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2. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Author

Doré, Hugo, Guyet, Ulysse, Leconte, Jade, Farrant, Gregory K., Alric, Benjamin, Ratin, Morgane, Ostrowski, Martin, Ferrieux, Mathilde, Brillet-Guéguen, Loraine, Hoebeke, Mark, Siltanen, Jukka, Le Corguillé, Gildas, Corre, Erwan, Wincker, Patrick, Scanlan, David J., Eveillard, Damien, Partensky, Frédéric, and Garczarek, Laurence

Published
2023
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3. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Author

Denoeud, France, primary, Godfroy, Olivier, additional, Cruaud, Corinne, additional, Heesch, Svenja, additional, Nehr, Zofia, additional, Tadrent, Nachida, additional, Couloux, Arnaud, additional, Brillet-Guéguen, Loraine, additional, Delage, Ludovic, additional, Mckeown, Dean, additional, Motomura, Taizo, additional, Sussfeld, Duncan, additional, Fan, Xiao, additional, Mazéas, Lisa, additional, Terrapon, Nicolas, additional, Barrera-Redondo, Josué, additional, Petroll, Romy, additional, Reynes, Lauric, additional, Choi, Seok-Wan, additional, Jo, Jihoon, additional, Uthanumallian, Kavitha, additional, Bogaert, Kenny, additional, Duc, Céline, additional, Ratchinski, Pélagie, additional, Lipinska, Agnieszka, additional, Noel, Benjamin, additional, Murphy, Eleanor A., additional, Lohr, Martin, additional, Khatei, Ananya, additional, Hamon-Giraud, Pauline, additional, Vieira, Christophe, additional, Akerfors, Svea Sanja, additional, Akita, Shingo, additional, Avia, Komlan, additional, Badis, Yacine, additional, Barbeyron, Tristan, additional, Belcour, Arnaud, additional, Berrabah, Wahiba, additional, Blanquart, Samuel, additional, Bouguerba-Collin, Ahlem, additional, Bringloe, Trevor, additional, Cattolico, Rose Ann, additional, Cormier, Alexandre, additional, Cruz de Carvalho, Helena, additional, Dallet, Romain, additional, De Clerck, Olivier, additional, Debit, Ahmed, additional, Denis, Erwan, additional, Destombe, Christophe, additional, Dinatale, Erica, additional, Dittami, Simon, additional, Drula, Elodie, additional, Faugeron, Sylvain, additional, Got, Jeanne, additional, Graf, Louis, additional, Groisillier, Agnès, additional, Guillemin, Marie-Laure, additional, Harms, Lars, additional, Hatchett, William John, additional, Henrissat, Bernard, additional, Hoarau, Galice, additional, Jollivet, Chloé, additional, Jueterbock, Alexander, additional, Kayal, Ehsan, additional, Kogame, Kazuhiro, additional, Bars, Arthur Le, additional, Leblanc, Catherine, additional, Ley, Ronja, additional, Liu, Xi, additional, Lopez, Pascal Jean, additional, Lopez, Philippe, additional, Manirakiza, Eric, additional, Massau, Karine, additional, Mauger, Stéphane, additional, Mest, Laetitia, additional, Michel, Gurvan, additional, Monteiro, Catia, additional, Nagasato, Chikako, additional, Nègre, Delphine, additional, Pelletier, Eric, additional, Phillips, Naomi, additional, Potin, Philippe, additional, Rensing, Stefan A., additional, Rousselot, Ellyn, additional, Rousvoal, Sylvie, additional, Schroeder, Declan, additional, Scornet, Delphine, additional, Siegel, Anne, additional, Tirichine, Leila, additional, Tonon, Thierry, additional, Valentin, Klaus, additional, Verbruggen, Heroen, additional, Weinberger, Florian, additional, Wheeler, Glen, additional, Kawai, Hiroshi, additional, Peters, Akira F., additional, Yoon, Hwan Su, additional, Hervé, Cécile, additional, Ye, Naihao, additional, Bapteste, Eric, additional, Valero, Myriam, additional, Markov, Gabriel V., additional, Corre, Erwan, additional, Coelho, Susana M., additional, Wincker, Patrick, additional, Aury, Jean-Marc, additional, and Cock, J. Mark, additional

