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

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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2. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M., Formenti, Giulio, Mouton, Alice, De Panis, Diego, Marins, Luísa S., Leitão, Henrique G., Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, De Pooter, Tim, Joris, Geert, Strazisar, Mojca, Wood, Jonathan M. D., Herron, Katie E., Seehausen, Ole, Watts, Phillip C., Shaw, Felix, Davey, Robert P., Minotto, Alice, Fernández, José M., Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C., Amorim, Isabel R., Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, BedHom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo A. V., Dias, Guilherme Borges, Bosse, Mirte, Brown, Tom, Bruggmann, Rémy, Buena-Atienza, Elena, Burgin, Josephine, Buzan, Elena, Cariani, Alessia, Casadei, Nicolas, Chiara, Matteo, Chozas, Sergio, Čiampor, Jr., Fedor, Crottini, Angelica, Cruaud, Corinne, Cruz, Fernando, Dalen, Love, De Biase, Alessio, del Campo, Javier, Delic, Teo, Dennis, Alice B., Derks, Martijn F. L., Diroma, Maria Angela, Djan, Mihajla, Duprat, Simone, Eleftheriadi, Klara, Feulner, Philine G. D., Flot, Jean-François, Forni, Giobbe, Fosso, Bruno, Fournier, Pascal, Fournier-Chambrillon, Christine, Gabaldon, Toni, Garg, Shilpa, Gissi, Carmela, Giupponi, Luca, Gomez-Garrido, Jessica, González, Josefa, Grilo, Miguel L., Grüning, Björn, Guerin, Thomas, Guiglielmoni, Nadege, Gut, Marta, Haesler, Marcel P., Hahn, Christoph, Halpern, Balint, Harrison, Peter W., Heintz, Julia, Hindrikson, Maris, Höglund, Jacob, Howe, Kerstin, Hughes, Graham M., Istace, Benjamin, Cock, Mark J., Janžekovič, Franc, Jonsson, Zophonias O., Joye-Dind, Sagane, Koskimäki, Janne J., Krystufek, Boris, Kubacka, Justyna, Kuhl, Heiner, Kusza, Szilvia, Labadie, Karine, Lähteenaro, Meri, Lantz, Henrik, Lavrinienko, Anton, Leclère, Lucas, Lopes, Ricardo Jorge, Madsen, Ole, Magdelenat, Ghislaine, Magoga, Giulia, Manousaki, Tereza, Mappes, Tapio, Marques, Joao Pedro, Redondo, Gemma I. Martinez, Maumus, Florian, McCarthy, Shane A., Megens, Hendrik-Jan, Melo-Ferreira, Jose, Mendes, Sofia L., Montagna, Matteo, Moreno, Joao, Mosbech, Mai-Britt, Moura, Mónica, Musilova, Zuzana, Myers, Eugene, Nash, Will J., Nater, Alexander, Nicholson, Pamela, Niell, Manuel, Nijland, Reindert, Noel, Benjamin, Noren, Karin, Oliveira, Pedro H., Olsen, Remi-Andre, Ometto, Lino, Oomen, Rebekah A., Ossowski, Stephan, Palinauskas, Vaidas, Palsson, Snaebjorn, Panibe, Jerome P., Pauperio, Joana, Pavlek, Martina, Payen, Emilie, Pawlowska, Julia, Pellicer, Jaume, Pesole, Graziano, Pimenta, Joao, Pippel, Martin, Pirttilä, Anna Maria, Poulakakis, Nikos, Rajan, Jeena, M.C. Rego, Rúben, Resendes, Roberto, Resl, Philipp, Riesgo, Ana, Rodin-Morch, Patrik, Soares, Andre E. R., Fernandes, Carlos Rodriguez, Romeiras, Maria M., Roxo, Guilherme, Rüber, Lukas, Ruiz-Lopez, Maria Jose, Saarma, Urmas, da Silva, Luis P., Sim-Sim, Manuela, Soler, Lucile, Sousa, Vitor C., Santos, Carla Sousa, Spada, Alberto, Stefanovic, Milomir, Steger, Viktor, Stiller, Josefin, Stöck, Matthias, Struck, Torsten H., Sudasinghe, Hiranya, Tapanainen, Riikka, Tellgren-Roth, Christian, Trindade, Helena, Tukalenko, Yevhen, Urso, Ilenia, Vacherie, Benoit, Van Belleghem, Steven M., Van Oers, Kees, Vargas-Chavez, Carlos, Velickovic, Nevena, Vella, Noel, Vella, Adriana, Vernesi, Cristiano, Vicente, Sara, Villa, Sara, Pettersson, Olga Vinnere, Volckaert, Filip A. M., Voros, Judit, Wincker, Patrick, Winkler, Sylke, Ciofi, Claudio, Waterhouse, Robert M., and Mazzoni, Camila J.

