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1. Creative Labour Regulation: Indeterminacy and Protection in an Uncertain World

Author: D. McCann, S. Lee, P. Belser, C. Fenwick, J. Howe, M. Luebker and D. McCann, S. Lee, P. Belser, C. Fenwick, J. Howe, M. Luebker
Published: 2014

2. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean—Atlantic Gradient

Author: Trouche, B., Brandt, M.I., Belser, C., Orejas, Covadonga, Pesant, S., Poulain, J., Wincker, P., Auguet, J.C., Arnaud-Haond, S., Maignien, L., Trouche, B., Brandt, M.I., Belser, C., Orejas, Covadonga, Pesant, S., Poulain, J., Wincker, P., Auguet, J.C., Arnaud-Haond, S., and Maignien, L.
Abstract: Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.
Published: 2021

3. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Author: Gorsky, Gabriel, Bourdin, Guillaume, Lombard, Fabien, Pedrotti, Maria Luiza, Audrain, Samuel, Bin, Nicolas, Boss, Emmanuel, 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, Haentjens, Nils, Hertau, Martin, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Moulin, Clementine, Moucherie, Yohann, Pesant, Stephane, Picheral, Marc, Poulain, Julie, Pujo-pay, Mireille, Reverdin, Gilles, Romac, Sarah, Sullivan, Mathew B., Trainic, Miri, Tressol, Marc, Trouble, 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., Thurber, Rebecca Lisette Vega, Zoccola, Didier, Planes, Serge, Allemand, Denis, Karsenti, Eric, Planes, S., Banaig, B., Boissin, E., Iwankow, G., Allemand, D., Zoccola, D., Reynaud, S., Beraud, E., Djerbi, N., Forcioli, D., Furla, P., Gilson, E., Mcmind, R., Ottaviani, A., Rottinger, E., Rouan, A., Zamoum, T., Flume, B. C. C., Pogoreutz, C., Voolstra, C. R., Rothig, T., Ziegler, M., Paoli, L., Ruscheweyh, H-j, Salazar, G., Sunagawa, S., Flores, J. M., Koren, I, Trainic, M., Lang-yona, N., Vardi, A., Conan, P., Ghiglione, J-f, Pujo-pay, M., Galand, P. E., Hochart, C., Audrain, S., Bourgois, E., Hertau, M., Lancelot, J., Monmarche, D., Moulin, C., Moucherie, Y., Trouble, R., Boss, E., Bourdin, G., Haentjens, N., Karp-boss, L., Agostini, S., Mitsuhashi, G., Kitano, Y., Da Silva, O., Dolan, J. R., Gorsky, G., Lemee, R., Lombard, F., Pedrotti, M-l, Cronin, D., Sullivan, M., Armstrong, E., Aury, J-m, Barbe, V, Belser, C., Carradec, Q., Labadie, K., Le-hoang, J., Noel, B., Poulain, J., Wincker, P., Klinges, G., Vega-thunder, R., Bonnival, E., De Vargas, C., Henry, N., Marie, D., Romac, S., Pesant, S., Miguel-gorda, M., Thomas, O. P., Bowler, C., Friedrich, R., Cassar, N., Lin, Y., John, S. G., Kelly, R. L., Cohen, N. R., Reverdin, G., Filee, J., Pedrotti, Maria Luiza, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Laboratoires d'excellence - LabexMER Marine Excellence Research: a changing ocean - - LabexMER2010 - ANR-10-LABX-0019 - LABX - OLD, 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), University of Maine, Tara Expéditions, Institut de biologie de l'Ecole Normale Supérieure (IBENS), 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), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Nicholas School of the Environment, Duke University [Durham], Mercator Océan, Société Civile CNRS Ifremer IRD Météo-France SHOM, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Woods Hole Oceanographic Institution (WHOI), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-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), University of Southern California (USC), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Department of Civil, Environmental and Geodetic Engineering [Columbus], Ohio State University [Columbus] (OSU), Laboratoire d'aérologie (LAERO), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universität Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Dpt génétique médicale [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Centre Scientifique de Monaco (CSM), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), European Molecular Biology Laboratory [Heidelberg] (EMBL), TARA, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, trace metals, Ocean Engineering, neuston, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Oceanography, 01 natural sciences, Pacific ocean, taxonomy, neuston/plankton genomics/taxonomy/imaging, ddc:570, Ecosystem, 14. Life underwater, lcsh:Science, Reef, 0105 earth and related environmental sciences, Water Science and Technology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, geography, geography.geographical_feature_category, aerosols, NCP, IOP, microplastic, plankton genomics, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ACL, 010604 marine biology & hydrobiology, Community structure, imaging, Pelagic zone, Plankton, Inlet, neuston/plankton genomics/taxonomy/imaging, aerosols, NCP, IOP, trace metals, microplastic, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, 13. Climate action, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Neuston
Abstract: Interactions 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. ISSN:2296-7745
Published: 2019

4. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean

Author: Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-francois, Gilson, Eric, Lombard, Fabien, Moulin, Clementine, Pesant, Stephane, Poulain, Julie, Reynaud, Stephanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Trouble, Romain, De Vargas, Colomban, Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, Planes, S., Allemand, D., Agostini, S., Armstrong, E., Audrain, S., Aury, J-m, Banaig, B., Barbe, V, Belser, C., Beraud, E., Boissin, E., Bonnival, E., Boss, E., Bourdin, G., Bourgois, E., Bowler, C., Carradec, Q., Cassar, N., Cohen, N. R., Conan, P., Cronin, D. R., Da Silva, O., De Vargas, C., Djerbi, N., Dolan, J. R., Herta, Dominguez G., Du J, Filee, J., Flores, J. M., Forcioli, D., Friedrich, R., Furla, P., Galand, P. E., Ghiglione, J-f, Gilson, E., Gorsky, G., Guinther, M., Haentjens, N., Henry, N., Hertau, M., Hochart, C., Hume, B. C. C., Iwankow, G., John, S. G., Karp-boss, L., Kelly, R. L., Kitano, Y., Klinges, G., Koren, I, Labadie, K., Lancelot, J., Lang-yona, N., Le-hoang, J., Lemee, R., Lin, Y., Lombard, F., Marie, D., Mcmind, R., Miguel-gordo, M., Trainic, M., Monmarche, D., Moulin, C., Mucherie, Y., Noel, B., Ottaviani, A., Paoli, L., Pedrotti, M-l, Pesant, S., Pogoreutz, C., Poulain, J., Pujo-pay, M., Reverdin, G., Reynaud, S., Romac, S., Rothig, T., Rottinger, E., Rouan, A., Ruscheweyh, H-j, Salazar, G., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Trouble, R., Vardi, A., Vega-thunder, R., Voolstra, C. R., Wincker, P., Zahed, A., Zamoum, T., Ziegler, M., Zoccola, D., Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre Scientifique de Monaco (CSM), Tara Expéditions, Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, University of Maine, 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 (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), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), 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 Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), ECOlogy of MArine Plankton (ECOMAP), 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)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Ohio State University [Columbus] (OSU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), University of Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Department of Earth Sciences [USC Los Angeles], University of Southern California (USC), Martin Ryan Institute, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Derby [United Kingdom], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-17-CE02-0020,CORALGENE,Complexité génomique de l'holobionte ' corail ' à l'échelle du Pacifique(2017), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (AD2M), 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)-Centre National de la Recherche Scientifique (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)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Justus-Liebig-Universität Gießen (JLU), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0301 basic medicine, Topography, Coral reefs, Effects of global warming on oceans, Coral, Biodiversity, Marine and Aquatic Sciences, Ecosystem services, 0302 clinical medicine, Community Page, Oceans, Biology (General), Islands, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography.geographical_feature_category, Ecology, Microbiota, General Neuroscience, Eukaryota, Coral reef, Anthozoa, Plankton, Holobiont, Corals, Expeditions, General Agricultural and Biological Sciences, Marine ecosystems, QH301-705.5, Climate change, Marine Biology, Biology, Ecosystems, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, ddc:570, Animals, Metabolomics, Marine ecosystem, 14. Life underwater, Symbiosis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Landforms, geography, Pacific Ocean, General Immunology and Microbiology, ACL, Ecology and Environmental Sciences, Organisms, Biology and Life Sciences, Geomorphology, Bodies of Water, 15. Life on land, Invertebrates, 030104 developmental biology, 13. Climate action, Earth Sciences, Reefs, Metagenomics, Reef ecosystems, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery
Abstract: Coral 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., This Community Page article presents the Tara Pacific expedition, which aims to shed 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 reef systems.
Published: 2019

5. Oak genome reveals facets of long lifespan

Author: Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., Faye, S., Francillonne, N., Labadie, K., Le Provost, G., Lesur, I., Bartholomé, J., Faivre-Rampant, P., Kohler, A., Leplé, J.-C., Chantret, N., Chen, J., Diévart, A., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Bogeat-Triboulot, M.-B., Bouffaud, Marie-Lara, Brachi, B., Chancerel, E., Cohen, D., Couloux, A., Da Silva, C., Dossat, C., Ehrenmann, F., Gaspin, C., Grima-Pettenati, J., Guichoux, E., Hecker, A., Herrmann, Sylvie, Hugueney, P., Hummel, I., Klopp, C., Lalanne, C., Lascoux, M., Lasserre, E., Lemainque, A., Desprez-Loustau, M.-L., Luyten, I., Madoui, M.-A., Mangenot, S., Marchal, C., Maumus, F., Mercier, J., Michotey, C., Panaud, O., Picault, N., Rouhier, N., Rué, O., Rustenholz, C., Salin, F., Soler, M., Tarkka, Mika, Velt, A., Zanne, A.E., Martin, F., Wincker, P., Quesneville, H., Kremer, A., Salse, J., Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., Faye, S., Francillonne, N., Labadie, K., Le Provost, G., Lesur, I., Bartholomé, J., Faivre-Rampant, P., Kohler, A., Leplé, J.-C., Chantret, N., Chen, J., Diévart, A., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Bogeat-Triboulot, M.-B., Bouffaud, Marie-Lara, Brachi, B., Chancerel, E., Cohen, D., Couloux, A., Da Silva, C., Dossat, C., Ehrenmann, F., Gaspin, C., Grima-Pettenati, J., Guichoux, E., Hecker, A., Herrmann, Sylvie, Hugueney, P., Hummel, I., Klopp, C., Lalanne, C., Lascoux, M., Lasserre, E., Lemainque, A., Desprez-Loustau, M.-L., Luyten, I., Madoui, M.-A., Mangenot, S., Marchal, C., Maumus, F., Mercier, J., Michotey, C., Panaud, O., Picault, N., Rouhier, N., Rué, O., Rustenholz, C., Salin, F., Soler, M., Tarkka, Mika, Velt, A., Zanne, A.E., Martin, F., Wincker, P., Quesneville, H., Kremer, A., and Salse, J.
Abstract: Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
Published: 2018

6. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Author: Gouin, A., Bretaudeau, A., Nam, K., Gimenez, S., Aury, J., Duvic, B., Hilliou, F., Durand, N., Montagné, N., Darboux, I., Kuwar, S., Chertemps, T., Siaussat, D., Bretschneider, A., Moné, Y., Ahn, S., Hänniger, S., Grenet, A., Neunemann, D., Maumus, F., Luyten, I., Labadie, K., Xu, W., Koutroumpa, F., Escoubas, J., Llopis, A., Maïbèche-Coisne, M., Salasc, F., Tomar, A., Anderson, A., Khan, S., Dumas, P., Orsucci, M., Guy, J., Belser, C., Alberti, A., Noel, B., Couloux, A., Mercier, J., Nidelet, S., Dubois, E., Liu, N., Boulogne, I., Mirabeau, O., Le Goff, G., Gordon, K., Oakeshott, J., Consoli, F., Volkoff, A., Fescemyer, H., Marden, J., Luthe, D., Herrero, S., Heckel, D., Wincker, P., Kergoat, G., Amselem, J., Quesneville, H., Groot, A., Jacquin-Joly, E., Nègre, N., Lemaitre, C., Legeai, F., and Fournier, E.
Subjects: fungi
Abstract: Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
Published: 2017

7. The pea genome

Author: Kreplak, Jonathan, Madoui, Mohammed-Amin, Labadie, Karine, Aubert, Gregoire, Bayer, Philippe, Capal, P., Klein, Anthony, KOUGBEADJO, Ayité, Vrana, J., Gali, K.K., Fournier, Carine, d'Agata, Léo, Taran, B., Belser, C., Le Paslier, Marie-Christine, Bendahmane, Abdelhafid, Berges, Helene, Barbe, Valérie, McGee, Rebecca, Lichtenzveig, Judith, Coyne, Clarice J., Warkentin, Tom D., Batley, J., Macas, Jiří, Edwards, Dave, Dolezel, Jaroslav, Wincker, Patrick, Burstin, Judith, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Bayer Cropscience, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), USDA-ARS : Agricultural Research Service, Molecular Biology, Bioinformatics, Evolutionary Biology, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), University of Western Australia, Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), School of Plant Biology, The University of Western Australia (UWA), and Noble Research Institute.
Subjects: [SDV]Life Sciences [q-bio], education, [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: International audience; The International Pea Genome Consortium Pea (Pisum sativum L.) has long been a model for plant genetics. It is also a widely grown pulse crop producing protein-rich seeds in a sustainable manner. Thanks to large national and international programs, and driven by innovations in sequencing technology, informatics and biotechnology, many genomic resources are now available for pea. An atlas of the expression of its genes in many tissues, high density genetic mapping, and the ongoing sequencing of its genome have provided useful tools for dissecting traits of interest. We will present how the pea genome draft sequence opens the way to explore genetic diversity of pea.
Published: 2017

8. Towards the genome sequence of pea : a tribute to Mendel

Author: Madoui , Mohammed-Amin, Labadie , K., Kreplak , Jonathan, Aubert , Gregoire, d'Agata , Léo, Capal , P., Fournier , Carine, KOUGBEADJO , Ayité, Vrana , J., Gali , K., Taran , B., Belser , C., Le Paslier , Marie-Christine, McGee , Rebecca, Edwards , D., Batley , J., Bendahmane , Abdelhafid, Berges , Helene, Barbe , V., Tayeh , Nadim, Klein , Anthony, Lichtenzveig , Judith, Aury , J-M., Coyne , C.J., Warkentin , T., Dolezel , J., Wincker , P., Burstin , Judith, 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), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, The University of Western Australia (UWA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Molecular Biology, Bioinformatics, Evolutionary Biology, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Western Region Plant Introduction Station, Legume Society., Institut de Biologie François JACOB (JACOB), 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 de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institute of Experimental Botany ASCR, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Génoscope, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), University of Saskatchewan [Saskatoon] ( U of S ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), USDA-ARS, University of Western Australia, UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Centre National de Ressources Génomiques Végétales ( CNRGV ), and Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC )
Subjects: pea, genome, sequence, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], food and beverages
Abstract: BAP GEAPSI BAP GEAPSIBAPGEAPSI; Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery of the laws of inheritance and kept this model status until the advent of molecular biology at the end of the 20th century. Pea is also one of the world’s oldest domesticated crops. It is currently the third most widely grown pulse crop, as its seeds serve as a protein-rich food for humans and livestock alike. While several legume species genome's draft sequences have been produced, progress in pea genomics has lagged behind largely as a consequence of its complex and large genome size. The pea genome is large (ca 4.45 Gb), probably resulting from recent expansion of retrotransposons followed by sequence diversification. The Pea Genome International Project has undertaken several complementary strategies in order to produce a high-quality draft sequence of the species. We will present how this draft sequence opens the way to renew strategies in pea breeding.
Published: 2016

9. The novel association of SMN protein with a ribonucleoprotein complex containing two major nucleolar proteins is altered in Spinal Muscular Atrophy

Author: Lefebvre, S., Burlet, P., Viollet, L., Bertrandy, S., Huber, C., Belser, C., Vial, E., and Munnich, A.
Subjects: Motor neurons -- Genetic aspects, Spinal muscular atrophy -- Genetic aspects, Genetic disorders -- Research, Biological sciences
Published: 2001

10. A new variant for Autosomal Recessive Spinal Muscular Atrophy in Childhood

Author: Viollet, L., Leclair-Richard, D., Burlet, P., Belser, C., Vial, E., Bertrandy, S., Lefebvre, S., and Munnich, A.
Subjects: Genetic research -- Analysis, Human genetics -- Research, Spinal muscular atrophy -- Genetic aspects, Biological sciences
Published: 2000

