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1. Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

Author: Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Agence Nationale de la Recherche (France), Région Midi-Pyrénées, Labex TULIP, European Research Council, Ministerio de Educación, Cultura y Deporte (España), Salguero-Linares, José Manuel, Serrano, Irene, Ruiz-Solani, Nerea, Salas-Gómez, Marta, Phukan, Ujjal J., González, Víctor M., Bernardo-Faura, Martí, Valls, Marc, Rengel, David, Coll, Núria S., Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Agence Nationale de la Recherche (France), Région Midi-Pyrénées, Labex TULIP, European Research Council, Ministerio de Educación, Cultura y Deporte (España), Salguero-Linares, José Manuel, Serrano, Irene, Ruiz-Solani, Nerea, Salas-Gómez, Marta, Phukan, Ujjal J., González, Víctor M., Bernardo-Faura, Martí, Valls, Marc, Rengel, David, and Coll, Núria S.
Abstract: Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response (HR). This type of cell death occurs precisely at the site of pathogen recognition, and it is restricted to a few cells. Extensive research has shed light on how plant immune receptors are mechanistically activated. However, two central key questions remain largely unresolved: how does cell death zonation take place, and what are the mechanisms that underpin this phenomenon? Consequently, bona fide transcriptional indicators of HR are lacking, which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation. In this study, to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana–Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity. Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes, expression profiles, and biological processes derived from tissue undergoing HR and that of its surroundings. Furthermore, we generated a pipeline based on concatenated pairwise comparisons between time, zone, and treatment that enabled us to define 13 robust transcriptional HR markers. Among these genes, the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death. This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria, opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level.
Published: 2022

2. Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Author: German Research Foundation, European Commission, Academy of Finland, Natural Sciences and Engineering Research Council of Canada, Federal Ministry of Education and Research (Germany), European Research Council, Labex TULIP, Agence Nationale de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Russian Foundation for Basic Research, Tarbiat Modares University, Aurora Organic Dairy, Slovak Research and Development Agency, Wageningen University and Research Centre, International Atomic Energy Agency, Fundação de Amparo à Pesquisa do Estado de São Paulo, Oklahoma State University, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Royal Canadian Geographical Society, Environmental Protection Agency (Ireland), University of Hawaii at Manoa, U.S. Navy, Department of Science and Technology (India), Department of Defense (US), Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministry of Education, Youth and Sports (Czech Republic), Colorado Wheat Research Foundation, Zone Atelier Alpes, Austrian Science Fund, Rentenbank, Welsh Government, European Agricultural Fund for Rural Development, Finnish Ministry of Agriculture and Forestry, Science Foundation Ireland, University of Toronto, Haliburton Forest & Wildlife Reserve, Arts and Sciences, Northern Kentucky University, University of Innsbruck, Higher Education Commission (Pakistan), Kerala Forest Research Institute, Universidad Complutense de Madrid, Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Fondo para la Investigación Científica y Tecnológica (Argentina), Universidad Nacional de Luján, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fonds de Recherche du Québec, Institute for Environmental Science and Policy, University of Illinois, Casey Tree, College of Liberal Arts and Social Sciences, DePaul University, Comisión Interministerial de Ciencia y Tecnología, CICYT (España), Japan Society for the Promotion of Science, McKnight Foundation, Russian Academy of Sciences, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Ministère de l'Europe et des Affaires étrangères (France), Bavarian Ministry for Food, Agriculture and Forestry, Ministero dell'Istruzione, dell'Università e della Ricerca, Idaho Agricultural Experiment Station, Estonian Science Foundation, Ministry of the Environment, Conservation and Parks (Ontario), National Natural Science Foundation of China, Australian Research Council, Phillips, Helen, R. P., Bach, Elizabeth M., Bartz, Marie L. C., Bennett, Joanne, Beugnon, Rémy, Briones, María J. I., Brown, George, Ferlian, Olga, Gongalsky, Konstantin B., Guerra, Carlos A., König-Ries, Birgitta, Holdsworth, Andrew R., Coors, Anja, Crotty, Felicity V., Crumsey, Jasmine M., Dávalos, Andrea, Diaz Cosin, Darío J., Loss, Scott R., Dobson, Annise M., Dominguez, Anahí, Esteban Duhour, Andrés, Schirrmann, Michael, Eekeren, Nick van, Holmstrup, Martin, Emmerling, Christoph, Falco, Liliana B., Fernández, Rosa, Fonte, Steven J., Fragoso, Carlos, Franco, André L. C., Marichal, Raphael, Fusilero, Abegail T., Moreno, Gerardo, Geraskina, Anna P., Gholami, Shaieste, Hopfensperger, Kristine N., González, Grizelle, Gundale, Michael J., Gutiérrez López, Mónica, Hackenberger, Branimir K., Hackenberger, Davorka K., Hernández, Luis M., Hirth, Jeff R., Morón-Ríos, Alejandro, Huerta Lwanga, Esperanza, Huhta, Veikko, Hurisso, Tunsisa T., Iannone III, Basil V., Iordache, Madalina, Ramirez, Kelly S., Irmler, Ulrich, Minamiya, Yukio, Ivask, Mari, Jesus Lidon, Juan B., Motohiro, Hasegawa, Johnson-Maynard, Jodi L., Joschko, Monika, Kaneko, Nobuhiro, Kanianska, Radoslava, Keith, Aidan M., Kernecker, Maria L., Scharenbroch, Bryant C., Koné, Armand W., Kooch, Yahya, Hendrik Moos, Jan, Muys, Bart, Kukkonen, Sanna T., Lalthanzara, H., Lammel, Daniel R., Lebedev, Iurii M., Le Cadre, Edith, Lincoln, Noa K., López-Hernández, Danilo, Neirynck, Johan, Krebs, Julia, Norgrove, Lindsey, Novo, Marta, Nuutinen, Visa, Choi, Amy, Nuzzo, Victoria, Schmidt, Olaf, Rahman, P. Mujeeb, Pansu, Johan, Paudel, Shishir, Pérès, Guénola, Pérez-Camacho, Lorenzo, Ponge, Jean-François, Orgiazzi, Alberto, Prietzel, Jörg, Wall, Diana H., Rapoport, Irina B., Imtiaz Rashid, Muhammad, Schröder, Boris, Rebollo, Salvador, Rodríguez, Miguel Á., Roth, Alexander M., Rousseau, Guillaume X., Rozen, Anna, Sayad, Ehsan, Schaik, Loes van, Brose, Ulrich, Seeber, Julia, Shashkov, Maxim P., Singh, Jaswinder, Smith, Sandy M., Steinwandter, Michael, Capowiez, Yvan, Szlavecz, Katalin, Russell, David, Talavera, José A., Trigo, Dolores, Decaëns, Thibaud, Tsukamoto, Jiro, Uribe-López, Sheila, Valença, Anne W. de, Virto, Iñigo, Wackett, Adrian A., Warren, Matthew W., Cavagnaro, Timothy R., Webster, Emily R., Wehr, Nathaniel H., Schwarz, Benjamin, Lavelle, Patrick, Wironen, Michael B., Wolters, Volkmar, Wu, Pengfei, Zenkova, Irina V. Z., Zhang, Weixin, Cameron, Erin K., Eisenhauer, Nico, Loreau, Michel, Mathieu, Jérôme, Mulder, Christian, Putten, Wim H. van der, Rillig, Matthias C., Matula, Radim, Thakur, Madhav P., Clause, Julia, Vries, Franciska T. de, Wardle, David A., Ammer, Sabine, Arai, Miwa, Ayuke, Fredrick O., Baker, Geoff H., Baretta, Dilmar, Barkusky, Dietmar, Hishi, Takuo, Beauséjour, Robin, Bedano, José C., Cluzeau, Daniel, Birkhofer, Klaus, Blanchart, Eric, Blossey, Bernd, Bolger, Thomas, Bradley, Robert L., Brossard, Michel, Burtis, James C., German Research Foundation, European Commission, Academy of Finland, Natural Sciences and Engineering Research Council of Canada, Federal Ministry of Education and Research (Germany), European Research Council, Labex TULIP, Agence Nationale de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Russian Foundation for Basic Research, Tarbiat Modares University, Aurora Organic Dairy, Slovak Research and Development Agency, Wageningen University and Research Centre, International Atomic Energy Agency, Fundação de Amparo à Pesquisa do Estado de São Paulo, Oklahoma State University, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Royal Canadian Geographical Society, Environmental Protection Agency (Ireland), University of Hawaii at Manoa, U.S. Navy, Department of Science and Technology (India), Department of Defense (US), Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministry of Education, Youth and Sports (Czech Republic), Colorado Wheat Research Foundation, Zone Atelier Alpes, Austrian Science Fund, Rentenbank, Welsh Government, European Agricultural Fund for Rural Development, Finnish Ministry of Agriculture and Forestry, Science Foundation Ireland, University of Toronto, Haliburton Forest & Wildlife Reserve, Arts and Sciences, Northern Kentucky University, University of Innsbruck, Higher Education Commission (Pakistan), Kerala Forest Research Institute, Universidad Complutense de Madrid, Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Fondo para la Investigación Científica y Tecnológica (Argentina), Universidad Nacional de Luján, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fonds de Recherche du Québec, Institute for Environmental Science and Policy, University of Illinois, Casey Tree, College of Liberal Arts and Social Sciences, DePaul University, Comisión Interministerial de Ciencia y Tecnología, CICYT (España), Japan Society for the Promotion of Science, McKnight Foundation, Russian Academy of Sciences, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Ministère de l'Europe et des Affaires étrangères (France), Bavarian Ministry for Food, Agriculture and Forestry, Ministero dell'Istruzione, dell'Università e della Ricerca, Idaho Agricultural Experiment Station, Estonian Science Foundation, Ministry of the Environment, Conservation and Parks (Ontario), National Natural Science Foundation of China, Australian Research Council, Phillips, Helen, R. P., Bach, Elizabeth M., Bartz, Marie L. C., Bennett, Joanne, Beugnon, Rémy, Briones, María J. I., Brown, George, Ferlian, Olga, Gongalsky, Konstantin B., Guerra, Carlos A., König-Ries, Birgitta, Holdsworth, Andrew R., Coors, Anja, Crotty, Felicity V., Crumsey, Jasmine M., Dávalos, Andrea, Diaz Cosin, Darío J., Loss, Scott R., Dobson, Annise M., Dominguez, Anahí, Esteban Duhour, Andrés, Schirrmann, Michael, Eekeren, Nick van, Holmstrup, Martin, Emmerling, Christoph, Falco, Liliana B., Fernández, Rosa, Fonte, Steven J., Fragoso, Carlos, Franco, André L. C., Marichal, Raphael, Fusilero, Abegail T., Moreno, Gerardo, Geraskina, Anna P., Gholami, Shaieste, Hopfensperger, Kristine N., González, Grizelle, Gundale, Michael J., Gutiérrez López, Mónica, Hackenberger, Branimir K., Hackenberger, Davorka K., Hernández, Luis M., Hirth, Jeff R., Morón-Ríos, Alejandro, Huerta Lwanga, Esperanza, Huhta, Veikko, Hurisso, Tunsisa T., Iannone III, Basil V., Iordache, Madalina, Ramirez, Kelly S., Irmler, Ulrich, Minamiya, Yukio, Ivask, Mari, Jesus Lidon, Juan B., Motohiro, Hasegawa, Johnson-Maynard, Jodi L., Joschko, Monika, Kaneko, Nobuhiro, Kanianska, Radoslava, Keith, Aidan M., Kernecker, Maria L., Scharenbroch, Bryant C., Koné, Armand W., Kooch, Yahya, Hendrik Moos, Jan, Muys, Bart, Kukkonen, Sanna T., Lalthanzara, H., Lammel, Daniel R., Lebedev, Iurii M., Le Cadre, Edith, Lincoln, Noa K., López-Hernández, Danilo, Neirynck, Johan, Krebs, Julia, Norgrove, Lindsey, Novo, Marta, Nuutinen, Visa, Choi, Amy, Nuzzo, Victoria, Schmidt, Olaf, Rahman, P. Mujeeb, Pansu, Johan, Paudel, Shishir, Pérès, Guénola, Pérez-Camacho, Lorenzo, Ponge, Jean-François, Orgiazzi, Alberto, Prietzel, Jörg, Wall, Diana H., Rapoport, Irina B., Imtiaz Rashid, Muhammad, Schröder, Boris, Rebollo, Salvador, Rodríguez, Miguel Á., Roth, Alexander M., Rousseau, Guillaume X., Rozen, Anna, Sayad, Ehsan, Schaik, Loes van, Brose, Ulrich, Seeber, Julia, Shashkov, Maxim P., Singh, Jaswinder, Smith, Sandy M., Steinwandter, Michael, Capowiez, Yvan, Szlavecz, Katalin, Russell, David, Talavera, José A., Trigo, Dolores, Decaëns, Thibaud, Tsukamoto, Jiro, Uribe-López, Sheila, Valença, Anne W. de, Virto, Iñigo, Wackett, Adrian A., Warren, Matthew W., Cavagnaro, Timothy R., Webster, Emily R., Wehr, Nathaniel H., Schwarz, Benjamin, Lavelle, Patrick, Wironen, Michael B., Wolters, Volkmar, Wu, Pengfei, Zenkova, Irina V. Z., Zhang, Weixin, Cameron, Erin K., Eisenhauer, Nico, Loreau, Michel, Mathieu, Jérôme, Mulder, Christian, Putten, Wim H. van der, Rillig, Matthias C., Matula, Radim, Thakur, Madhav P., Clause, Julia, Vries, Franciska T. de, Wardle, David A., Ammer, Sabine, Arai, Miwa, Ayuke, Fredrick O., Baker, Geoff H., Baretta, Dilmar, Barkusky, Dietmar, Hishi, Takuo, Beauséjour, Robin, Bedano, José C., Cluzeau, Daniel, Birkhofer, Klaus, Blanchart, Eric, Blossey, Bernd, Bolger, Thomas, Bradley, Robert L., Brossard, Michel, and Burtis, James C.
Abstract: Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.
Published: 2021

3. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species: Intraspecific dispersal of C4 physiology

Author: European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), Labex TULIP, Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., Christin, Pascal-Antoine, European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), Labex TULIP, Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., and Christin, Pascal-Antoine
Abstract: C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.
Published: 2020

4. An epigenetic molluscicide

Author: Nelia Luviano, Ludovic Halby, Corinne Jallet, Paola B. Arimondo, Celine Cosseau, Christoph Grunau, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This study is set within the framework of the « Laboratoire d’Excellence (LabEx) » TULIP (ANR-10-LABX-41) and CeMEB (ANR- 10-LABX-04-01). N.L. was supported by a PhD grant of the Region Occitanie, France and the UPVD, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010)
Subjects: molluscicide, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, schistosomiases, epigenetics, DNA methylation inhibitor, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Biomphalaria glabrata
Abstract: Biomphalaria glabratais a fresh-water mollusk that serves as obligatory intermediate host toSchistosoma mansoni, agent of the neglected tropical disease schistosomiasis that affects roughly 250 Mio people. One of the ways to control the pathogenic agent is to interrupt the life cycle by eliminating the intermediate snail host though foal treatment of water bodies with molluscicides. Currently recommended molluscicides were developed in the 1950ths and lack sufficient specificity, e.g., they are toxic to fish. To provide new lead compounds for the development of a new type of molluscicides we used a rational approach based on the hypotheses that interfering with an important epigenetic mark, DNA methylation, would impede development of the snail host. We present here the compound 29, analogues-based compound that mimic substrates of DNA methyltransferases. We show that compound 29 has (i) low cytotoxicity for human cells, (ii) it inhibits DNA methylation, and (iii) it decreases fecundity inB.glabrata. It is therefore conceivable to produce compounds that act as specific epigenetic molluscicides.
Published: 2023

5. A dual legume-rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses

Author: Laurent Sauviac, Antoine Rémy, Emeline Huault, Mélanie Dalmasso, Théophile Kazmierczak, Marie‐Françoise Jardinaud, Ludovic Legrand, Corentin Moreau, Bryan Ruiz, Anne‐Claire Cazalé, Sophie Valière, Benjamin Gourion, Laurence Dupont, Véronique Gruber, Eric Boncompagni, Eliane Meilhoc, Pierre Frendo, Florian Frugier, Claude Bruand, Frugier, Florian, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universite Paris-Saclay, French National Research Agency (ANR), European Commission, Labex SPS, Labex TULIP, EUR SPS, Labex Signalife, EUR TULIP GS, IDEX UCA JEDI, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: S4o, root nodule, senescence, Physiology, [SDV]Life Sciences [q-bio], NAC transcription factor, RNA sequencing, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV] Life Sciences [q-bio], cytokinin, Gene Expression Regulation, Plant, RNA, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nitrogen Fixation, Medicago truncatula, cytokinin, NAC transcription factor, nitrogen fixation, RNA sequencing, root nodule, S4o, senescence, symbiosis, Root Nodules, Plant, Symbiosis, Transcriptome, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins, Rhizobium
Abstract: International audience; Senescence determines plant organ lifespan depending on aging and environmental cues. During the endosymbiotic interaction with rhizobia, legume plants develop a specific organ, the root nodule, which houses nitrogen (N)-fixing bacteria. Unlike earlier processes of the legume-rhizobium interaction (nodule formation, N fixation), mechanisms controlling nodule senescence remain poorly understood. To identify nodule senescence-associated genes, we performed a dual plant-bacteria RNA sequencing approach on Medicago truncatula-Sinorhizobium meliloti nodules having initiated senescence either naturally (aging) or following an environmental trigger (nitrate treatment or salt stress). The resulting data allowed the identification of hundreds of plant and bacterial genes differentially regulated during nodule senescence, thus providing an unprecedented comprehensive resource of new candidate genes associated with this process. Remarkably, several plant and bacterial genes related to the cell cycle and stress responses were regulated in senescent nodules, including the rhizobial RpoE2-dependent general stress response. Analysis of selected core nodule senescence plant genes allowed showing that MtNAC969 and MtS40, both homologous to leaf senescence-associated genes, negatively regulate the transition between N fixation and senescence. In contrast, overexpression of a gene involved in the biosynthesis of cytokinins, well-known negative regulators of leaf senescence, may promote the transition from N fixation to senescence in nodules.
Published: 2022
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6. Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection

Author: Manon Fallet, Caroline Montagnani, Bruno Petton, Luc Dantan, Julien de Lorgeril, Sébastien Comarmond, Cristian Chaparro, Eve Toulza, Simon Boitard, Jean-Michel Escoubas, Agnès Vergnes, Jacqueline Le Grand, Ingo Bulla, Yannick Gueguen, Jérémie Vidal-Dupiol, Christoph Grunau, Guillaume Mitta, Céline Cosseau, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), 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), The present study was supported by the ANR project DECIPHER (ANR-14-CE19-0023), by the 'Chercheur d’Avenir' project TRANSGIGAS (Region Languedoc Roussillon), by the EU funded project VIVALDI (H2020 program, n°678589) and by Ifremer, CNRS, Université de Montpellier and Université de Perpignan Via Domitia. With the support of LabEx CeMEB, an ANR 'Investissements d’Avenir 'Laboratoires d'Excellences' program through the Environmental Epigenomics Platform (ANR-10-LABX-0004) and LabEx TULIP (ANR‐10‐LABX‐0041)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), and European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016)
Subjects: Microbiology (medical), animal structures, DNA methylation, Oyster, Innate immune shaping, Microbiota, Epigenetic, Aquaculture, Microbiology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Immune System, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, bacteria, Crassostrea, Transcriptome
Abstract: Background The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation — and, importantly, protection from infectious disease — is still an open question. Results Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS. Conclusions We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease. tag the videobyte/videoabstract in this section
Published: 2022
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7. Mating Interactions between Schistosoma bovis and S. mansoni and Compatibility of Their F1 Progeny with Biomphalaria glabrata and Bulinus truncatus

Author: Amos Mathias Onyekwere, Alejandra De Elias-Escribano, Julien Kincaid-Smith, Sarah Dametto, Jean-François Allienne, Anne Rognon, Maria Dolores Bargues, Jérôme Boissier, Alex Ekwueme Federal University Ndufu-Alike, Ikwo (AE-FUNAI), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Departamento de Parasitologia, Universitat de València (UV)-Facultad de farmacia, Facultad de Farmacia, Universitat de València (UV), CIBER de Enfermedades Infecciosas, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), This research was funded by Campus France, France and Tertiary Education Trust Fund (TETfund), Nigeria and was supported by the program HySWARM (ANR-18-CE35-0001) from the French Research National Agency respectively awarded to J.B. and A.M.O. is funded by Campus France. M.D.B. and A.D.E.-E. were funded by the Red de Investigacion de Centros de Enfermedades Tropicales-RICET (RD16/0027/0023) of the PN de I+D+I, ISCIII-Subdireccion General de Redes y Centros de Investigacion Cooperativa RETICS, Ministry of Health and Consumption, Madrid, by CIBER de Enfermedades Infecciosas (CB21/13/00056), ISCIII, Ministry of Science and Education, Madrid, Spain, by the PROMETEO Program, Programa de Ayudas para Grupos de Investigacion de Excelencia (2021/004), Generalitat Valenciana, Valencia, Spain and by BEFPI/2021/019. This study is set within the framework of the 'Laboratoires d'Excellence (LABEX)' TULIP (ANR-10-LABX-0041)., ANR-18-CE35-0001,HySWARM,Hybrid Swarm: rôle de l'hybridation dans les capacités invasives, l'épidémiologie et le diagnostic de la schistosomiase(2018), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: Microbiology (medical), mating interactions, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Schistosoma mansoni, compatibility, Microbiology, Biomphalaria glabrata, Schistosoma bovis, F1 progeny, Bulinus truncatus, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Virology, parasitic diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract: Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the pairing behavior between Schistosoma bovis and S. mansoni in mixed infections in mice. We used six mate choice experiments to assess mating interactions between the two schistosome species. We show that mating between the two Schistosoma species is not random and that S. mansoni exhibits greater mate recognition compared to S. bovis. We also performed reciprocal crosses (male S. mansoni × female S. bovis) and (female S. mansoni × male S. bovis) that produce active swimming miracidia. These miracidia were genotyped by ITS2 sequencing and proposed for mollusc infection. Molecular analyses show that all the miracidia are parthenogenetically produced (i.e., their harbor the mother ITS2 genotype) and as a consequence can only infect the mollusc of the maternal species. Offspring produced by male S. mansoni × female S. bovis pairing can only infect Bulinus truncatus whereas offspring produced by female S. mansoni × male S. bovis can only infect Biomphalaria glabrata snails. Evolutionary and epidemiological consequences are discussed.
Published: 2022
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8. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses

Author: Yannick Gueguen, J. de Lorgeril, Samuel Dupont, C. Salmeron, G. Tanguy, Caroline Montagnani, J.Y. Bou Khalil, Jean-Christophe Auguet, Jean-Michel Escoubas, Bruno Petton, B. La Scola, Eve Toulza, A. Lokmer, Christelle Desnues, Guillaume Mitta, David Pecqueur, Erwan Corre, Laure Guillou, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), 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)-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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), The present study was supported by: the DHOF program of the UMR5244/IHPE (http://ihpe.univ-perp.fr/en/ihpe-transversal-holobiont/), the Ifremer project HémoMicrobiote, EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future (ANR-10-INBS-02), the ANR projects DECIPHER (ANR-14-CE19–0023) and ENVICOPAS (ANR-15-CE35–0004), the EU funded project VIVALDI (H2020 program, n°678589), by Ifremer, CNRS, Université de Montpellier, Université de Perpignan via Domitia, by the IHU Méditerranée Infection, Marseille, France, by the French Government under the «Investissements d’avenir» program (reference: Méditerranée Infection 10-IAHU-03) and by the Région Provence-Alpes-Côte d’Azur and by the European funding FEDER PRIMI. This study is set within the framework of the 'Laboratoires d’Excellences (LABEX)' TULIP (ANR-10-LABX-41)., ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), ANR-15-CE35-0004,ENVICOPAS,Impact des changements environnementaux sur les organismes pathogènes dans les écosystèmes côtiers(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Éco-Anthropologie (EAE), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), 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), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Parasitologie fonctionnelle et évolutive (PFE), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Radiopathologie et Thérapies Expérimentales [IRSN, Fontenay-aux-Roses] (PRP-HOM - SRBE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Oyster, animal structures, Early-life microbiota, lcsh:QR1-502, Zoology, medicine.disease_cause, Within-host ecosystem, lcsh:Microbiology, 03 medical and health sciences, biology.animal, medicine, Trans-kingdom interactions, Human virome, Microbiome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ecological niche, 0303 health sciences, lcsh:Veterinary medicine, biology, 030306 microbiology, Host (biology), Oyster genetic background, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Protist, General Medicine, Pacific oyster, biology.organism_classification, Transplantation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Crassostrea gigas, lcsh:SF600-1100, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acln, Hemolymph microbiota dynamics, Research Article
Abstract: Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
Published: 2020
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9. Analysis of temporal patterns in animal movement networks

Author: Guillaume Le Loc’h, Mathieu Lihoreau, Thibault Dubois, Cristian Pasquaretta, Virginie P. Delepoulle, Philipp Heeb, Tamara Gómez-Moracho, Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), XeriusTracking SARL, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), This work was funded by the CNRS, a grant from the Agence Nationale de la Recherche to M.L. (ANR‐16‐CE02‐0010), and the Laboratoire d'Excellence (LABEX) TULIP (ANR‐10‐LABX‐41). We acknowledge Prof. Lars Chittka and Dr. Joe Woodgate for providing access to the harmonic radar (bumblebee trajectory) and XeriusTracking for the GPS data (black kite trajectory)., ANR-16-CE02-0010,Mov-It,Le mouvement des ongulés au sein de paysages hétérogènes: identification des processus comportementaux reliant les changements globaux aux performances démographiques et à la gestion spatialement explicite(2016), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Centre de Recherches sur la Cognition Animale (CRCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-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 Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 0303 health sciences, movement networks, Computer science, business.industry, Movement (music), [SDV]Life Sciences [q-bio], Ecological Modeling, Argos, 010603 evolutionary biology, 01 natural sciences, GPS tracking, spatial networks, 03 medical and health sciences, Harmonic radar, movement ecology, Computer vision, Artificial intelligence, harmonic radar, business, animal trajectories, motifs time series, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: We implemented our method in R. We provide the codes and the bumblebee and black kite datasets in Dryad Digital Repository https://doi.org/10.5061/dryad.47d7wm390 (Pasquaretta et al., 2015). The roe deer dataset was obtained from MOVEBANK (Wikelski & Kays, 2020). Animal Identifier: Sandro (M06), from Cagnacci et al. (2011) (https://www.movebank.org/). The wolf dataset was obtained from MOVEBANK (Wikelski & Kays, 2020), Animal identifier: Zimzik, from Kaczensky et al. (2006) (https://www.movebank.org/).We implemented our method in R. We provide the codes and the bumblebee and black kite datasets in Dryad Digital Repository https://doi.org/10.5061/dryad.47d7wm390 (Pasquaretta et al., 2015). The roe deer dataset was obtained from MOVEBANK (Wikelski & Kays, 2020). Animal Identifier: Sandro (M06), from Cagnacci et al. (2011) (https://www.movebank.org/). The wolf dataset was obtained from MOVEBANK (Wikelski & Kays, 2020), Animal identifier: Zimzik, from Kaczensky et al. (2006) (https://www.movebank.org/).; International audience; 1. Understanding how animal movements change across space and time is a fundamental question in ecology. While classical analyses of trajectories give insightful descriptors of spatial patterns, a satisfying method for assessing the temporal succession of such patterns is lacking.2. Network analyses are increasingly used to capture properties of complex animal trajectories in simple graphical metrics. Here, building on this approach, we introduce a method that incorporates time into movement network analyses based on temporal sequences of network motifs.3. We illustrate our method using four example trajectories (bumblebee, black kite, roe deer, wolf) collected with different technologies (harmonic radar, platform terminal transmitter, global positioning system). First, we transformed each trajectory into a spatial network by defining the animal's coordinates as nodes and movements in between as edges. Second, we extracted temporal sequences of network motifs from each movement network and compared the resulting behavioural profiles to topological features of the original trajectory. Finally, we compared each sequence of motifs with simulated Brownian and Lévy random motions to statistically determine differences between trajectories and classical movement models.4. Our analysis of the temporal sequences of network motifs in individual movement networks revealed successions of spatial patterns corresponding to changes in behavioural modes that can be attributed to specific spatio‐temporal events of each animal trajectory. Future applications of our method to multi‐layered movement and social network analysis yield considerable promises for extending the study of complex movement patterns at the population level.
Published: 2020
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10. Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection

Author: Fallet, Manon, Montagnani, C., Petton, Bruno, de Lorgeril, Julien, Comarmond, Sébastien, Chaparro, Cristian, Toulza, Eve, Boitard, Simon, Escoubas, Jean-Michel, Vergnes, Agnès, Le Grand, Jacqueline, Bulla, Ingo, Gueguen, Yannick, Vidal-Dupiol, Jérémie, Grunau, Christoph, Mitta, Guillaume, Cosseau, Céline, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), The present study was supported by the ANR project DECIPHER (ANR-14-CE19-0023), by the 'Chercheur d’Avenir' project TRANSGIGAS (Region Languedoc Roussillon), by the EU funded project VIVALDI (H2020 program, n°678589) and by Ifremer, CNRS, Université de Montpellier and Université de Perpignan Via Domitia. With the support of LabEx CeMEB, an ANR 'Investissements d’Avenir 'Laboratoires d'Excellences' program through the Environmental Epigenomics Platform (ANR-10-LABX-0004) and LabEx TULIP (ANR‐10‐LABX‐0041)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016)
Subjects: oyster, DNA methylation, animal structures, aquaculture, innate immune shaping, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], microbiota, bacteria, epigenetic
Abstract: Background The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation – and, importantly, protection from infectious disease – is still an open question. Results Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific Oyster Mortality Syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS. Conclusions We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease.
Published: 2022
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11. New insights into the role of DNA methylation in Biomphalaria glabrata infection susceptibility

Author: Luviano, Nelia, Lopez, Marie, Gawehns, Fleur, Chaparro, Cristian, Arimondo, Paola, Halby, Ludovic, Verhoeven, Koen, Pujol, Benoit, Gourbal, Benjamin, Duval, David, Ittiprasert, Wannaporn, Allienne, Jean-François, Pouzol, Damien, Tavernier, Geneviève, Cosseau, Celine, Grunau, Christoph, Netherlands Institute of Ecology (NIOO), Terrestrial Ecology (TE), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Pharmacochimie de la Régulation Epigénétique du Cancer (ETaC), PIERRE FABRE-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), 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), Georgetown University [Washington] (GU), Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by Wellcome Trust strategic award (107475/Z/15/Z) and by a PhD grant to NL from the Region Occitanie (EPIPARA project) and the University of Perpignan Via Domitia graduate school ED305. With the support of LabEx CeMEB, an ANR'Investissements d’avenir' program (ANR-10-LABX-04-01) through the Environmental Epigenomics Platform and the 'projets de recherche exploratoires du CeMEB 2018' project 'Epigenetics of inbreeding depression (EPID)'. This study is set within the framework of the 'Laboratoires d'Excellences (LABEX)' TULIP (ANR-10-LABX-41). BQR UPVD provided funding for the Nanoject III Programmable Nanoliter Injector., FIOCRUZ, ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: [SDE]Environmental Sciences
Abstract: Introduction As for many transmissible diseases non-pharmacological interventions are one of the most effective ways to control schistosoma infections. One of theses, the control of the intermediate host, is also recognized by WHO as a key element to eradication of the disease in humans. Biomphalaria snails can show remarkable resistance to schistosomes and prevalence is low in snail populations even in regions where the parasite is highly present in the vertebrate host.Resistance is a heritable trait, but it shows also high plasticity e.g., snails can be become resistant to the same parasite strain after a primary infection. One of the components of heritable plasticity is epigenetic information that refers to the heritable but reversible changes in gene function, and one of the bearers of epigenetic information is DNA methylation. We reasoned that modifying DNA methylation in the snail would have potentially positive effects on resistance traits. Methods We developed chemical DNA methylation modulators to which the snails were exposed to modify their pan-genomic methylation and we established a method for targeted DNA methylation modifications based on dCas9/Crispr. For heritability of resistance measure we used epigenetic recombinant inbred lines (EpiRILs) and experimental infections. Results We applied a dCas9-SunTag-DNMT3A complex and synthetic sgRNA to transfect B. glabrata embryos and observed an increase of CpG methylation at the target site in 50% of the hatching snails. DNA methylations were also introduced in an inbred B.glabrata line by chemical treatment in F0. This led to phenotypic variation in F3 and methylation differences in F3. Both increase and decrease (up to 100% and down to 20% prevalence from 86% control) of infection success indicating variation in complex resistance/compatibility trait. Conclusions We show that DNA methylation can be modified in B.glabrata both chemically and dCas-based, and pan-genomic or targeted. These modifications produce heritable phenotypic variants and have an influence on infection susceptibility confirming the epigenetic component of this trait. A rational of DNA methylation-based vector control will be presented.
Published: 2022

12. Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

Author: Jose Salguero-Linares, Irene Serrano, Nerea Ruiz-Solani, Marta Salas-Gómez, Ujjal Jyoti Phukan, Victor Manuel González, Martí Bernardo-Faura, Marc Valls, David Rengel, Nuria S. Coll, Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Agence Nationale de la Recherche (France), Région Midi-Pyrénées, Labex TULIP, European Research Council, University of Barcelona, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Georg-August-University = Georg-August-Universität Göttingen, Centre for Research in Agricultural Genomics (CRAG), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de pharmacologie et de biologie structurale (IPBS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), fellowship PID2019-108595RBI00 funded by Spanish MCIN/AEI/10.13039/501100011033 (to N.S.C. and M.V.), fellowship BES-2017-080210 funded by MCIN/AEI/10.13039/501100011033 and by ``ESF Investing in your future' (to J.S.-L.), FPU19/03778 funded by MU (o Ministerio de Universidades) (to N.R.S.), by the ``Severo Ochoa Programme for Centres of Excellence in R&D' (SEV-2015-0533 and CEX2019-000902-S funded by MCIN/AEI/10.13039/501100011033), and by the CERCA Programme/Generalitat de Catalunya. Work at the LIPM was supported by the INRA SPE department (AAP2014), the Re ' gion Midi-Pyre ' ne ' es (grant 13050322), grants PID2019-108595RB-I00 funded by MCIN/AEI/10.13039/501100011033, AGL2016-78002-R funded by MCIN/AEI/10.13039/501100011033 and by ``ERDF A way of making Europe', ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
Subjects: hypersensitive response, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Arabidopsis thaliana, Arabidopsis, Pseudomonas syringae, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Effector-triggered immunity, pattern-triggered immunity, Pattern-triggered immunity, Plant immunity, effector-triggered immunity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Plant Immunity, Molecular Biology, Plant Diseases, Cell Death, Arabidopsis Proteins, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Cell death indicator, cell death indicator, Hypersensitive response, Immunitat de les plantes, Plants immunity
Abstract: Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response (HR). This type of cell death occurs precisely at the site of pathogen recognition, and it is restricted to a few cells. Extensive research has shed light on how plant immune receptors are mechanistically activated. However, two central key questions remain largely unresolved: how does cell death zonation take place, and what are the mechanisms that underpin this phenomenon? Consequently, bona fide transcriptional indicators of HR are lacking, which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation. In this study, to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana–Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity. Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes, expression profiles, and biological processes derived from tissue undergoing HR and that of its surroundings. Furthermore, we generated a pipeline based on concatenated pairwise comparisons between time, zone, and treatment that enabled us to define 13 robust transcriptional HR markers. Among these genes, the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death. This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria, opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level., Research at CRAG was supported by grants PID2019-108595RB-I00 funded by MCIN/AEI/10.13039/501100011033 and AGL2016-78002-R funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” (to N.S.C. and M.V.); fellowship PID2019-108595RB-I00 funded by Spanish MCIN/AEI/10.13039/501100011033 (to N.S.C. and M.V.); fellowship BES-2017-080210 funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future” (to J.S.-L.); FPU19/03778 funded by MU (o Ministerio de Universidades) (to N.R.-S.); by the “Severo Ochoa Programme for Centres of Excellence in R&D” (SEV-2015-0533 and CEX2019-000902-S funded by MCIN/AEI/10.13039/501100011033); and by the CERCA Programme/Generalitat de Catalunya. Work at the LIPM was supported by the INRA SPE department (AAP2014), the Région Midi-Pyrénées (grant 13050322), and the French Laboratory of Excellence project “TULIP” (ANR-10-LABX-41; ANR-11-IDEX-0002-02). I.S. was supported by an AgreenSkills fellowship within the EU Marie-Curie FP7 COFUND People Programme (grant agreement 267196).
Published: 2022
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13. The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor

Author: Koen J. F. Verhoeven, Slavica Ivanovic, Fleur Gawehns, Christoph Grunau, Patrice David, Nelia Luviano, Cristian Chaparro, Céline Cosseau, Paola B. Arimondo, Marie Lopez, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Pierre Fabre (Centre de R&D Pierre Fabre), PIERRE FABRE, Netherlands Institute of Ecology (NIOO-KNAW), Chimie biologique épigénétique - Epigenetic Chemical Biology (EpiCBio), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported by Wellcome Trust strategic award [107475/Z/15/Z] and by a PhD grant to NL from the Region Occitanie (EPIPARA project) and the University of Perpignan Via Domitia graduate school ED305. With the support of LabEx CeMEB, an ANR 'Investissements d’avenir' program (ANR-10-LABX-04-01) through the Environmental Epigenomics Platform and the 'projets de recherche exploratoires du CeMEB 2018' project 'Epigenetics of inbreeding depression (EPID)'. This study is set within the framework of the 'Laboratoires d'Excellences (LABEX)' TULIP (ANR‐10‐LABX‐41)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Pharmacochimie de la Régulation Epigénétique du Cancer (ETaC), PIERRE FABRE-Centre National de la Recherche Scientifique (CNRS), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Royal Netherlands Academy of Arts and Sciences (KNAW), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), and Terrestrial Ecology (TE)
Subjects: [SDV]Life Sciences [q-bio], Bisulfite sequencing, DNA Methyltransferase Inhibitor, Locus (genetics), [CHIM.THER]Chemical Sciences/Medicinal Chemistry, QH426-470, Biology, Plan_S-Compliant-OA, Epigenesis, Genetic, Epigenome, chemistry.chemical_compound, 03 medical and health sciences, 0302 clinical medicine, Epigenetic inheritance, Genetics, Animals, Biomphalaria glabrata, Epimutation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, Epigenetics, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 0303 health sciences, Mollusks, Biomphalaria, Research, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Phenotypic trait, Methylation, DNA Methylation, biology.organism_classification, Invertebrates, 5-Methylcytosine, DNMT inhibitors, chemistry, Mollusca, international, 030220 oncology & carcinogenesis, DNA methylation, 030217 neurology & neurosurgery
Abstract: Background 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. Results Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. Conclusions Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.
Published: 2021
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14. HpaP Sequesters HrpJ, an Essential Component of Ralstonia solanacearum Virulence That Triggers Necrosis in Arabidopsis

Author: Aurélie Le Ru, Stéphane Genin, Fabrice Roux, Narjes Razavi, Céline Henry, Marie Turner, Fabienne Vailleau, David Rengel, C. Sabbagh, Fabien Lonjon, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41 French Ministry of National Education and Research, Lebanon ('Municipalite de Nabatieh'), Lebanon ('Association de Specialisation et d'Orientation Scientifique'), INRA Plant Health and Environment division (SPE), French National Research Agency (ANR) : ANR-2010-JCJC-1710-01, and Occitanie Regional Council
Subjects: bacterial pathogenesis, genome-wide association mapping, Physiology, Mutant, Virulence, 03 medical and health sciences, proteomics, Arabidopsis, plant responses to pathogens, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Secretion, Pathogen, 030304 developmental biology, 0303 health sciences, Ralstonia solanacearum, biology, 030306 microbiology, Effector, arabidopsis thaliana, food and beverages, General Medicine, biology.organism_classification, Cell biology, secretome, type III secretion control, Agronomy and Crop Science, effectors
Abstract: International audience; The Gram-negative bacterium Ralstonia solanacearum, the causal agent of bacterial wilt, is a worldwide major crop pathogen whose virulence strongly relies on a type III secretion system (T3SS). This extracellular apparatus allows the translocation of proteins, called type III effectors (T3Es), directly into the host cells. To date, very few data are available in plant-pathogenic bacteria concerning the role played by type III secretion (T3S) regulators at the posttranslational level. We have demonstrated that HpaP, a putative T3S substrate specificity switch protein of R. solanacearum, controls T3E secretion. To better understand the role of HpaP on T3S control, we analyzed the secretomes of the GMI1000 wild-type strain as well as the hpaP mutant using a mass spectrometry experiment (liquid chromatography tandem mass spectrometry). The secretomes of both strains appeared to be very similar and highlighted the modulation of the secretion of few type III substrates. Interestingly, only one type III-associated protein, HrpJ, was identified as specifically secreted by the hpaP mutant. HrpJ appeared to be an essential component of the T3SS, essential for T3S and pathogenicity. We further showed that HrpJ is specifically translocated in planta by the hpaP mutant and that HrpJ can physically interact with HpaP. Moreover, confocal microscopy experiments demonstrated a cytoplasmic localization for HrpJ once in planta. When injected into Arabidopsis thaliana leaves, HrpJ is able to trigger a necrosis on 16 natural accessions. A genome-wide association mapping revealed a major association peak with 12 highly significant single-nucleotide polymorphisms located on a plant acyl-transferase.
Published: 2020
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15. Host effects in high ectomycorrhizal diversity tropical rainforests on ultramafic soils in New Caledonia