Published
2024
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3. The NEREA Augmented Observatory: an integrative approach to marine coastal ecology

Author

Campese, Lucia, Russo, Luca, Abagnale, Maria, Alberti, Adriana, Bachi, Giancarlo, Balestra, Cecilia, Bellardini, Daniele, Buondonno, Angela, Cardini, Ulisse, Carotenuto, Ylenia, Checcucci, Giovanni, Chiusano, Maria Luisa, D’Ambra, Isabella, d’Ippolito, Giuliana, Di Capua, Iole, Donnarumma, Vincenzo, Fontana, Angelo, Furia, Marta, Galarza-Verkovitch, Denisse, Gallia, Roberto, Labadie, Karine, Leone, Serena, Licandro, Priscilla, Longo, Antonio, Maselli, Maira, Merquiol, Louise, Murano, Carola, Oliveira, Pedro H., Passarelli, Augusto, Percopo, Isabella, Perdereau, Aude, Piredda, Roberta, Raffini, Francesca, Roncalli, Vittoria, Ruscheweyh, Hans-Joachim, Russo, Ennio, Saggiomo, Maria, Santinelli, Chiara, Sarno, Diana, Sunagawa, Shinichi, Tramontano, Ferdinando, Trano, Anna Chiara, Uttieri, Marco, Wincker, Patrick, Zampicinini, Gianpaolo, Casotti, Raffaella, Conversano, Fabio, D’Alelio, Domenico, Iudicone, Daniele, Margiotta, Francesca, and Montresor, Marina

Published
2024
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4. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Belser, Caroline, Poulain, Julie, Labadie, Karine, Gavory, Frederick, Alberti, Adriana, Guy, Julie, Carradec, Quentin, Cruaud, Corinne, da Silva, Corinne, Engelen, Stefan, Mielle, Paul, Perdereau, Aude, Samson, Gaelle, Gaz, Shahinaz, Team, Genoscope Technical, Voolstra, Christian R, Galand, Pierre E, Flores, J. Michel, Hume, Benjamin Cc, Perna, Gabriela, Ziegler, Maren, Ruscheweyh, Hans-Joachim, Boissin, Emilie, Romac, Sarah, Bourdin, Guillaume, Iwankow, Guillaume, Moulin, Clémentine, García, David A Paz, Coordinators, Tara Pacific Consortium, Scarpelli, Claude, Jacoby, E Krame, Oliveira, Pedro H, Aury, Jean-Marc, Allemand, Denis, Planes, Serge, and Wincker, Patrick

Subjects
Quantitative Biology - Quantitative Methods
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 host coral 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.

Published
2022

5. High altitude horse use and early horse transport in eastern Eurasia: New evidence from melting ice

Author

Taylor, William Timothy Treal, primary, Hart, Isaac A, additional, Tuvshinjargal, Tumurbaatar, additional, Bayarsaikhan, Jamsranjav, additional, Jarman, Nicholas L, additional, Bittner, Peter, additional, López Calle, Paula, additional, Blakeslee, Logan A, additional, Zahir, Muhammad, additional, Chauvey, Lorelei, additional, Tressières, Gaëtan, additional, Tonasso-Calvière, Laure, additional, Schiavinato, Stéphanie, additional, Cruaud, Corinne, additional, Aury, Jean-Marc, additional, Oliveira, Pedro H, additional, Wincker, Patrick, additional, and Orlando, Ludovic, additional

Published
2024
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7. Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.