Published
2024
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4. Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Author

Denoeud, France, Godfroy, Olivier, Cruaud, Corinne, Heesch, Svenja, Nehr, Zofia, Tadrent, Nachida, Couloux, Arnaud, Brillet-guéguen, Loraine, Delage, Ludovic, Mckeown, Dean, Motomura, Taizo, Sussfeld, Duncan, Fan, Xiao, Mazéas, Lisa, Terrapon, Nicolas, Barrera-redondo, Josué, Petroll, Romy, Reynes, Lauric, Choi, Seok-wan, Jo, Jihoon, Uthanumallian, Kavitha, Bogaert, Kenny, Duc, Céline, Ratchinski, Pélagie, Lipinska, Agnieszka, Noel, Benjamin, Murphy, Eleanor A., Lohr, Martin, Khatei, Ananya, Hamon-giraud, Pauline, Vieira, Christophe, Akerfors, Svea Sanja, Akita, Shingo, Avia, Komlan, Badis, Yacine, Barbeyron, Tristan, Belcour, Arnaud, Berrabah, Wahiba, Blanquart, Samuel, Bouguerba-collin, Ahlem, Bringloe, Trevor, Cattolico, Rose Ann, Cormier, Alexandre, Cruz De Carvalho, Helena, Dallet, Romain, De Clerck, Olivier, Debit, Ahmed, Denis, Erwan, Destombe, Christophe, Dinatale, Erica, Dittami, Simon, Drula, Elodie, Faugeron, Sylvain, Got, Jeanne, Graf, Louis, Groisillier, Agnès, Guillemin, Marie-laure, Harms, Lars, Hatchett, William John, Henrissat, Bernard, Hoarau, Galice, Jollivet, Chloé, Jueterbock, Alexander, Kayal, Ehsan, Kogame, Kazuhiro, Le Bars, Arthur, Leblanc, Catherine, Ley, Ronja, Liu, Xi, Lopez, Pascal Jean, Lopez, Philippe, Manirakiza, Eric, Massau, Karine, Mauger, Stéphane, Mest, Laetitia, Michel, Gurvan, Monteiro, Catia, Nagasato, Chikako, Nègre, Delphine, Pelletier, Eric, Phillips, Naomi, Potin, Philippe, Rensing, Stefan A., Rousselot, Ellyn, Rousvoal, Sylvie, Schroeder, Declan, Scornet, Delphine, Siegel, Anne, Tirichine, Leila, Tonon, Thierry, Valentin, Klaus, Verbruggen, Heroen, Weinberger, Florian, Wheeler, Glen, Kawai, Hiroshi, Peters, Akira F., Yoon, Hwan Su, Hervé, Cecile, Ye, Naihao, Bapteste, Eric, Valero, Myriam, Markov, Gabriel V., Corre, Erwan, Coelho, Susana M., Wincker, Patrick, Aury, Jean-marc, Cock, J. Mark, Denoeud, France, Godfroy, Olivier, Cruaud, Corinne, Heesch, Svenja, Nehr, Zofia, Tadrent, Nachida, Couloux, Arnaud, Brillet-guéguen, Loraine, Delage, Ludovic, Mckeown, Dean, Motomura, Taizo, Sussfeld, Duncan, Fan, Xiao, Mazéas, Lisa, Terrapon, Nicolas, Barrera-redondo, Josué, Petroll, Romy, Reynes, Lauric, Choi, Seok-wan, Jo, Jihoon, Uthanumallian, Kavitha, Bogaert, Kenny, Duc, Céline, Ratchinski, Pélagie, Lipinska, Agnieszka, Noel, Benjamin, Murphy, Eleanor A., Lohr, Martin, Khatei, Ananya, Hamon-giraud, Pauline, Vieira, Christophe, Akerfors, Svea Sanja, Akita, Shingo, Avia, Komlan, Badis, Yacine, Barbeyron, Tristan, Belcour, Arnaud, Berrabah, Wahiba, Blanquart, Samuel, Bouguerba-collin, Ahlem, Bringloe, Trevor, Cattolico, Rose Ann, Cormier, Alexandre, Cruz De Carvalho, Helena, Dallet, Romain, De Clerck, Olivier, Debit, Ahmed, Denis, Erwan, Destombe, Christophe, Dinatale, Erica, Dittami, Simon, Drula, Elodie, Faugeron, Sylvain, Got, Jeanne, Graf, Louis, Groisillier, Agnès, Guillemin, Marie-laure, Harms, Lars, Hatchett, William John, Henrissat, Bernard, Hoarau, Galice, Jollivet, Chloé, Jueterbock, Alexander, Kayal, Ehsan, Kogame, Kazuhiro, Le Bars, Arthur, Leblanc, Catherine, Ley, Ronja, Liu, Xi, Lopez, Pascal Jean, Lopez, Philippe, Manirakiza, Eric, Massau, Karine, Mauger, Stéphane, Mest, Laetitia, Michel, Gurvan, Monteiro, Catia, Nagasato, Chikako, Nègre, Delphine, Pelletier, Eric, Phillips, Naomi, Potin, Philippe, Rensing, Stefan A., Rousselot, Ellyn, Rousvoal, Sylvie, Schroeder, Declan, Scornet, Delphine, Siegel, Anne, Tirichine, Leila, Tonon, Thierry, Valentin, Klaus, Verbruggen, Heroen, Weinberger, Florian, Wheeler, Glen, Kawai, Hiroshi, Peters, Akira F., Yoon, Hwan Su, Hervé, Cecile, Ye, Naihao, Bapteste, Eric, Valero, Myriam, Markov, Gabriel V., Corre, Erwan, Coelho, Susana M., Wincker, Patrick, Aury, Jean-marc, and Cock, J. Mark