11. Mutant SMN protein (472del5) in Spinal Muscular Atrophy enters the nucleolus

Author: Lefebvre, S., Bertrandy, S., Burlet, P., Belser, C., Viollet, L., and Munnich, A.
Subjects: Spinal muscular atrophy -- Genetic aspects, RNA -- Physiological aspects, Biological sciences
Published: 2000

12. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Author: Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., Murat, F., Ueno, S., Bartholomé, J., Lalanne, C., Ehrenmann, F., Noirot, C., Burban, C., Léger, V., Amselem, J., Belser, C., Quesneville, H., Stierschneider, M., Fluch, S., Feldhahn, Lasse, Tarkka, Mika, Herrmann, Sylvie, Buscot, Francois, Klopp, C., Kremer, A., Salse, J., Aury, J.-M., Plomion, C., Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., Murat, F., Ueno, S., Bartholomé, J., Lalanne, C., Ehrenmann, F., Noirot, C., Burban, C., Léger, V., Amselem, J., Belser, C., Quesneville, H., Stierschneider, M., Fluch, S., Feldhahn, Lasse, Tarkka, Mika, Herrmann, Sylvie, Buscot, Francois, Klopp, C., Kremer, A., Salse, J., Aury, J.-M., and Plomion, C.
Abstract: Background Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
Published: 2015

13. Genomic resources for functional analysis in Medicago truncatula and related crop species

Author: Debellé, Frederic, Belser, C., Aury, J.M., Labadie, K., Roux, Brice, Sallet, Erika, Carrere, Sebastien, Wincker, P., Schiex, Thomas, Julier, Bernadette, Gamas, Pascal, Gouzy, Jerome, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA)
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2012

14. Rigid Rodlike Dinuclear Ru/Os Complexes of a Novel Bridging Ligand. Intercomponent Energy and Electron-Transfer Processes

Author: c Stefan Bernhard, Luisa De Cola, a and, b Francesco Barigelletti, a Vincenzo Balzani, Peter Belser, c, and Lucia Flamigni b
Subjects: chemistry.chemical_compound, Electron transfer, Crystallography, Reaction rate constant, chemistry, Excited state, Adamantane, Energy transfer, General Engineering, Bridging ligand, Physical and Theoretical Chemistry, Luminescence, Photochemistry
Abstract: The PF6- salts of the dinuclear complexes [(bpy)2Ru(PAP)Ru(bpy)2]4+ (RuIIPAPRuII), [(bpy)2Os(PAP)Os(bpy)2]4+ (OsIIPAPOsII), and [(bpy)2Ru(PAP)Os(bpy)2]4+ (RuIIPAPOsII) have been prepared, where bpy = 2,2‘-bipyridine and PAP is a rodlike bridging ligand made of an adamantane-based spacer collinear with the coordination axis of two 1,10-phenanthroline units. In the prepared complexes, the metal−metal distance is 2.1 nm. In the RuIIPAPOsII compound, photoinduced energy transfer from the RuII-based to the OsII-based unit takes place with rate constant 5.2 × 107 s-1 at room temperature and 2.4 × 107 s-1 at 77 K. In the mixed-valence RuIIPAPOsIII compound, the luminescent excited state of the RuII-based unit is quenched via electron transfer by the OsIII-based unit with rate constant 7.2 × 106 s-1. The rate constant for the back-electron-transfer reaction is 8.3 × 103 s-1.
Published: 1996

15. High-power rf cavity R&D for the PEP-II B factory

Author: Rimmer, R, Lambertson, Glen R, Hodgson, J, Ko, K, Ng, C, Pendleton, R, Reuter, E, Schwarz, H, Skarpaas, K V, Adams, F, Burton, B, De Jong, M, Lipsett, M G, Belser, C, Franks, M, and McCarville, T
Subjects: Engineering
Published: 1994

16. Detection and discrimination of fauna in the aerosphere using Doppler weather surveillance radar

Author: Gauthreaux, S. A., primary, Livingston, J. W., additional, and Belser, C. G., additional
Published: 2007
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17. Evaluation of the ISAS system after two years of practical experience in forensic police work

Author: Belser, C., Ineichen, M., and Pfefferli, P.
Published: 1996
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18. Status of the PEP-II low-energy ring vacuum system

Author: Cheng, D., primary, Hunt, D., additional, Hsieh, H., additional, Meneghetti, J., additional, Kennedy, K., additional, Stevens, T., additional, Jones, G., additional, Miller, T., additional, Colomb, D., additional, Bertolini, L., additional, Belser, C., additional, Kerns, J., additional, and Daly, E., additional
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19. Status and early commissioning of the PEP-II High Energy Ring

Author: Wienands, U., primary, Reuter, E., additional, Bellomo, P., additional, Fisher, A., additional, Gracia, J., additional, Gray, R., additional, Pietryka, M., additional, Taylor, T., additional, Bharadwaj, V., additional, Iverson, R., additional, Kulikov, A., additional, Seeman, J.T., additional, Turner, J., additional, Belser, C., additional, Zisman, M., additional, and Zholents, S., additional
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20. Status of the PEP-II low-energy ring vacuum system.

Author: Cheng, D., Hunt, D., Hsieh, H., Meneghetti, J., Kennedy, K., Stevens, T., Jones, G., Miller, T., Colomb, D., Bertolini, L., Belser, C., Kerns, J., and Daly, E.
Published: 1997
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21. Status and early commissioning of the PEP-II High Energy Ring.

Author: Wienands, U., Reuter, E., Bellomo, P., Fisher, A., Gracia, J., Gray, R., Pietryka, M., Taylor, T., Bharadwaj, V., Iverson, R., Kulikov, A., Seeman, J.T., Turner, J., Belser, C., Zisman, M., and Zholents, S.
Published: 1997
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22. Evaluation of anomalous systemic and pulmonary venous return in a young child with heterotaxy: a case study--implications for military dependent care.

