and Microbiology, Geography, General Neuroscience, Ocean current, fungi, Community structure, General Medicine, 15. Life on land, Plankton, Oceanography, 13. Climate action, Metagenomics, metabarcoding, ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton., We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions.
Published: 2022

33. Unveiling hidden eukaryotes: diversity of Endomyxa (Rhizaria) in coastal marine habitats

Author: Berney, Cédric, primary, Ciaghi, Stefan, additional, Romac, Sarah, additional, Mahé, Frédéric, additional, de Vargas, Colomban, additional, Jaillon, Olivier, additional, Kirchmair, Martin, additional, Bass, David, additional, and Neuhauser, Sigrid, additional
Published: 2022
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34. Patrimoine éphémère : Et si les assureurs allaient nous sauver ? Ed. 1

Author: Jaillon, Olivier, Jaillon, Olivier, Jaillon, Olivier, and Jaillon, Olivier
Abstract: Nous sommes entrés dans la société du patrimoine éphémère, dominée par le règne des usages fractionnés et le recul de la possession. Particulièrement visible dans le comportement des millennials, cette lame de fond submerge peu à peu tous les domaines de notre vie. Aujourd'hui, tout se loue : portables, ordinateurs, vêtements ou encore vélos et trottinettes en libre-service... L'accès à la propriété et la possession d'objets emblématiques de la société de consommation ne sont plus considérés comme des priorités par la nouvelle génération, qui découvre d'autres voies pour se réaliser et s'affirmer. Plus qu'une mutation associée au foisonnement des dispositifs digitaux, nous vivons une métamorphose radicale des mentalités. Dans ce contexte, les assureurs sont un stabilisateur économique et social qui permet aux communautés humaines de résister aux chocs et de se développer dans la durée. Olivier Jaillon livre dans cet essai une analyse éclairante des ruptures technologiques et anthropologiques en cours. N'hésitant pas à briser des tabous au sujet de l'héritage et de l'accumulation des richesses, l'auteur défend sa conviction profonde : en facilitant le passage du patrimoine tangible au patrimoine éphémère, les assureurs auront un impact direct sur l'accomplissement de nos aspirations individuelles et collectives. Moins de contraintes, moins d'inégalités, plus de libertés et de solidarités. Ces maîtres-mots ont vocation à devenir les principes directeurs de l'assurance de demain.
Published: 2020

35. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author: Delmont, Tom O, Gaia, Morgan, Hinsinger, Damien D, Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Coordinators, Tara Oceans, Sunagawa, Shinichi, Acinas, Silvia G, Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Pelletier, Eric, Delmont, Tom O, Gaia, Morgan, Hinsinger, Damien D, Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Coordinators, Tara Oceans, Sunagawa, Shinichi, Acinas, Silvia G, Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, and Pelletier, Eric
Abstract: Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
Published: 2022

36. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author: Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Pelletier, Eric, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, and Pelletier, Eric
Abstract: Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
Published: 2022

37. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, and Tara Oceans Coordinators
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.
Published: 2022

38. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author: Delmont, Tom O., primary, Gaia, Morgan, additional, Hinsinger, Damien D., additional, Frémont, Paul, additional, Vanni, Chiara, additional, Fernandez-Guerra, Antonio, additional, Eren, A. Murat, additional, Kourlaiev, Artem, additional, d'Agata, Leo, additional, Clayssen, Quentin, additional, Villar, Emilie, additional, Labadie, Karine, additional, Cruaud, Corinne, additional, Poulain, Julie, additional, Da Silva, Corinne, additional, Wessner, Marc, additional, Noel, Benjamin, additional, Aury, Jean-Marc, additional, de Vargas, Colomban, additional, Bowler, Chris, additional, Karsenti, Eric, additional, Pelletier, Eric, additional, Wincker, Patrick, additional, Jaillon, Olivier, additional, Sunagawa, Shinichi, additional, Acinas, Silvia G., additional, Bork, Peer, additional, Sardet, Christian, additional, Stemmann, Lars, additional, Lescot, Magali, additional, Babin, Marcel, additional, Gorsky, Gabriel, additional, Grimsley, Nigel, additional, Guidi, Lionel, additional, Hingamp, Pascal, additional, Kandels, Stefanie, additional, Iudicone, Daniele, additional, Ogata, Hiroyuki, additional, Pesant, Stéphane, additional, Sullivan, Matthew B., additional, Not, Fabrice, additional, Lee, Karp-Boss, additional, Boss, Emmanuel, additional, Cochrane, Guy, additional, Follows, Michael, additional, Poulton, Nicole, additional, Raes, Jeroen, additional, Sieracki, Mike, additional, and Speich, Sabrina, additional
Published: 2022
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39. Equatorial to Polar genomic variability of the picoalga Bathycoccus prasinos