Author

Pan, Jianfei, Liu, Xuexue, Baca, Mateusz, Calvière‐Tonasso, Laure, Schiavinato, Stéphanie, Chauvey, Loreleï, Tressières, Gaétan, Perdereau, Aude, Aury, Jean‐Marc, Oliveira, Pedro H., Wincker, Patrick, Abdykanova, Aida, Arsuaga, Juan Luis, Bayarsaikhan, Jamsranjav, Belinskiy, Andrey B., Carbonell, Eudald, Davoudi, Hossein, Lira Garrido, Jaime, Gilbert, Allan S., and Hermes, Taylor

Subjects
BACTERIAL toxins, FOSSIL DNA, EQUUS, EQUIDAE, HORSES, DONKEYS
Abstract

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome‐wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4‐kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown. [ABSTRACT FROM AUTHOR]

Published
2024
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9. The defensome of complex bacterial communities

Author

Beavogui, Angelina, primary, Lacroix, Auriane, additional, Wiart, Nicolas, additional, Poulain, Julie, additional, Delmont, Tom O., additional, Paoli, Lucas, additional, Wincker, Patrick, additional, and Oliveira, Pedro H., additional

Published
2024
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12. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

Author

Oliveira, Pedro H., Ribis, John W., Garrett, Elizabeth M., Trzilova, Dominika, Kim, Alex, Sekulovic, Ognjen, Mead, Edward A., Pak, Theodore, Zhu, Shijia, Deikus, Gintaras, Touchon, Marie, Lewis-Sandari, Martha, Beckford, Colleen, Zeitouni, Nathalie E., Altman, Deena R., Webster, Elizabeth, Oussenko, Irina, Bunyavanich, Supinda, Aggarwal, Aneel K., Bashir, Ali, Patel, Gopi, Wallach, Frances, Hamula, Camille, Huprikar, Shirish, Schadt, Eric E., Sebra, Robert, van Bakel, Harm, Kasarskis, Andrew, Tamayo, Rita, Shen, Aimee, and Fang, Gang