Author: Kinney JB, Gilman MD, Bolt SL, Zenger DC, Belser C, Stillman CA, Sahn DJ, Kinney, James Bedford, Gilman, Matthew David, Bolt, Stephen Laurence, Zenger, David Charles, Belser, Charlotte, Stillman, Charles Allen, and Sahn, David Jonathan
Abstract: The case of a young male patient with a complex admixture lesion who required a comprehensive anatomic evaluation before palliative cardiac surgery is presented. We describe a safe anesthesia protocol for obtaining the late-acquisition, gadolinium-enhanced, magnetic resonance angiographic images necessary to define the complex pulmonary and systemic venous anatomic features of his cardiac admixture lesion. Subspecialty physician staffing implications for the care of military dependants with congenital heart disease who might benefit from evaluation using this safe simple protocol and readily available magnetic resonance imaging technology are addressed. [ABSTRACT FROM AUTHOR]
Published: 2008
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23. Assembly for producing oil from a stratum of oil shale in situ

Author: Belser, C
Published: 1955

24. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

Author: Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, Seehausen O, Watts PC, Shaw F, Davey RP, Minotto A, Fernández JM, Böhne A, Alegria C, Alioto T, Alves PC, Amorim IR, Aury JM, Backstrom N, Baldrian P, Baltrunaite L, Barta E, BedHom B, Belser C, Bergsten J, Bertrand L, Bilandija H, Binzer-Panchal M, Bista I, Blaxter M, Borges PAV, Dias GB, Bosse M, Brown T, Bruggmann R, Buena-Atienza E, Burgin J, Buzan E, Cariani A, Casadei N, Chiara M, Chozas S, Čiampor F Jr, Crottini A, Cruaud C, Cruz F, Dalen L, De Biase A, Del Campo J, Delic T, Dennis AB, Derks MFL, Diroma MA, Djan M, Duprat S, Eleftheriadi K, Feulner PGD, Flot JF, Forni G, Fosso B, Fournier P, Fournier-Chambrillon C, Gabaldon T, Garg S, Gissi C, Giupponi L, Gomez-Garrido J, González J, Grilo ML, Grüning B, Guerin T, Guiglielmoni N, Gut M, Haesler MP, Hahn C, Halpern B, Harrison PW, Heintz J, Hindrikson M, Höglund J, Howe K, Hughes GM, Istace B, Cock MJ, Janžekovič F, Jonsson ZO, Joye-Dind S, Koskimäki JJ, Krystufek B, Kubacka J, Kuhl H, Kusza S, Labadie K, Lähteenaro M, Lantz H, Lavrinienko A, Leclère L, Lopes RJ, Madsen O, Magdelenat G, Magoga G, Manousaki T, Mappes T, Marques JP, Redondo GIM, Maumus F, McCarthy SA, Megens HJ, Melo-Ferreira J, Mendes SL, Montagna M, Moreno J, Mosbech MB, Moura M, Musilova Z, Myers E, Nash WJ, Nater A, Nicholson P, Niell M, Nijland R, Noel B, Noren K, Oliveira PH, Olsen RA, Ometto L, Oomen RA, Ossowski S, Palinauskas V, Palsson S, Panibe JP, Pauperio J, Pavlek M, Payen E, Pawlowska J, Pellicer J, Pesole G, Pimenta J, Pippel M, Pirttilä AM, Poulakakis N, Rajan J, M C Rego R, Resendes R, Resl P, Riesgo A, Rodin-Morch P, Soares AER, Fernandes CR, Romeiras MM, Roxo G, Rüber L, Ruiz-Lopez MJ, Saarma U, da Silva LP, Sim-Sim M, Soler L, Sousa VC, Santos CS, Spada A, Stefanovic M, Steger V, Stiller J, Stöck M, Struck TH, Sudasinghe H, Tapanainen R, Tellgren-Roth C, Trindade H, Tukalenko Y, Urso I, Vacherie B, Van Belleghem SM, Van Oers K, Vargas-Chavez C, Velickovic N, Vella N, Vella A, Vernesi C, Vicente S, Villa S, Pettersson OV, Volckaert FAM, Voros J, Wincker P, Winkler S, Ciofi C, Waterhouse RM, and Mazzoni CJ
Published: 2024
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25. Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres.

Author: Boideau F, Huteau V, Maillet L, Brunet A, Coriton O, Deniot G, Trotoux G, Taburel-Lodé M, Eber F, Gilet M, Baron C, Boutte J, Richard G, Aury JM, Belser C, Labadie K, Morice J, Falentin C, Martin O, Falque M, Chèvre AM, and Rousseau-Gueutin M
Subjects: Recombination, Genetic genetics, Crossing Over, Genetic, Brassica rapa genetics, Chromosomes, Plant genetics, Centromere genetics, Brassica napus genetics, Ploidies, Meiosis genetics
Abstract: Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
Published: 2024
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26. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