Abstract

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. We show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage. Finally, analysis of microevolutionary patterns within the genusEctocarpusindicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales.

Published
2024
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5. The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga

Author

Dittami, Simon M., Corre, Erwan, Brillet-Guéguen, Loraine, Lipinska, Agnieszka P., Pontoizeau, Noé, Aite, Meziane, Avia, Komlan, Caron, Christophe, Cho, Chung Hyun, Collén, Jonas, Cormier, Alexandre, Delage, Ludovic, Doubleau, Sylvie, Frioux, Clémence, Gobet, Angélique, González-Navarrete, Irene, Groisillier, Agnès, Hervé, Cécile, Jollivet, Didier, KleinJan, Hetty, Leblanc, Catherine, Liu, Xi, Marie, Dominique, Markov, Gabriel V., Minoche, André E., Monsoor, Misharl, Pericard, Pierre, Perrineau, Marie-Mathilde, Peters, Akira F., Siegel, Anne, Siméon, Amandine, Trottier, Camille, Yoon, Hwan Su, Himmelbauer, Heinz, Boyen, Catherine, and Tonon, Thierry

Published
2020
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6. Origin and evolutionary trajectories of brown algal sex chromosomes

Author

Barrera-Redondo, Josué, primary, Lipinska, Agnieszka P., additional, Liu, Pengfei, additional, Dinatale, Erica, additional, Cossard, Guillaume, additional, Bogaert, Kenny, additional, Hoshino, Masakazu, additional, Avia, Komlan, additional, Leiria, Goncalo, additional, Avdievich, Elena, additional, Liesner, Daniel, additional, Luthringer, Rémy, additional, Godfroy, Olivier, additional, Heesch, Svenja, additional, Nehr, Zofia, additional, Brillet-Guéguen, Loraine, additional, Peters, Akira F., additional, Hoarau, Galice, additional, Pearson, Gareth, additional, Aury, Jean-Marc, additional, Wincker, Patrick, additional, Denoeud, France, additional, Cock, J Mark, additional, Haas, Fabian B., additional, and Coelho, Susana M, additional

Published
2024
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7. The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species

