Ogata Hiroyuki

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Ogata
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Hiroyuki
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  • Article
    The ocean sampling day consortium
    (BioMed Central, 2015-06-19) Kopf, Anna ; Bicak, Mesude ; Kottmann, Renzo ; Schnetzer, Julia ; Kostadinov, Ivaylo ; Lehmann, Katja ; Fernandez-Guerra, Antonio ; Jeanthon, Christian ; Rahav, Eyal ; Ullrich, Matthias S. ; Wichels, Antje ; Gerdts, Gunnar ; Polymenakou, Paraskevi ; Kotoulas, Georgios ; Siam, Rania ; Abdallah, Rehab Z. ; Sonnenschein, Eva C. ; Cariou, Thierry ; O’Gara, Fergal ; Jackson, Stephen ; Orlic, Sandi ; Steinke, Michael ; Busch, Julia ; Duarte, Bernardo ; Caçador, Isabel ; Canning-Clode, Joao ; Bobrova, Oleksandra ; Marteinsson, Viggo ; Reynisson, Eyjolfur ; Loureiro, Clara Magalhaes ; Luna, Gian Marco ; Quero, Grazia Marina ; Loscher, Carolin R. ; Kremp, Anke ; DeLorenzo, Marie E. ; Øvreås, Lise ; Tolman, Jennifer ; LaRoche, Julie ; Penna, Antonella ; Frischer, Marc ; Davis, Timothy ; Katherine, Barker ; Meyer, Christopher P. ; Ramos, Sandra ; Magalhaes, Catarina ; Jude-Lemeilleur, Florence ; Aguirre-Macedo, Ma Leopoldina ; Wang, Shiao ; Poulton, Nicole ; Jones, Scott ; Collin, Rachel ; Fuhrman, Jed A. ; Conan, Pascal ; Alonso, Cecilia ; Stambler, Noga ; Goodwin, Kelly ; Yakimov, Michail M. ; Baltar, Federico ; Bodrossy, Levente ; Van De Kamp, Jodie ; Frampton, Dion M. F. ; Ostrowski, Martin ; Van Ruth, Paul ; Malthouse, Paul ; Claus, Simon ; Deneudt, Klaas ; Mortelmans, Jonas ; Pitois, Sophie ; Wallom, David ; Salter, Ian ; Costa, Rodrigo ; Schroeder, Declan C. ; Kandil, Mahrous M. ; Amaral, Valentina ; Biancalana, Florencia ; Santana, Rafael ; Pedrotti, Maria Luiza ; Yoshida, Takashi ; Ogata, Hiroyuki ; Ingleton, Timothy ; Munnik, Kate ; Rodriguez-Ezpeleta, Naiara ; Berteaux-Lecellier, Veronique ; Wecker, Patricia ; Cancio, Ibon ; Vaulot, Daniel ; Bienhold, Christina ; Ghazal, Hassan ; Chaouni, Bouchra ; Essayeh, Soumya ; Ettamimi, Sara ; Zaid, El Houcine ; Boukhatem, Noureddine ; Bouali, Abderrahim ; Chahboune, Rajaa ; Barrijal, Said ; Timinouni, Mohammed ; El Otmani, Fatima ; Bennani, Mohamed ; Mea, Marianna ; Todorova, Nadezhda ; Karamfilov, Ventzislav ; ten Hoopen, Petra ; Cochrane, Guy R. ; L’Haridon, Stephane ; Bizsel, Kemal Can ; Vezzi, Alessandro ; Lauro, Federico M. ; Martin, Patrick ; Jensen, Rachelle M. ; Hinks, Jamie ; Gebbels, Susan ; Rosselli, Riccardo ; De Pascale, Fabio ; Schiavon, Riccardo ; dos Santos, Antonina ; Villar, Emilie ; Pesant, Stephane ; Cataletto, Bruno ; Malfatti, Francesca ; Edirisinghe, Ranjith ; Herrera Silveira, Jorge A. ; Barbier, Michele ; Turk, Valentina ; Tinta, Tinkara ; Fuller, Wayne J. ; Salihoglu, Ilkay ; Serakinci, Nedime ; Ergoren, Mahmut Cerkez ; Bresnan, Eileen ; Iriberri, Juan ; Fronth Nyhus, Paul Anders ; Bente, Edvardsen ; Karlsen, Hans Erik ; Golyshin, Peter N. ; Gasol, Josep M. ; Moncheva, Snejana ; Dzhembekova, Nina ; Johnson, Zackary ; Sinigalliano, Christopher D. ; Gidley, Maribeth Louise ; Zingone, Adriana ; Danovaro, Roberto ; Tsiamis, Georgios ; Clark, Melody S. ; Costa, Ana Cristina ; El Bour, Monia ; Martins, Ana M. ; Collins, R. Eric ; Ducluzeau, Anne-Lise ; Martinez, Jonathan ; Costello, Mark J. ; Amaral-Zettler, Linda A. ; Gilbert, Jack A. ; Davies, Neil ; Field, Dawn ; Glockner, Frank Oliver
    Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
  • Article
    Pan genome of the phytoplankton Emiliania underpins its global distribution
    (Nature Publishing Group, 2013-07-10) Read, Betsy A. ; Kegel, Jessica ; Klute, Mary J. ; Kuo, Alan J. ; Lefebvre, Stephane C. ; Maumus, Florian ; Mayer, Christoph ; Miller, John ; Monier, Adam ; Salamov, Asaf ; Young, Jeremy ; Aguilar, Maria ; Claverie, Jean-Michel ; Frickenhaus, Stephan ; Gonzalez, Karina ; Herman, Emily K. ; Lin, Yao-Cheng ; Napier, Johnathan ; Ogata, Hiroyuki ; Sarno, Analissa F. ; Shmutz, Jeremy ; Schroeder, Declan C. ; de Vargas, Colomban ; Verret, Frederic ; von Dassow, Peter ; Valentin, Klaus ; Van de Peer, Yves ; Wheeler, Glen L. ; Emiliania huxleyi Annotation Consortium ; Dacks, Joel B. ; Delwiche, Charles F. ; Dyhrman, Sonya T. ; Glockne, Gernot ; Joh, Uwe ; Richards, Thomas ; Worden, Alexandra Z. ; Zhang, Xiaoyu ; Grigoriev, Igor V.
    Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space3. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
  • Article
    Life-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, Colomban
    Emiliania 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.