Author: Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, Seehausen O, Watts PC, Shaw F, Davey RP, Minotto A, Fernández JM, Böhne A, Alegria C, Alioto T, Alves PC, Amorim IR, Aury JM, Backstrom N, Baldrian P, Baltrunaite L, Barta E, BedHom B, Belser C, Bergsten J, Bertrand L, Bilandija H, Binzer-Panchal M, Bista I, Blaxter M, Borges PAV, Dias GB, Bosse M, Brown T, Bruggmann R, Buena-Atienza E, Burgin J, Buzan E, Cariani A, Casadei N, Chiara M, Chozas S, Čiampor F Jr, Crottini A, Cruaud C, Cruz F, Dalen L, De Biase A, Del Campo J, Delic T, Dennis AB, Derks MFL, Diroma MA, Djan M, Duprat S, Eleftheriadi K, Feulner PGD, Flot JF, Forni G, Fosso B, Fournier P, Fournier-Chambrillon C, Gabaldon T, Garg S, Gissi C, Giupponi L, Gomez-Garrido J, González J, Grilo ML, Grüning B, Guerin T, Guiglielmoni N, Gut M, Haesler MP, Hahn C, Halpern B, Harrison PW, Heintz J, Hindrikson M, Höglund J, Howe K, Hughes GM, Istace B, Cock MJ, Janžekovič F, Jonsson ZO, Joye-Dind S, Koskimäki JJ, Krystufek B, Kubacka J, Kuhl H, Kusza S, Labadie K, Lähteenaro M, Lantz H, Lavrinienko A, Leclère L, Lopes RJ, Madsen O, Magdelenat G, Magoga G, Manousaki T, Mappes T, Marques JP, Redondo GIM, Maumus F, McCarthy SA, Megens HJ, Melo-Ferreira J, Mendes SL, Montagna M, Moreno J, Mosbech MB, Moura M, Musilova Z, Myers E, Nash WJ, Nater A, Nicholson P, Niell M, Nijland R, Noel B, Noren K, Oliveira PH, Olsen RA, Ometto L, Oomen RA, Ossowski S, Palinauskas V, Palsson S, Panibe JP, Pauperio J, Pavlek M, Payen E, Pawlowska J, Pellicer J, Pesole G, Pimenta J, Pippel M, Pirttilä AM, Poulakakis N, Rajan J, M C Rego R, Resendes R, Resl P, Riesgo A, Rodin-Morch P, Soares AER, Fernandes CR, Romeiras MM, Roxo G, Rüber L, Ruiz-Lopez MJ, Saarma U, da Silva LP, Sim-Sim M, Soler L, Sousa VC, Santos CS, Spada A, Stefanovic M, Steger V, Stiller J, Stöck M, Struck TH, Sudasinghe H, Tapanainen R, Tellgren-Roth C, Trindade H, Tukalenko Y, Urso I, Vacherie B, Van Belleghem SM, Van Oers K, Vargas-Chavez C, Velickovic N, Vella N, Vella A, Vernesi C, Vicente S, Villa S, Pettersson OV, Volckaert FAM, Voros J, Wincker P, Winkler S, Ciofi C, Waterhouse RM, and Mazzoni CJ
Abstract: A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP., (© 2024. The Author(s).)
Published: 2024
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27. Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats.

Author: Mota APZ, Koutsovoulos GD, Perfus-Barbeoch L, Despot-Slade E, Labadie K, Aury JM, Robbe-Sermesant K, Bailly-Bechet M, Belser C, Péré A, Rancurel C, Kozlowski DK, Hassanaly-Goulamhoussen R, Da Rocha M, Noel B, Meštrović N, Wincker P, and Danchin EGJ
Subjects: Animals, Caenorhabditis elegans genetics, In Situ Hybridization, Fluorescence, Telomere genetics, Polyploidy, Tylenchoidea genetics, Tylenchida
Abstract: Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity., (© 2024. The Author(s).)
Published: 2024
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28. Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.

Author: Trouche B, Schauberger C, Bouderka F, Auguet JC, Belser C, Poulain J, Thamdrup B, Wincker P, Arnaud-Haond S, Glud RN, and Maignien L
Abstract: Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered., (© 2023. The Author(s).)
Published: 2023
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29. Publisher Correction: The DNA sequence and analysis of human chromosome 14.

Author: Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Brüls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Ségurens B, Anière F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Ménard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufossé-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guérin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier L, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quétier F, Waterston R, Hood L, and Weissenbach J
Published: 2023
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30. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.

Author: Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, and Wincker P
Subjects: Animals, Pacific Ocean, Acclimatization genetics, Coral Reefs, Transcriptome genetics, Anthozoa genetics
Abstract: Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming., (© 2023. The Author(s).)
Published: 2023
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31. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Author: Belser C, Poulain J, Labadie K, Gavory F, Alberti A, Guy J, Carradec Q, Cruaud C, Da Silva C, Engelen S, Mielle P, Perdereau A, Samson G, Gas S, Voolstra CR, Galand PE, Flores JM, Hume BCC, Perna G, Ziegler M, Ruscheweyh HJ, Boissin E, Romac S, Bourdin G, Iwankow G, Moulin C, Paz García DA, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Scarpelli C, Jacoby EK, Oliveira PH, Aury JM, Allemand D, Planes S, and Wincker P
Subjects: Animals, Biodiversity, Ecosystem, Anthozoa, Coral Reefs
Abstract: Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene., (© 2023. The Author(s).)
Published: 2023
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32. Diversity of the Pacific Ocean coral reef microbiome.

Author: Galand PE, Ruscheweyh HJ, Salazar G, Hochart C, Henry N, Hume BCC, Oliveira PH, Perdereau A, Labadie K, Belser C, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Armstrong EJ, Paz-García DA, Ziegler M, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Zoccola D, Voolstra CR, Thurber RV, Sunagawa S, Wincker P, Allemand D, and Planes S
Subjects: Animals, Coral Reefs, Pacific Ocean, Biodiversity, Fishes, Plankton, Anthozoa, Microbiota
Abstract: Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems., (© 2023. The Author(s).)
Published: 2023
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33. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence.