Author

Lipinska, Agnieszka P, primary, Krueger-Hadfield, Stacy A, additional, Godfroy, Olivier, additional, Dittami, Simon M, additional, Ayres-Ostrock, Lígia, additional, Bonthond, Guido, additional, Brillet-Guéguen, Loraine, additional, Coelho, Susana, additional, Corre, Erwan, additional, Cossard, Guillaume, additional, Destombe, Christophe, additional, Epperlein, Paul, additional, Faugeron, Sylvain, additional, Ficko-Blean, Elizabeth, additional, Beltrán, Jessica, additional, Lavaut, Emma, additional, Le Bars, Arthur, additional, Marchi, Fabiana, additional, Mauger, Stéphane, additional, Michel, Gurvan, additional, Potin, Philippe, additional, Scornet, Delphine, additional, Sotka, Erik E, additional, Weinberger, Florian, additional, Cabral de Oliveira, Mariana, additional, Guillemin, Marie-Laure, additional, Plastino, Estela M, additional, and Valero, Myriam, additional

Published
2023
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9. The Rhodoexplorer Platform for Red Algal Genomics and Whole Genome Assemblies for Several Gracilaria Species

Author

Lipinska, Agnieszka P., Krueger-Hadfield, Stacy A., Godfroy, Olivier, Dittami, Simon, Ayres-Ostrock, Lígia, Bonthond, Guido, Brillet-Guéguen, Loraine, Coelho, Susana, Corre, Erwan, Cossard, Guillaume, Destombe, Christophe, Epperlein, Paul, Faugeron, Sylvain, Ficko-Blean, Elizabeth, Beltrán, Jessica, Lavaut, Emma, Le Bars, Arthur, Marchi, Fabiana, Mauger, Stéphane, Michel, Gurvan, Potin, Philippe, Scornet, Delphine, Sotka, Erik E., Weinberger, Florian, de Oliveira, Mariana Cabral, Guillemin, Marie-Laure, Plastino, Estela M, Valero, Myriam, Castric, Vincent, Lipinska, Agnieszka P., Krueger-Hadfield, Stacy A., Godfroy, Olivier, Dittami, Simon, Ayres-Ostrock, Lígia, Bonthond, Guido, Brillet-Guéguen, Loraine, Coelho, Susana, Corre, Erwan, Cossard, Guillaume, Destombe, Christophe, Epperlein, Paul, Faugeron, Sylvain, Ficko-Blean, Elizabeth, Beltrán, Jessica, Lavaut, Emma, Le Bars, Arthur, Marchi, Fabiana, Mauger, Stéphane, Michel, Gurvan, Potin, Philippe, Scornet, Delphine, Sotka, Erik E., Weinberger, Florian, de Oliveira, Mariana Cabral, Guillemin, Marie-Laure, Plastino, Estela M, Valero, Myriam, and Castric, Vincent

Abstract

Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

Published
2023
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10. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Author

Doré, Hugo, primary, Guyet, Ulysse, additional, Leconte, Jade, additional, Farrant, Gregory K., additional, Alric, Benjamin, additional, Ratin, Morgane, additional, Ostrowski, Martin, additional, Ferrieux, Mathilde, additional, Brillet-Guéguen, Loraine, additional, Hoebeke, Mark, additional, Siltanen, Jukka, additional, Corguillé, Gildas Le, additional, Corre, Erwan, additional, Wincker, Patrick, additional, Scanlan, David J., additional, Eveillard, Damien, additional, Partensky, Frédéric, additional, and Garczarek, Laurence, additional

Published
2022
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11. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Author

Garczarek, Laurence, Guyet, Ulysse, Doré, Hugo, Farrant, Gregory, Hoebeke, Mark, Brillet-Guéguen, Loraine, Bisch, Antoine, Ferrieux, Mathilde, Siltanen, Jukka, Corre, Erwan, Le Corguillé, Gildas, Ratin, Morgane, Pitt, Frances, Ostrowski, Martin, Conan, Maël, Siegel, Anne, Labadie, Karine, Aury, Jean-Marc, Wincker, Patrick, Scanlan, David, Partensky, Frédéric, 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), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Warwick [Coventry], Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), 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), 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), and 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)