Published
2020
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13. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M, primary, Formenti, Giulio, additional, Mouton, Alice, additional, Ciofi, Claudio, additional, Waterhouse, Robert M, additional, Mazzoni, Camila J, additional, De Panis, Diego, additional, Schlude Marins, Luisa S, additional, Leitao, Henrique G, additional, Diedericks, Genevieve, additional, Kirangwa, Joseph, additional, Morselli, Marco, additional, Salces, Judit, additional, Escudero, Nuria, additional, Iannucci, Alessio, additional, Natali, Chiara, additional, Svardal, Hannes, additional, Fernandez, Rosa, additional, De Pooter, Tim, additional, Joris, Geert, additional, Strazisar, Mojca, additional, Wood, Jo, additional, Herron, Katie E, additional, Seehausen, Ole, additional, Watts, Phillip C, additional, Shaw, Felix, additional, Davey, Robert P, additional, Minotto, Alice, additional, Fernandez Gonzalez, Jose Maria, additional, Bohne, Astrid, additional, Alegria, Carla, additional, Alioto, Tyler, additional, Alves, Paulo C, additional, Amorim, Isabel R, additional, Aury, Jean-Marc, additional, Backstrom, Niclas, additional, Baldrian, Petr, additional, Ballarin, Loriano, additional, Baltrunaite, Laima, additional, Barta, Endre, additional, BedHom, Bertrand, additional, Belser, Caroline, additional, Bergsten, Johannes, additional, Bertrand, Laurie, additional, Bilandija, Helena, additional, Binzer-Panchal, Mahesh, additional, Bista, Iliana, additional, Blaxter, Mark, additional, Borges, Paulo AV, additional, Borges Dias, Guilherme, additional, Bosse, Mirte, additional, Brown, Tom, additional, Bruggmann, Remy, additional, Buena-Atienza, Elena, additional, Burgin, Josephine, additional, Buzan, Elena, additional, Casadei, Nicolas, additional, Chiara, Matteo, additional, Chozas, Sergio, additional, Ciampor, Fedor F, additional, Crottini, Angelica, additional, Cruaud, Corinne, additional, Cruz, Fernando, additional, Dalen, Love, additional, De Biase, Alessio, additional, del Campo, Javier, additional, Delic, Teo, additional, Dennis, Alice B, additional, Derks, Martijn FL, additional, Diroma, Maria Angela, additional, Djan, Mihajla, additional, Duprat, Simone, additional, Eleftheriadi, Klara, additional, Feulner, Philine GD, additional, Flot, Jean-Francois, additional, Forni, Giobbe, additional, Fosso, Bruno, additional, Fournier, Pascal, additional, Fournier-Chambrillon, Christine, additional, Gabaldon, Toni, additional, Garg, Shilpa, additional, Gissi, Carmela, additional, Giupponi, Luca, additional, Gomez-Garrido, Jessica, additional, Gonzalez, Josefa, additional, Grilo, Miguel L, additional, Gruening, Bjoern, additional, Guerin, Thomas, additional, Guiglielmoni, Nadege, additional, Gut, Marta, additional, Haesler, Marcel P, additional, Hahn, Christoph, additional, Halpern, Balint, additional, Harrison, Peter, additional, Heintz, Julia, additional, Hindrikson, Maris, additional, Hoglund, Jacob, additional, Howe, Kerstin, additional, Hughes, Graham, additional, Istace, Benjamin, additional, Cock, Mark J., additional, Jancekovic, Franc, additional, Jonsson, Zophonias O, additional, Joye-Dind, Sagane, additional, Koskimaki, Janne J., additional, Krystufek, Boris, additional, Kubacka, Justyna, additional, Kuhl, Heiner, additional, Kusza, Szilvia, additional, Labadie, Karine, additional, Lahteenaro, Meri, additional, Lantz, Henrik, additional, Lavrinienko, Anton, additional, Leclere, Lucas, additional, Lopes, Ricardo Jorge, additional, Madsen, Ole, additional, Magdelenat, Ghislaine, additional, Magoga, Giulia, additional, Manousaki, Tereza, additional, Mappes, Tapio, additional, Marques, Joao Pedro, additional, Martinez Redondo, Gemma I, additional, Maumus, Florian, additional, Megens, Hendrik-Jan, additional, Melo-Ferreira, Jose, additional, Mendes, Sofia L, additional, Montagna, Matteo, additional, Moreno, Joao, additional, Mosbech, Mai-Britt, additional, Moura, Monica, additional, Musilova, Zuzana, additional, Myers, Eugene, additional, Nash, Will J., additional, Nater, Alexander, additional, Nicholson, Pamela, additional, Niell, Manuel, additional, Nijland, Reindert, additional, Noel, Benjamin, additional, Noren, Karin, additional, Oliveira, Pedro H, additional, Olsen, Remi-Andre, additional, Ometto, Lino, additional, Ossowski, Stephan, additional, Palinauskas, Vaidas, additional, Palsson, Snaebjorn, additional, Panibe, Jerome P, additional, Pauperio, Joana, additional, Pavlek, Martina, additional, Payen, Emilie, additional, Pawlowska, Julia, additional, Pellicer, Jaume, additional, Pesole, Graziano, additional, Pimenta, Joao, additional, Pippel, Martin, additional, Pirttila, Anna Maria, additional, Poulakakis, Nikos, additional, Rajan, Jeena, additional, Rego, Ruben MC, additional, Resendes, Roberto, additional, Resl, Philipp, additional, Riesgo, Ana, additional, Rodin-Morch, Patrik, additional, Soares, Andre ER, additional, Rodriguez Fernandes, Carlos, additional, Romeiras, Maria M., additional, Roxo, Guilherme, additional, Ruber, Lukas, additional, Ruiz-Lopez, Maria Jose, additional, Saarma, Urmas, additional, Silva, Luis P, additional, Sim-Sim, Manuela, additional, Soler, Lucile, additional, Sousa, Vitor C, additional, Sousa Santos, Carla, additional, Spada, Alberto, additional, Stefanovic, Milomir, additional, Steger, Viktor, additional, Stiller, Josefin, additional, Stock, Matthias, additional, Struck, Torsten Hugo H, additional, Sudasinghe, Hiranya, additional, Tapanainen, Riikka, additional, Tellgren-Roth, Christian, additional, Trindade, Helena, additional, Tukalenko, Yevhen, additional, Urso, Ilenia, additional, Vacherie, Benoit, additional, Van Belleghem, Steven M, additional, van Oers, Kees, additional, Vargas-Chavez, Carlos, additional, Velickovic, Nevena, additional, Vella, Noel, additional, Vella, Adriana, additional, Vernesi, Cristiano, additional, Vicente, Sara, additional, Villa, Sara, additional, Vinnere Pettersson, Olga, additional, Volckaert, Filip AM, additional, Voros, Judit, additional, Wincker, Patrick, additional, and Winkler, Sylke, additional