Author: Guérin N, Ciccarella M, Flamant E, Frémont P, Mangenot S, Istace B, Noel B, Belser C, Bertrand L, Labadie K, Cruaud C, Romac S, Bachy C, Gachenot M, Pelletier E, Alberti A, Jaillon O, Wincker P, Aury JM, and Carradec Q
Subjects: Acclimatization genetics, Chromosomes, Genomics, Nitrates metabolism, Oceans and Seas, Phytoplankton genetics, Phytoplankton metabolism, Iron metabolism, Stramenopiles genetics
Abstract: The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment., (© 2022. The Author(s).)
Published: 2022
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34. Chromosome-scale assembly of the yellow mealworm genome.

Author: Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, and Madoui MA
Abstract: Background: The yellow mealworm beetle, Tenebrio molitor , is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor . Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm., Competing Interests: Competing interests: Fabrice Berro, Sona Gasparian and Thomas Lefebvre work for Ynsect, a private company breeding yellow mealworms. Ynsect is also the coordinator of the H2020 FARMYNG project that supports this study. No competing interests were disclosed for the other co-others., (Copyright: © 2022 Eleftheriou E et al.)
Published: 2022
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35. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding.

Author: Aury JM, Engelen S, Istace B, Monat C, Lasserre-Zuber P, Belser C, Cruaud C, Rimbert H, Leroy P, Arribat S, Dufau I, Bellec A, Grimbichler D, Papon N, Paux E, Ranoux M, Alberti A, Wincker P, and Choulet F
Subjects: Breeding, Chromosomes, Sequence Analysis, DNA methods, Genome, Triticum genetics
Abstract: Background: The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost., Results: Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan., Conclusions: We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)
Published: 2022
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36. Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection.

Author: Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P, and Barbe V
Subjects: Genome, Genomic Structural Variation, Genomics methods, High-Throughput Nucleotide Sequencing methods, Sequence Analysis, DNA methods, Nanopores
Abstract: Background: Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1)., Results: We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted., Conclusions: Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference., (© 2022. The Author(s).)
Published: 2022
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37. Epigenomic and structural events preclude recombination in Brassica napus.

Author: Boideau F, Richard G, Coriton O, Huteau V, Belser C, Deniot G, Eber F, Falentin C, Ferreira de Carvalho J, Gilet M, Lodé-Taburel M, Maillet L, Morice J, Trotoux G, Aury JM, Chèvre AM, and Rousseau-Gueutin M
Subjects: Chromosomes, Plant, Epigenomics, Genome, Plant, In Situ Hybridization, Fluorescence, Plant Breeding, Brassica napus genetics
Abstract: Meiotic recombination is a major evolutionary process generating genetic diversity at each generation in sexual organisms. However, this process is highly regulated, with the majority of crossovers lying in the distal chromosomal regions that harbor low DNA methylation levels. Even in these regions, some islands without recombination remain, for which we investigated the underlying causes. Genetic maps were established in two Brassica napus hybrids to detect the presence of such large nonrecombinant islands. The role played by DNA methylation and structural variations in this local absence of recombination was determined by performing bisulfite sequencing and whole genome comparisons. Inferred structural variations were validated using either optical mapping or oligo fluorescence in situ hybridization. Hypermethylated or inverted regions between Brassica genomes were associated with the absence of recombination. Pairwise comparisons of nine B. napus genome assemblies revealed that such inversions occur frequently and may contain key agronomic genes such as resistance to biotic stresses. We conclude that such islands without recombination can have different origins, such as DNA methylation or structural variations in B. napus. It is thus essential to take into account these features in breeding programs as they may hamper the efficient combination of favorable alleles in elite varieties., (© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.)
Published: 2022
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38. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient.

Author: Trouche B, Brandt MI, Belser C, Orejas C, Pesant S, Poulain J, Wincker P, Auguet JC, Arnaud-Haond S, and Maignien L
Abstract: Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Trouche, Brandt, Belser, Orejas, Pesant, Poulain, Wincker, Auguet, Arnaud-Haond and Maignien.)
Published: 2021
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39. Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.

Author: Belser C, Baurens FC, Noel B, Martin G, Cruaud C, Istace B, Yahiaoui N, Labadie K, Hřibová E, Doležel J, Lemainque A, Wincker P, D'Hont A, and Aury JM
Subjects: Nanopore Sequencing, Nanopores, Chromosomes, Plant genetics, Genome, Plant, Musa genetics, Telomere
Abstract: Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes., (© 2021. The Author(s).)
Published: 2021
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40. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case.

Author: Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chèvre AM, Wincker P, Rousseau-Gueutin M, and Aury JM
Abstract: With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology.
Published: 2021
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41. Population genomics of apricots unravels domestication history and adaptive events.

Author: Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrère S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen X, Pétriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T, and Decroocq V
Subjects: Chromosomes, Plant genetics, Disease Resistance genetics, Evolution, Molecular, Fruit classification, Fruit genetics, Fruit growth & development, Gene Flow, Genetic Variation, Life Cycle Stages genetics, Metagenomics, Phenotype, Phylogeny, Prunus armeniaca classification, Prunus armeniaca growth & development, Selection, Genetic, Domestication, Genome, Plant genetics, Prunus armeniaca genetics
Abstract: Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.
Published: 2021
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42. Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA.

Author: Brandt MI, Pradillon F, Trouche B, Henry N, Liautard-Haag C, Cambon-Bonavita MA, Cueff-Gauchard V, Wincker P, Belser C, Poulain J, Arnaud-Haond S, and Zeppilli D
Subjects: Animals, Mediterranean Sea, Biodiversity, Biomarkers analysis, DNA, Environmental analysis, Environmental Monitoring methods, Geologic Sediments analysis
Abstract: Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1-V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
Published: 2021
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43. Long-read assembly of the Brassica napus reference genome Darmor-bzh.