Subjects
Aquatic Organisms, Likelihood Functions, Geography, AcademicSubjects/SCI00010, QH, [SDV]Life Sciences [q-bio], Cyanobacteria, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR, User-Computer Interface, Bacterial Proteins, Databases, Genetic, [SDE]Environmental Sciences, Database Issue, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 05 Environmental Sciences, 06 Biological Sciences, 08 Information and Computing Sciences, Data Curation, Genome, Bacterial, Phylogeny, Information Systems, Developmental Biology
Abstract

International audience; Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

Published
2020

12. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Author

Doré, Hugo, Farrant, Gregory K., Guyet, Ulysse, Haguait, Julie, Humily, Florian, Ratin, Morgane, Pitt, Frances Diana, Ostrowski, Martin, Six, Christophe, Brillet-Guéguen, Loraine, Hoebeke, Mark, Bisch, Antoine, Le Corguillé, Gildas, Corre, Erwan, Labadie, Karine, Aury, Jean-Marc, Wincker, Patrick, Choi, Dong Han, Noh, Jae Hoon, Eveillard, Damien, Scanlan, David J., Partensky, Frédéric, Garczarek, Laurence, 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), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (LS2N - équipe COMBI), ANR-13-ADAP-0010,SAMOSA,Synechococcus as a model genus for studying adaptation of marine phytoplankton to environmental changes(2013), ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Marine cyanobacteria 1, amino-acid substitutions 6, amino-acid substitutions, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], comparative genomics, Microbiology, genomic islands, QH301, comparative genomics 4, evolution, QH426, 0502 Environmental Science and Management, 0503 Soil Sciences, 0605 Microbiology, ComputingMilieux_MISCELLANEOUS, Synechococcus 3, Original Research, Prochlorococcus, niche adaptation, Synechococcus, marine cyanobacteria, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], QR, niche adaptation 5, evolution 8, Prochlorococcus2, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], genomic islands 7, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

Published
2020

13. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803

Author

Guyet, Ulysse, Nguyen, Ngoc, Doré, Hugo, Haguait, Julie, Pittera, Justine, Conan, Maël, Ratin, Morgane, Corre, Erwan, Le Corguillé, Gildas, Brillet-Guéguen, Loraine, Hoebeke, Mark, Six, Christophe, Steglich, Claudia, Siegel, Anne, Eveillard, Damien, Partensky, Frédéric, Garczarek, Laurence, 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), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Department of Biology [Fribourg], University of Freiburg [Freiburg], ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
Synechococcus, Microbiology (medical), transcriptomics, temperature stress, [SDE]Environmental Sciences, light stress, marine cyanobacteria, UV radiations, Microbiology
Abstract

International audience; Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous highlight (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b 6 /f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.

Published
2020
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14. Additional file 5 of Comparative genomics applied to Mucor species with different lifestyles

Author

Lebreton, Annie, Corre, Erwan, Jany, Jean-Luc, Brillet-Guéguen, Loraine, Pèrez-Arques, Carlos, Garre, Victoriano, Misharl Monsoor, Debuchy, Robert, Meur, Christophe Le, Coton, Emmanuel, Barbier, Georges, and Meslet-Cladière, Laurence

Abstract

Additional file 5: Table S2. Extraction and sequencing information corresponding to the four newly sequenced Mucor isolates

Published
2020
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15. Additional file 4 of Comparative genomics applied to Mucor species with different lifestyles

Author

Lebreton, Annie, Corre, Erwan, Jany, Jean-Luc, Brillet-Guéguen, Loraine, Pèrez-Arques, Carlos, Garre, Victoriano, Misharl Monsoor, Debuchy, Robert, Meur, Christophe Le, Coton, Emmanuel, Barbier, Georges, and Meslet-Cladière, Laurence

Subjects
food and beverages
Abstract

Additional file 4: Table S1. Number of identified CAZyme encoding genes involved in the degradation of plant cell wall components (Cellulose active, Hemicellulose active and Pectin active). The presence of genes has been confirmed with manual annotation.