Published
2023
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14. The defensome of complex bacterial communities

Author

Beavogui, Angelina, primary, Lacroix, Auriane, additional, Wiart, Nicolas, additional, Poulain, Julie, additional, Delmont, Tom O., additional, Paoli, Lucas, additional, Wincker, Patrick, additional, and Oliveira, Pedro H., additional

Published
2023
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16. Diversity of the Pacific Ocean coral reef microbiome

Author

Galand, Pierre E., primary, Ruscheweyh, Hans-Joachim, additional, Salazar, Guillem, additional, Hochart, Corentin, additional, Henry, Nicolas, additional, Hume, Benjamin C. C., additional, Oliveira, Pedro H., additional, Perdereau, Aude, additional, Labadie, Karine, additional, Belser, Caroline, additional, Boissin, Emilie, additional, Romac, Sarah, additional, Poulain, Julie, additional, Bourdin, Guillaume, additional, Iwankow, Guillaume, additional, Moulin, Clémentine, additional, Armstrong, Eric J., additional, Paz-García, David A., additional, Ziegler, Maren, additional, Agostini, Sylvain, additional, Banaigs, Bernard, additional, Boss, Emmanuel, additional, Bowler, Chris, additional, de Vargas, Colomban, additional, Douville, Eric, additional, Flores, Michel, additional, Forcioli, Didier, additional, Furla, Paola, additional, Gilson, Eric, additional, Lombard, Fabien, additional, Pesant, Stéphane, additional, Reynaud, Stéphanie, additional, Thomas, Olivier P., additional, Troublé, Romain, additional, Zoccola, Didier, additional, Voolstra, Christian R., additional, Thurber, Rebecca Vega, additional, Sunagawa, Shinichi, additional, Wincker, Patrick, additional, Allemand, Denis, additional, and Planes, Serge, additional

Published
2023
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18. Diversity of the Pacific Ocean coral reef microbiome

Author

Galand, Pierre E., Ruscheweyh, Hans-Joachim, Salazar, Guillem, Hochart, Corentin, Henry, Nicolas, Hume, Benjamin C. C., Oliveira, Pedro H., Perdereau, Aude, Labadie, Karine, and Voolstra, Christian R.

Subjects
ddc:570
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. published

Published
2023

23. Complete Genome Sequence of Tepidibacter sp. Strain 8C15b, Isolated from Bank Sediments of Haiphong Bay, Vietnam

Author

Fouteau, Stéphanie, primary, Bui Van, Vuong, additional, Rouy, Zoé, additional, Beraud, Mélanie, additional, Cruaud, Corinne, additional, Cayol, Jean-Luc, additional, Chifflet, Sandrine, additional, Chu Van, Thuoc, additional, Pham The, Thu, additional, Vallenet, David, additional, Oliveira, Pedro H., additional, Mari, Xavier, additional, and Pradel, Nathalie, additional

Published
2022
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25. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, Genoscope Technical Team, Voolstra, Christian R., Galand, Pierre E., Michel Flores, J., Benjamin Cc Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Paz García, David A., Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Éric Douville, Didier Forcioli, Paola Furla, Éric Gilson, Fabien Lombard, Stephane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, Krame Jacoby, E., Oliveira, Pedro H., Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker, Génomique métabolique (UMR 8030), 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)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universität Konstanz, 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), Weizmann Institute of Science [Rehovot, Israël], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Tara Expéditions, Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), 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), 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), 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), Université Côte d'Azur (UCA), 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), European Molecular Biology Laboratory (EMBL), Centre Scientifique de Monaco (CSM), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), Menguy, Caroline, Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), and 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)

Subjects
FOS: Biological sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
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 host coral 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.

Published
2022
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37. Modeling and Maximum Power Tracking of a Solar-Wind Microgeneration System.