Author: Rousseau-Gueutin M, Belser C, Da Silva C, Richard G, Istace B, Cruaud C, Falentin C, Boideau F, Boutte J, Delourme R, Deniot G, Engelen S, de Carvalho JF, Lemainque A, Maillet L, Morice J, Wincker P, Denoeud F, Chèvre AM, and Aury JM
Subjects: Genome, High-Throughput Nucleotide Sequencing, Phenotype, Brassica napus genetics, Nanopores
Abstract: Background: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus., Findings: Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes., Conclusion: Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits., (© The Author(s) 2020. Published by Oxford University Press GigaScience.)
Published: 2020
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44. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa .

Author: Boutte J, Maillet L, Chaussepied T, Letort S, Aury JM, Belser C, Boideau F, Brunet A, Coriton O, Deniot G, Falentin C, Huteau V, Lodé-Taburel M, Morice J, Trotoux G, Chèvre AM, Rousseau-Gueutin M, and Ferreira de Carvalho J
Abstract: Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa 'Z1' genome vs. the B. rapa 'Chiifu' genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa 'Z1' and B. rapa 'Chiifu' at the origin of important length differences in some chromosomes. For instance, lengths of 'Z1' and 'Chiifu' A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu.' Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in 'Z1' genome compared to 'Chiifu' on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability., (Copyright © 2020 Boutte, Maillet, Chaussepied, Letort, Aury, Belser, Boideau, Brunet, Coriton, Deniot, Falentin, Huteau, Lodé-Taburel, Morice, Trotoux, Chèvre, Rousseau-Gueutin and Ferreira de Carvalho.)
Published: 2020
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45. BiSCoT: improving large eukaryotic genome assemblies with optical maps.

Author: Istace B, Belser C, and Aury JM
Abstract: Motivation: Long read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal., Results: We developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly., Availability: BiSCoT and improved assemblies are freely available on GitHub at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/., Competing Interests: The authors declare there are no competing interests., (©2020 Istace et al.)
Published: 2020
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46. Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers.

Author: Leroy T, Rougemont Q, Dupouey JL, Bodénès C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, and Plomion C
Subjects: Bayes Theorem, Genetic Speciation, Hybridization, Genetic, Gene Flow, Quercus genetics
Abstract: Oaks are dominant forest tree species widely distributed across the Northern Hemisphere, where they constitute natural resources of economic, ecological, social and historical value. Hybridisation and adaptive introgression have long been thought to be major drivers of their ecological success. Therefore, the maintenance of species barriers remains a key question, given the extent of interspecific gene flow. In this study, we made use of the tremendous genetic variation among four European white oak species (31 million single nucleotide polymorphisms (SNPs)) to infer the evolutionary history of these species, study patterns of genetic differentiation and identify reproductive barriers. We first analysed the ecological and historical relationships among these species and inferred a long-term strict isolation followed by a recent and extensive postglacial contact using approximate Bayesian computation. Assuming this demographic scenario, we then performed backward simulations to generate the expected distributions of differentiation under neutrality to scan their genomes for reproductive barriers. We finally identified important intrinsic and ecological functions driving the reproductive isolation. We discussed the importance of identifying the genetic basis for the ecological preferences between these oak species and its implications for the renewal of European forests under global warming., (© 2019 The Authors New Phytologist © 2019 New Phytologist Trust.)
Published: 2020
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47. A reference genome for pea provides insight into legume genome evolution.

Author: Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Bérard A, Vrbová I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelová H, Milec Z, Vrána J, Lee H, Kougbeadjo A, Térézol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Doležel J, Wincker P, and Burstin J
Subjects: Chromosome Mapping, Fabaceae classification, Gene Expression Regulation, Plant, Genetic Variation, Genomics, Phenotype, Phylogeny, Reference Standards, Repetitive Sequences, Nucleic Acid, Seed Storage Proteins genetics, Whole Genome Sequencing, Chromosomes, Plant genetics, Evolution, Molecular, Fabaceae genetics, Genome, Plant, Pisum sativum genetics, Plant Proteins genetics, Quantitative Trait Loci
Abstract: We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
Published: 2019
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48. Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster.

Author: Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E, and Ferrandon D
Abstract: We present the draft genome sequence of Tubulinosema ratisbonensis , a microsporidium species infecting Drosophila melanogaster A total of 3,013 protein-encoding genes and an array of transposable elements were identified. This work represents a necessary step to develop a novel model of host-parasite relationships using the highly tractable genetic model D. melanogaster ., (Copyright © 2019 Polonais et al.)
Published: 2019
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49. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.

Author: Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P, and Aury JM
Subjects: High-Throughput Nucleotide Sequencing methods, Optics and Photonics methods, Repetitive Sequences, Nucleic Acid genetics, Brassica genetics, Brassica rapa genetics, Chromosome Mapping methods, Chromosomes, Plant genetics, Genome, Plant genetics, Nanopores
Abstract: Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions 1-4 . However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.
Published: 2018
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50. Oak genome reveals facets of long lifespan.

Author: Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, and Salse J
Subjects: Biological Evolution, DNA, Plant genetics, Genetic Variation genetics, Longevity genetics, Mutation, Phylogeny, Sequence Analysis, DNA, Genome, Plant genetics, Quercus genetics
Abstract: Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes 1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times 2 . With 450 species spread throughout Asia, Europe and America 3 , oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical 4 and modelling 5 approaches have shown that intra-organismal genetic heterogeneity can be selected for 6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes 7 . However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
Published: 2018
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