Published
2020
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16. Herbivore-induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata

Author

Ritter, Andrés, Cabioch, Léa, Brillet-Guéguen, Loraine, Corre, Erwan, Cosse, Audrey, Dartevelle, Laurence, Duruflé, Harold, Fasshauer, Carina, Goulitquer, Sophie, Thomas, François, Correa, Juan, Potin, Philippe, Faugeron, Sylvain, Leblanc, Catherine, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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), Pontificia Universidad Católica de Chile (UC), Diatom Genomics [LCQB] (LCQB-DG), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Evolutionary Biology and Ecology of Algae (EBEA), 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)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)

Subjects
cDNA libraries, Algae, Forms of DNA, lcsh:Medicine, Plant Science, Fatty Acids, Nonesterified, Phaeophyta, Real-Time Polymerase Chain Reaction, Biochemistry, Extraction techniques, Plant-Animal Interactions, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Metabolomics, Herbivory, DNA libraries, Amino Acids, Molecular Biology Techniques, lcsh:Science, Molecular Biology, Expressed Sequence Tags, Behavior, Molecular Biology Assays and Analysis Techniques, Animal Behavior, Ecology, Plant Ecology, Ecology and Environmental Sciences, lcsh:R, Organisms, Biology and Life Sciences, DNA, Plants, Seaweed, Complementary DNA, RNA extraction, Trophic Interactions, Nucleic acids, Research and analysis methods, Grazing, Community Ecology, Amino Acid Analysis, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, Zoology, Research Article
Abstract

International audience; Kelps are founding species of temperate marine ecosystems, living in intertidal coastal areas where they are often challenged by generalist and specialist herbivores. As most sessile organisms, kelps develop defensive strategies to restrain grazing damage and preserve their own fitness during interactions with herbivores. To decipher some inducible defense and signaling mechanisms, we carried out metabolome and transcriptome analyses in two emblematic kelp species, Lessonia spicata from South Pacific coasts and Laminaria digitata from North Atlantic, when challenged with their main specialist herbivores. Mass spectrometry based metabolomics revealed large metabolic changes induced in these two brown algae following challenges with their own specialist herbivores. Targeted metabolic profiling of L. spicata further showed that free fatty acid (FFA) and amino acid (AA) metabolisms were particularly regulated under grazing. An early stress response was illustrated by the accumulation of Sulphur containing amino acids in the first twelve hours of herbivory pressure. At latter time periods (after 24 hours), we observed FFA liberation and eicosanoid oxylipins synthesis likely representing metabolites related to stress. Global transcriptomic analysis identified sets of candidate genes specifically induced by grazing in both kelps. qPCR analysis of the top candidate genes during a 48-hours time course validated the results. Most of these genes were particularly activated by herbivore challenge after 24 hours, suggesting that transcriptional reprogramming could be operated at this time period. We demonstrated the potential utility of these genes as molecular markers for herbivory by measuring their inductions in grazed individuals of field harvested L. digitata and L. spicata. By unravelling the regulation of some metabolites and genes following grazing pressure in two kelps representative of the two hemispheres, this work contributes to provide a set of herbivore-induced chemical and molecular responses in kelp species, showing similar inducible responses upon specialist herbivores in their respective ecosystems.

Published
2017

17. Specific Targeting of Plant and Apicomplexa Parasite Tubulin through Differential Screening Using In Silico and Assay-Based Approaches

Author

Soleilhac, Emmanuelle, primary, Brillet-Guéguen, Loraine, additional, Roussel, Véronique, additional, Prudent, Renaud, additional, Touquet, Bastien, additional, Dass, Sheena, additional, Aci-Sèche, Samia, additional, Kasam, Vinod, additional, Barette, Caroline, additional, Imberty, Anne, additional, Breton, Vincent, additional, Vantard, Marylin, additional, Horvath, Dragos, additional, Botté, Cyrille, additional, Tardieux, Isabelle, additional, Roy, Sylvaine, additional, Maréchal, Eric, additional, and Lafanechère, Laurence, additional

Published
2018
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18. Community-Driven Data Analysis Training for Biology