Author: Leconte, Jade, primary, Timsit, Youri, additional, Delmont, Tom O, additional, Lescot, Magali, additional, Piganeau, Gwenaël, additional, Wincker, Patrick, additional, and Jaillon, Olivier, additional
Published: 2022
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40. List of Contributors

Author: Álvarez-Dios, José Antonio, primary, Aleström, Peter, additional, Bekaert, Michaël, additional, Berthelot, Camille, additional, Bobe, Julien, additional, Boudinot, Pierre, additional, Bouza, Carmen, additional, Claros, Manuel Gonzalo, additional, Cousin, Xavier, additional, Crollius, Hugues Roest, additional, Fernández, Jesús, additional, Figueras, Antonio, additional, Gómez-Tato, Antonio, additional, Genêt, Carine, additional, Guiguen, Yann, additional, Hermida, Miguel, additional, Jaillon, Olivier, additional, Jakobsen, Kjetill S., additional, Jentoft, Sissel, additional, Jiang, Yanliang, additional, Jin, Xingkun, additional, Jin, Yulin, additional, Li, Jiongtang, additional, Liu, Shikai, additional, Liu, Zhanjiang, additional, MacKenzie, Simon, additional, Manchado, Manuel, additional, Marandel, Lucie, additional, Martínez, Paulino, additional, McAndrew, Brendan J., additional, Moreira Sanmartín, Rebeca, additional, Nederbragt, Alexander J., additional, Novoa, Beatriz, additional, Panserat, Stéphane, additional, Pardo, Belén G., additional, Penman, David J., additional, Pereiro, Patricia, additional, Piferrer, Francesc, additional, Planas, Josep V., additional, Quillet, Edwige, additional, Rebordinos, Laureana, additional, Ribas, Laia, additional, Rise, Matthew L., additional, Roberts, Steven, additional, Robledo, Diego, additional, Rodríguez-Ramilo, Silvia T., additional, Rubiolo, Juan A., additional, Star, Bastiaan, additional, Sun, Xiaowen, additional, Taboada, Xoana, additional, Tan, Suxu, additional, Tørresen, Ole Kristian, additional, Viñas, Ana, additional, Volff, Jean-Nicolas, additional, Wehner, Stefanie, additional, Winther-Larsen, Hanne C., additional, Xu, Jian, additional, Xu, Peng, additional, Yang, Yujia, additional, and Yuan, Zihao, additional
Published: 2016
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41. The rainbow trout genome, an important landmark for aquaculture and genome evolution

Author: Bobe, Julien, primary, Marandel, Lucie, additional, Panserat, Stéphane, additional, Boudinot, Pierre, additional, Berthelot, Camille, additional, Quillet, Edwige, additional, Volff, Jean-Nicolas, additional, Genêt, Carine, additional, Jaillon, Olivier, additional, Crollius, Hugues Roest, additional, and Guiguen, Yann, additional
Published: 2016
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42. Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