Author

de Oliveira, Pedro H. T. de M. and Cerqueira Revoredo, Téo

Subjects
*ARTIFICIAL satellite tracking, *SOLAR wind, *TRACKING algorithms, *WIND turbines, *METEOROLOGICAL stations, *HYBRID systems, *RENEWABLE energy sources
Abstract

The global energy scenario is changing, and clean generation is leading the way. As new ways of producing energy becomes more popular, microgeneration takes a greater share of the market, supplying both isolated and grid connected systems. In such context, hybrid systems that combine two or more different types of sources are a promising approach, although their valuable application depends on many intrinsic and ambient factors and should be thoroughly evaluated. To assess system performance in advance, not only to better predict its operation but also to well design it for specific applications without the need to install it on site, accurate computational models that reflect its real behavior should be developed. Aiming to contribute on this matter, this work presents a dynamic model for a solar-wind microgeneration system, which allows the evaluation of the system's behavior under different demand scenarios, as well as to implement different energy management strategies. In addition to the base model comprised a photovoltaic panel, a wind turbine, an inverter, and an energy storage element, this work presents the implementation and performance comparison of two different maximum power point tracking algorithms based on soft computing techniques and on real data collected at a meteorological station. Results validate the hybrid microgeneration model and provides insight on the specification of maximum power point tracking algorithms for specific applications. [ABSTRACT FROM AUTHOR]

Published
2022
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39. Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition

Author

Lewis Leslie A, Astatke Mekbib, Umekubo Peter T, Alvi Shaheen, Saby Robert, Afrose Jehan, Oliveira Pedro H, Monteiro Gabriel A, and Prazeres Duarte MF

Subjects
Curvature propensity plot data, extensive sequence-specific binding, figure-of-eight transposition intermediate, hydroxyl radical footprinting, minicircle junction, selective binding, synaptic complex, transpososome, Genetics, QH426-470
Abstract

Abstract Background Transposition in IS3, IS30, IS21 and IS256 insertion sequence (IS) families utilizes an unconventional two-step pathway. A figure-of-eight intermediate in Step I, from asymmetric single-strand cleavage and joining reactions, is converted into a double-stranded minicircle whose junction (the abutted left and right ends) is the substrate for symmetrical transesterification attacks on target DNA in Step II, suggesting intrinsically different synaptic complexes (SC) for each step. Transposases of these ISs bind poorly to cognate DNA and comparative biophysical analyses of SC I and SC II have proven elusive. We have prepared a native, soluble, active, GFP-tagged fusion derivative of the IS2 transposase that creates fully formed complexes with single-end and minicircle junction (MCJ) substrates and used these successfully in hydroxyl radical footprinting experiments. Results In IS2, Step I reactions are physically and chemically asymmetric; the left imperfect, inverted repeat (IRL), the exclusive recipient end, lacks donor function. In SC I, different protection patterns of the cleavage domains (CDs) of the right imperfect inverted repeat (IRR; extensive in cis) and IRL (selective in trans) at the single active cognate IRR catalytic center (CC) are related to their donor and recipient functions. In SC II, extensive binding of the IRL CD in trans and of the abutted IRR CD in cis at this CC represents the first phase of the complex. An MCJ substrate precleaved at the 3' end of IRR revealed a temporary transition state with the IRL CD disengaged from the protein. We propose that in SC II, sequential 3' cleavages at the bound abutted CDs trigger a conformational change, allowing the IRL CD to complex to its cognate CC, producing the second phase. Corroborating data from enhanced residues and curvature propensity plots suggest that CD to CD interactions in SC I and SC II require IRL to assume a bent structure, to facilitate binding in trans. Conclusions Different transpososomes are assembled in each step of the IS2 transposition pathway. Recipient versus donor end functions of the IRL CD in SC I and SC II and the conformational change in SC II that produces the phase needed for symmetrical IRL and IRR donor attacks on target DNA highlight the differences.