Author

Batut, Bérénice, primary, Hiltemann, Saskia, additional, Bagnacani, Andrea, additional, Baker, Dannon, additional, Bhardwaj, Vivek, additional, Blank, Clemens, additional, Bretaudeau, Anthony, additional, Brillet-Guéguen, Loraine, additional, Čech, Martin, additional, Chilton, John, additional, Clements, Dave, additional, Doppelt-Azeroual, Olivia, additional, Erxleben, Anika, additional, Freeberg, Mallory Ann, additional, Gladman, Simon, additional, Hoogstrate, Youri, additional, Hotz, Hans-Rudolf, additional, Houwaart, Torsten, additional, Jagtap, Pratik, additional, Larivière, Delphine, additional, Le Corguillé, Gildas, additional, Manke, Thomas, additional, Mareuil, Fabien, additional, Ramírez, Fidel, additional, Ryan, Devon, additional, Sigloch, Florian Christoph, additional, Soranzo, Nicola, additional, Wolff, Joachim, additional, Videm, Pavankumar, additional, Wolfien, Markus, additional, Wubuli, Aisanjiang, additional, Yusuf, Dilmurat, additional, Taylor, James, additional, Backofen, Rolf, additional, Nekrutenko, Anton, additional, and Grüning, Björn, additional

Published
2018
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19. The genome of Ectocarpus subulatus – a highly stress-tolerant brown alga

Author

Dittami, Simon M., primary, Corre, Erwan, additional, Brillet-Guéguen, Loraine, additional, Lipinska, Agnieszka P., additional, Pontoizeau, Noé, additional, Aite, Meziane, additional, Avia, Komlan, additional, Caron, Christophe, additional, Cho, Chung Hyun, additional, Collén, Jonas, additional, Cormier, Alexandre, additional, Delage, Ludovic, additional, Doubleau, Sylvie, additional, Frioux, Clémence, additional, Gobet, Angélique, additional, González-Navarrete, Irene, additional, Groisillier, Agnès, additional, Hervé, Cécile, additional, Jollivet, Didier, additional, KleinJan, Hetty, additional, Leblanc, Catherine, additional, Liu, Xi, additional, Marie, Dominique, additional, Markov, Gabriel V., additional, Minoche, André E., additional, Monsoor, Misharl, additional, Pericard, Pierre, additional, Perrineau, Marie-Mathilde, additional, Peters, Akira F., additional, Siegel, Anne, additional, Siméon, Amandine, additional, Trottier, Camille, additional, Yoon, Hwan Su, additional, Himmelbauer, Heinz, additional, Boyen, Catherine, additional, and Tonon, Thierry, additional

Published
2018
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20. Community-driven data analysis training for biology

Author

Batut, Bérénice, primary, Hiltemann, Saskia, additional, Bagnacani, Andrea, additional, Baker, Dannon, additional, Bhardwaj, Vivek, additional, Blank, Clemens, additional, Bretaudeau, Anthony, additional, Brillet-Guéguen, Loraine, additional, Čech, Martin, additional, Chilton, John, additional, Clements, Dave, additional, Doppelt-Azeroual, Olivia, additional, Erxleben, Anika, additional, Freeberg, Mallory Ann, additional, Gladman, Simon, additional, Hoogstrate, Youri, additional, Hotz, Hans-Rudolf, additional, Houwaart, Torsten, additional, Jagtap, Pratik, additional, Larivière, Delphine, additional, Corguillé, Gildas Le, additional, Manke, Thomas, additional, Mareuil, Fabien, additional, Ramírez, Fidel, additional, Ryan, Devon, additional, Sigloch, Florian Christoph, additional, Soranzo, Nicola, additional, Wolff, Joachim, additional, Videm, Pavankumar, additional, Wolfien, Markus, additional, Wubuli, Aisanjiang, additional, Yusuf, Dilmurat, additional, Network, Galaxy Training, additional, Backofen, Rolf, additional, Taylor, James, additional, Nekrutenko, Anton, additional, and Grüning, Björn, additional

Published
2017
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26. Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus.