Author: Denoeud, France, Henriet, Simon, Mungpakdee, Sutada, Aury, Jean-Marc, Da Silva, Corinne, Brinkmann, Henner, Mikhaleva, Jana, Olsen, Lisbeth Charlotte, Jubin, Claire, Cañestro, Cristian, Bouquet, Jean-Marie, Danks, Gemma, Poulain, Julie, Campsteijn, Coen, Adamski, Marcin, Cross, Ismael, Yadetie, Fekadu, Muffato, Matthieu, Louis, Alexandra, Butcher, Stephen, Tsagkogeorga, Georgia, Konrad, Anke, Singh, Sarabdeep, Jensen, Marit Flo, Cong, Evelyne Huynh, Eikeseth-Otteraa, Helen, Noel, Benjamin, Anthouard, Véronique, Porcel, Betina M., Kachouri-Lafond, Rym, Nishino, Atsuo, Ugolini, Matteo, Chourrout, Pascal, Nishida, Hiroki, Aasland, Rein, Huzurbazar, Snehalata, Westhof, Eric, Delsuc, Frédéric, Lehrach, Hans, Reinhardt, Richard, Weissenbach, Jean, Roy, Scott W., Artiguenave, François, Postlethwait, John H., Manak, J. Robert, Thompson, Eric M., Jaillon, Olivier, Du Pasquier, Louis, Boudinot, Pierre, Liberles, David A., Volff, Jean-Nicolas, Philippe, Hervé, Lenhard, Boris, Crollius, Hugues Roest, Wincker, Patrick, and Chourrout, Daniel
Published: 2010

43. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela, Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea, Picheral, Marc, Henry, Nicolas, Acinas, Silvia, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sullivan, Matthew, Sunagawa, Shinichi, Wincker, Patrick, Stemmann, Lars, Lombard, Fabien, 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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU]Sciences of the Universe [physics], fungi
Abstract: International audience; Abstract Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO 2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
Published: 2021

44. Giant Viruses Encode Actin-Related Proteins

Author: Da Cunha, Violette, primary, Gaia, Morgan, additional, Ogata, Hiroyuki, additional, Jaillon, Olivier, additional, Delmont, Tom O, additional, and Forterre, Patrick, additional
Published: 2022
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45. Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses

Author: Gaïa, Morgan, primary, Meng, Lingjie, additional, Pelletier, Eric, additional, Forterre, Patrick, additional, Vanni, Chiara, additional, Fernandez-Guerra, Antonio, additional, Jaillon, Olivier, additional, Wincker, Patrick, additional, Ogata, Hiroyuki, additional, Krupovic, Mart, additional, and Delmont, Tom O., additional
Published: 2021
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46. Environmental vulnerability of the global ocean epipelagic plankton community interactome

Author: Chaffron, Samuel, Delage, Erwan, Budinich, Marko, Vintache, Damien, Henry, Nicolas, Nef, Charlotte, Ardyna, Mathieu, Zayed, Ahmed A., Junger, Pedro C., Galand, Pierre E., Lovejoy, Connie, Murray, Alison, Sarmento, Hugo, Tara Oceans Coordinators, Acinas, Silvia G., Babin, Marcel, Iudicone, Daniele, Jaillon, Olivier, Karsenti, Eric, Wincker, Patrick, Karp-Boss, Lee, Sullivan, Matthew B., Bowler, Chris, Vargas, Colomban de, Eveillard, Damien, Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Helmut Horten Foundation, Ministerio de Ciencia, Innovación y Universidades (España), European Research Council, European Commission, Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), and Natural Sciences and Engineering Research Council of Canada
Subjects: fungi, [SDE]Environmental Sciences, sense organs
Abstract: This article is contribution number 120 of Tara Oceans.-- 15 pages, 4 figures, supplementary materials https://www.science.org/doi/suppl/10.1126/sciadv.abg1921/suppl_file/sciadv.abg1921_SM.pdf.-- Data and materials availability: Data described here are available at the EBI under the project identifiers PRJEB402 and PRJEB7988 and at PANGAEA (96). All data (raw abundance matrices and interactome graphML files) needed to evaluate the conclusions of the paper are available in the Supplementary Materials. A web server for exploring and searching the global ocean interactome is available at https://saas.ls2n.fr/Tara-Oceans-interactome/, Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network—the community interactome—and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change, We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ETH and the Helmut Horten Foundation, MEXT/JSPS/KAKENHI (projects 16H06429, 16K21723, 16H06437, and 18H02279), the Spanish Ministry of Economy and Competitiveness (project MAGGY-CTM2017-87736-R), ERC Advanced Award Diatomic (grant agreement 835067 to CB), the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant to SC), and the H2020 European Commission project AtlantECO (award number 862923). […]. E.D. is supported by the RFI ATLANSTIC2020 grant (PROBIOSTIC grant to DE). M.Bu. received financial support from the French Facility for Global Environment (FFEM) as part of the “Ocean Plankton, Climate and Development” project. P.C.J. was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP (PhD grant 2017/26786-1). H.S. is supported by a Brazilian Research Council (CNPq) productivity grant (process 309514/2017-7) and FAPESP (grant 2014/14139-3). […] Additional funding from the Natural Sciences and Engineering Council (NSERC) Canada Discovery program is gratefully acknowledged., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021

47. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, Winckler, Patrick, 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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fonds Français pour l'Environnement Mondial, European Commission, and Agencia Estatal de Investigación (España)
Subjects: Multidisciplinary, Ecology, Abundance (ecology), FOS: Biological sciences, Ectotherm, fungi, Environmental science, Climate model, Ecosystem, Plankton, Zooplankton, Copepod, Latitude
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump, This article is contribution number 121 of Tara Oceans.-- 19 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41598-021-94615-5.-- Data availability: Median ESD and abundance values by zooplankton groups are available at https://doi.org/10.17632/nwvjwccgvh.1. Zooplankton imaging datasets from the Tara Oceans expeditions are available through the collaborative web Ecotaxa application and repository under the addresses: https://ecotaxa.obs-vlfr.fr/prj/377, https://ecotaxa.obs-vlfr.fr/prj/2245, https://ecotaxa.obs-vlfr.fr/prj/378 for the WP2 net; https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for the Bongo net; https://ecotaxa.obs-vlfr.fr/prj/415, https://ecotaxa.obs-vlfr.fr/prj/409, https://ecotaxa.obs-vlfr.fr/prj/408, https://ecotaxa.obs-vlfr.fr/prj/411, https://ecotaxa.obs-vlfr.fr/prj/412 for the Régent net. Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582, Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (http://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, The French Ministry of Research, and the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). M.C.B. acknowledges postdoc fellowships from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES) (99999.000487/2016-03) and the Fonds Français pour l'Environnement Mondial (FFEM). F.B. received support from ETH Zürich and from the European Union’s Horizon 2020 research and innovation program under grant agreement n°SEP-210591007, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2021

48. Variability of the Nonstructural 5A Protein of Hepatitis C Virus Type 3a Isolates and Relation to Interferon Sensitivity

Author: Agence Nationale de Recherche sur le SIDA AC11 Group, Castelain, Sandrine, Khorsi, Hafida, Roussel, Juliette, François, Catherine, Jaillon, Olivier, Capron, Dominique, Penin, François, Wychowski, Czeslaw, Meurs, Eliane, and Duverlie, Gilles
Published: 2002

49. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence

Author: Guérin, Nina, primary, Ciccarella, Marta, additional, Flamant, Elisa, additional, Frémont, Paul, additional, Mangenot, Sophie, additional, Istace, Benjamin, additional, Noel, Benjamin, additional, Romac, Sarah, additional, Bachy, Charles, additional, Gachenot, Martin, additional, Pelletier, Eric, additional, Alberti, Adriana, additional, Jaillon, Olivier, additional, Cruaud, Corinne, additional, Wincker, Patrick, additional, Aury, Jean-Marc, additional, and Carradec, Quentin, additional
Published: 2021
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50. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Author: Massana, Ramon, Gobet, Angélique, Audic, Stéphane, Bass, David, Bittner, Lucie, Boutte, Christophe, Chambouvet, Aurélie, Christen, Richard, Claverie, Jean-Michel, Decelle, Johan, Dolan, John R., Dunthorn, Micah, Edvardsen, Bente, Forn, Irene, Forster, Dominik, Guillou, Laure, Jaillon, Olivier, Kooistra, Wiebe H. C. F., Logares, Ramiro, Mahé, Frédéric, Not, Fabrice, Ogata, Hiroyuki, Pawlowski, Jan, Pernice, Massimo C., Probert, Ian, Romac, Sarah, Richards, Thomas, Santini, Sébastien, Shalchian-Tabrizi, Kamran, Siano, Raffaele, Simon, Nathalie, Stoeck, Thorsten, Vaulot, Daniel, Zingone, Adriana, and de Vargas, Colomban
Published: 2015
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