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ArticleExpanding Tara oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition (2016-2018)(Frontiers Media, 2019-12-11) Gorsky, Gabriel ; Bourdin, Guillaume ; Lombard, Fabien ; Pedrotti, Maria Luiza ; Audrain, Samuel ; Bin, Nicolas ; Boss, Emmanuel S. ; Bowler, Chris ; Cassar, Nicolas ; Caudan, Loic ; Chabot, Genevieve ; Cohen, Natalie R. ; Cron, Daniel ; De Vargas, Colomban ; Dolan, John R. ; Douville, Eric ; Elineau, Amanda ; Flores, J. Michel ; Ghiglione, Jean-Francois ; Haëntjens, Nils ; Hertau, Martin ; John, Seth G. ; Kelly, Rachel L. ; Koren, Ilan ; Lin, Yajuan ; Marie, Dominique ; Moulin, Clémentine ; Moucherie, Yohann ; Pesant, Stephane ; Picheral, Marc ; Poulain, Julie ; Pujo-Pay, Mireille ; Reverdin, Gilles ; Romac, Sarah ; Sullivan, Mathew B. ; Trainic, Miri ; Tressol, Marc ; Troublé, Romain ; Vardi, Assaf ; Voolstra, Christian R. ; Wincker, Patrick ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Gilson, Eric ; Reynaud, Stephanie ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Vega Thurber, Rebecca ; Zoccola, Didier ; Planes, Serge ; Allemand, Denis ; Karsenti, EricInteractions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.
ArticleGenome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita(Nature Publishing Group, 2008-07-27) Abad, Pierre ; Gouzy, Jerome ; Aury, Jean-Marc ; Castagnone-Sereno, Philippe ; Danchin, Etienne G. J. ; Deleury, Emeline ; Perfus-Barbeoch, Laetitia ; Anthouard, Veronique ; Artiguenave, Francois ; Blok, Vivian C. ; Caillaud, Marie-Cecile ; Coutinho, Pedro M. ; Da Silva, Corinne ; De Luca, Francesca ; Deau, Florence ; Esquibet, Magali ; Flutre, Timothe ; Goldstone, Jared V. ; Hamamouch, Noureddine ; Hewezi, Tarek ; Jaillon, Olivier ; Jubin, Claire ; Leonetti, Paola ; Magliano, Marc ; Maier, Tom R. ; Markov, Gabriel V. ; McVeigh, Paul ; Pesole, Graziano ; Poulain, Julie ; Robinson-Rechavi, Marc ; Sallet, Erika ; Segurens, Beatrice ; Steinbach, Delphine ; Tytgat, Tom ; Ugarte, Edgardo ; van Ghelder, Cyril ; Veronico, Pasqua ; Baum, Thomas J. ; Blaxter, Mark ; Bleve-Zacheo, Teresa ; Davis, Eric L ; Ewbank, Jonathan J. ; Favery, Bruno ; Grenier, Eric ; Henrissat, Bernard ; Jones, John T. ; Laudet, Vincent ; Maule, Aaron G. ; Quesneville, Hadi ; Rosso, Marie-Noelle ; Schiex, Thomas ; Smant, Geert ; Weissenbach, Jean ; Wincker, PatrickPlant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall–degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
ArticleGenomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga(Nature Publishing Group, 2013-07-21) Flot, Jean-Francois ; Hespeels, Boris ; Li, Xiang ; Noel, Benjamin ; Arkhipova, Irina R. ; Danchin, Etienne G. J. ; Hejno, Andreas ; Henrissat, Bernard ; Koszul, Romain ; Aury, Jean-Marc ; Barbe, Valerie ; Barthelemy, Roxane-Marie ; Bast, Jens ; Bazykin, Georgii A. ; Chabrol, Olivier ; Couloux, Arnaud ; Da Rocha, Martine ; Da Silva, Corinne ; Gladyshev, Eugene A. ; Gouret, Philippe ; Hallatschek, Oskar ; Hecox-Lea, Bette ; Labadie, Karine ; Lejeune, Benjamin ; Piskurek, Oliver ; Poulain, Julie ; Rodriguez, Fernando ; Ryan, Joseph F. ; Vakhrusheva, Olga A. ; Wajnberg, Eric ; Wirth, Benedicte ; Yushenova, Irina A. ; Kellis, Manolis ; Kondrashov, Alexey S. ; Mark Welch, David B. ; Pontarotti, Pierre ; Weissenbach, Jean ; Wincker, Patrick ; Jaillon, Olivier ; Van Doninck, KarineLoss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
ArticleThe Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean(Public Library of Science, 2019-09-23) Planes, Serge ; Allemand, Denis ; Agostini, Sylvain ; Banaigs, Bernard ; Boissin, Emilie ; Boss, Emmanuel S. ; Bourdin, Guillaume ; Bowler, Chris ; Douville, Eric ; Flores, J. Michel ; Forcioli, Didier ; Furla, Paola ; Galand, Pierre E. ; Ghiglione, Jean-Francois ; Gilson, Eric ; Lombard, Fabien ; Moulin, Clémentine ; Pesant, Stephane ; Poulain, Julie ; Reynaud, Stephanie ; Romac, Sarah ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Thomas, Olivier P. ; Troublé, Romain ; de Vargas, Colomban ; Vega Thurber, Rebecca ; Voolstra, Christian R. ; Wincker, Patrick ; Tara Pacific ConsortiumCoral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
ArticleLife-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton(Nature Publishing Group, 2014-12-02) von Dassow, Peter ; John, Uwe ; Ogata, Hiroyuki ; Probert, Ian ; Bendif, El Mahdi ; Kege, Jessica U. ; Audic, Stephane ; Wincker, Patrick ; Da Silva, Corinne ; Claverie, Jean-Michel ; Doney, Scott C. ; Glover, David M. ; Flores, Daniella Mella ; Herrera, Yeritza ; Lescot, Magali ; Garet-Delmas, Marie-Jose ; de Vargas, ColombanEmiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.