Author

Nègre, Delphine, Aite, Méziane, Belcour, Arnaud, Frioux, Clémence, Brillet-Guéguen, Loraine, Liu, Xi, Bordron, Philippe, Godfroy, Olivier, Lipinska, Agnieszka P., Leblanc, Catherine, Siegel, Anne, Dittami, Simon M., Corre, Erwan, and Markov, Gabriel V.

Subjects
SACCHARINA, ABSCISIC acid, BIOSYNTHESIS, METABOLIC profile tests, ALGAE, METABOLIC models, BROWN algae, LAMINARIA
Abstract

Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of Saccharina japonica and Cladosiphon okamuranus has provided the necessary data for the reconstruction of Genome–Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of Ectocarpus siliculosus to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by Saccharina japonica, its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches. [ABSTRACT FROM AUTHOR]

Published
2019
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27. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.

Author

Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury JM, Wincker P, Scanlan DJ, and Partensky F

Subjects
Bacterial Proteins genetics, Geography, Likelihood Functions, Phylogeny, User-Computer Interface, Aquatic Organisms genetics, Cyanobacteria genetics, Data Curation, Databases, Genetic, Genome, Bacterial, Information Systems
Abstract

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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28. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.

Author

Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, and Garczarek L

Abstract

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus , we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters ( Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton., (Copyright © 2020 Doré, Farrant, Guyet, Haguait, Humily, Ratin, Pitt, Ostrowski, Six, Brillet-Guéguen, Hoebeke, Bisch, Le Corguillé, Corre, Labadie, Aury, Wincker, Choi, Noh, Eveillard, Scanlan, Partensky and Garczarek.)

Published
2020
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29. Herbivore-induced chemical and molecular responses of the kelps Laminaria digitata and Lessonia spicata.

Author

Ritter A, Cabioch L, Brillet-Guéguen L, Corre E, Cosse A, Dartevelle L, Duruflé H, Fasshauer C, Goulitquer S, Thomas F, Correa JA, Potin P, Faugeron S, and Leblanc C

Subjects
Amino Acids metabolism, Expressed Sequence Tags, Fatty Acids, Nonesterified metabolism, Metabolomics, Phaeophyceae genetics, Phaeophyceae metabolism, Real-Time Polymerase Chain Reaction, Transcriptome, Herbivory, Phaeophyceae physiology
Abstract

Kelps are founding species of temperate marine ecosystems, living in intertidal coastal areas where they are often challenged by generalist and specialist herbivores. As most sessile organisms, kelps develop defensive strategies to restrain grazing damage and preserve their own fitness during interactions with herbivores. To decipher some inducible defense and signaling mechanisms, we carried out metabolome and transcriptome analyses in two emblematic kelp species, Lessonia spicata from South Pacific coasts and Laminaria digitata from North Atlantic, when challenged with their main specialist herbivores. Mass spectrometry based metabolomics revealed large metabolic changes induced in these two brown algae following challenges with their own specialist herbivores. Targeted metabolic profiling of L. spicata further showed that free fatty acid (FFA) and amino acid (AA) metabolisms were particularly regulated under grazing. An early stress response was illustrated by the accumulation of Sulphur containing amino acids in the first twelve hours of herbivory pressure. At latter time periods (after 24 hours), we observed FFA liberation and eicosanoid oxylipins synthesis likely representing metabolites related to stress. Global transcriptomic analysis identified sets of candidate genes specifically induced by grazing in both kelps. qPCR analysis of the top candidate genes during a 48-hours time course validated the results. Most of these genes were particularly activated by herbivore challenge after 24 hours, suggesting that transcriptional reprogramming could be operated at this time period. We demonstrated the potential utility of these genes as molecular markers for herbivory by measuring their inductions in grazed individuals of field harvested L. digitata and L. spicata. By unravelling the regulation of some metabolites and genes following grazing pressure in two kelps representative of the two hemispheres, this work contributes to provide a set of herbivore-induced chemical and molecular responses in kelp species, showing similar inducible responses upon specialist herbivores in their respective ecosystems.

Published
2017
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