Published
2012
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40. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

Author

Oliveira, Pedro H., primary, Ribis, John W., additional, Garrett, Elizabeth M., additional, Trzilova, Dominika, additional, Kim, Alex, additional, Sekulovic, Ognjen, additional, Mead, Edward A., additional, Pak, Theodore, additional, Zhu, Shijia, additional, Deikus, Gintaras, additional, Touchon, Marie, additional, Lewis-Sandari, Martha, additional, Beckford, Colleen, additional, Zeitouni, Nathalie E., additional, Altman, Deena R., additional, Webster, Elizabeth, additional, Oussenko, Irina, additional, Bunyavanich, Supinda, additional, Aggarwal, Aneel K., additional, Bashir, Ali, additional, Patel, Gopi, additional, Wallach, Frances, additional, Hamula, Camille, additional, Huprikar, Shirish, additional, Schadt, Eric E., additional, Sebra, Robert, additional, van Bakel, Harm, additional, Kasarskis, Andrew, additional, Tamayo, Rita, additional, Shen, Aimee, additional, and Fang, Gang, additional

Published
2019
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43. Epigenomic and functional characterization of a core DNA methyltransferase in the human pathogenClostridium difficile

Author

Oliveira, Pedro H., primary, Ribis, John W., additional, Garrett, Elizabeth M., additional, Trzilova, Dominika, additional, Kim, Alex, additional, Sekulovic, Ognjen, additional, Mead, Edward A., additional, Pak, Theodore, additional, Zhu, Shijia, additional, Deikus, Gintaras, additional, Touchon, Marie, additional, Beckford, Colleen, additional, Zeitouni, Nathalie E., additional, Altman, Deena, additional, Webster, Elizabeth, additional, Oussenko, Irina, additional, Bunyavanich, Supinda, additional, Aggarwal, Aneel K., additional, Bashir, Ali, additional, Patel, Gopi, additional, Hamula, Camille, additional, Huprikar, Shirish, additional, Schadt, Eric E., additional, Sebra, Robert, additional, van Bakel, Harm, additional, Kasarskis, Andrew, additional, Tamayo, Rita, additional, Shen, Aimee, additional, and Fang, Gang, additional

Published
2018
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44. Host range and genetic plasticity explain the coexistence of integrative and extrachromosomal mobile genetic element

Author

Agence Nationale de la Recherche (France), European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Cury, Jean, Oliveira, Pedro H., Cruz, Fernando de la, Rocha, Eduardo P. C., Agence Nationale de la Recherche (France), European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Cury, Jean, Oliveira, Pedro H., Cruz, Fernando de la, and Rocha, Eduardo P. C.

Abstract

Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element’s host range.

Published
2018

47. Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

Author

MIT-Portugal Program, Massachusetts Institute of Technology. Department of Chemical Engineering, Monteiro, Gabriel A., Jones, Kristala L., Prazeres, Duarte Miguel, Gonçalves, Geisa A. L., Oliveira, Pedro H., Gomes, Ana G., Lewis, Leslie A., MIT-Portugal Program, Massachusetts Institute of Technology. Department of Chemical Engineering, Monteiro, Gabriel A., Jones, Kristala L., Prazeres, Duarte Miguel, Gonçalves, Geisa A. L., Oliveira, Pedro H., Gomes, Ana G., and Lewis, Leslie A.

Abstract

Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability., Fundação para a Ciência e a Tecnologia (PTDC/EBB-EBI/113650/2009), MIT-Portugal Program

Published
2016

50. Acquisition and Processing of Ventricular Structures from the M-Mode Echocardiogram

Author

Oliveira, João Pedro Estima de and Oliveira, Pedro H. H. Guedes de

Subjects
cardiovascular system, cardiovascular diseases
Abstract

This work describes a system for M-mode echocardiogram processing. In order to characterize the left ventricle functions and dimensions, the system detects in real time the ventricular structures and processes them off-line for parameter extraction. (...), Neste trabalho apresenta-se um sistema para tratamento do sinal ecocardiográfico, sobre o qual se faz a determinação, em tempo real, das estruturas do ventrículoesquerdo, cujos contornos em modo-M são processados a posteriori com o fim de extrair parâmetros caracterizadores das funções e dimensões ventriculares. O sistema total é constituído por uma parte electrónica, dedicada à detecção e digitalização das estruturas ecocardiográficas, a qual é controlada por ummicrocomputador que, por sua vez, suporta a secção de processamento do ecocardiograma modo-M.(...)

Published
1999

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