Author: Sarah Gigante, Thomas Ibanez, Laurent Maggia, Julie Goxe, Kelly Letellier, Stéphane McCoy, Véronique Gourmelon, Monique Gardes, Jennifer Read, Jean-Michel Bellanger, Fabian Carriconde, Equipe Sol & Végétation (SolVeg), Institut Agronomique Néo-Calédonien (IAC), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Vale Nouvelle-Calédonie, Partenaires INRAE, School of Biological Sciences, University of East Anglia [Norwich] (UEA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Labex TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02
Subjects: 0106 biological sciences, F40 - Écologie végétale, Biodiversity, Plant Science, Rainforest, Biology, 010603 evolutionary biology, 01 natural sciences, Ectosymbiosis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Forêt tropicale humide, Ectomycorrhizal fungi, Champignon du sol, Ecology, Evolution, Behavior and Systematics, Ultramafic soils, New caledonian rainforests, Ecology, Ecological Modeling, P34 - Biologie du sol, Tropics, Species diversity, High fungal diversity, Arillastrum, respiratory system, 15. Life on land, biology.organism_classification, Biodiversity hotspot, Ectomycorhize, Cortinarius, Host preference, Biodiversité, Host density, human activities, Communauté végétale, 010606 plant biology & botany
Abstract: International audience; Tropical rainforests have been thought to have low prevalence and diversity of ectomycorrhizal symbioses. However, to date, tropical regions have been poorly sampled for ectomycorrhizal fungi. Here, we investigated ectomycorrhizal fungal community diversity and the role of host plants in shaping this diversity in three main ultramafic rainforests in New Caledonia, an archipelago renowned for its exceptional plant diversity and recognized as a biodiversity hotspot. Sampling of ectomycorrhizal root tips and fruit bodies in Nothofagus aequilateralis-dominated, Arillastrum gummiferum-dominated and mixed rainforests showed high fungal diversity with, in total, 28 lineages and 311 operational taxonomic units (OTUs), of which 95% might be endemic. We also found that host preference and host density influenced ectomycorrhizal community composition and contributed to the high fungal diversity of New Caledonian rainforests. Finally, the/cortinarius lineage dominated the below- and above-ground communities, which suggests that this lineage plays a central role in ultramafic ecosystems functioning.
Published: 2019
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16. Phylogeny and divergence dating of the ladybird beetle tribe Coccinellini Latreille (Coleoptera: Coccinellidae: Coccinellinae)

Author: Lúcia Massutti de Almeida, Karen Salazar, Gael J. Kergoat, Romain Nattier, Alexandra Magro, Alice Michel-Salzat, Pascaline Chifflet‐Belle, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidade Federal do Parana [Curitiba] (UFPR), Universidade Federal do Paraná (UFPR), Laboratório de Sistemática e Bioecologia de Coleoptera, Departamento de Zoologia, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The financial support in the doctoral studies to Karen Salazar was provided by the government agency Colciencias-Colombia (program number 756-2016). Alexandra Magro was supported by the ‘Laboratoires d’Excellence’ LabEx TULIP (ANR-10-LABX-0041) and CEBA (ANR-10-LABX-0025), and Lucia M. Almeida by CNPq.(308992/2017-2)., ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: 0106 biological sciences, 0303 health sciences, biology, [SDV]Life Sciences [q-bio], Tribe (biology), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Divergence, 03 medical and health sciences, Coccinellini, Coccinellinae, Phylogenetics, Evolutionary biology, Insect Science, Coccinellidae, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: International audience; We reconstruct a comprehensively sampled molecular phylogeny for the second most species-rich tribe of the ladybird beetle family Coccinellidae, the charismatic Coccinellini. We analysed a dataset consisting of five nuclear and three mitochondrial gene fragments from 150 taxa to provide a detailed phylogeny and estimates of historical divergence times using Bayesian relaxed clocks and primary fossil calibrations and an assessment of the evolution of feeding habits. The results of phylogenetic analyses provide strong support for the monophyly of the tribe Coccinellini, highlight the existence of four major clades and most sampled Coccinellini genera (30 out of 34) were recovered monophyletic. Our dating analyses suggest an Early Cretaceous origin for Coccinellidae at ca. 140 millions years ago (Ma) and a Late Cretaceous origin for the tribe Coccinellini at ca. 83.8 Ma. Ancestral character state estimation of feeding habits highlights a high level of phylogenetic niche conservatism on aphids and indicates that the most common recent ancestor of Coccinellini likely also fed on aphids. Our reconstruction of feeding habits and assessment of the aphid fossil record suggests that the diversification of Coccinellini paralleled that of Aphididae, although with substantial variation in host-breadth and the tendency for a few specialized lineages towards non-aphid feeding.
Published: 2021
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17. The Ecology of the Genome and the Dynamics of the Biological Dark Matter

Author: Anne Nguyen, Sébastien Gourbière, Alheli Flores-Ferrer, Sylvain Glémin, Olivier Panaud, Jean-Marc Deragon, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Sussex, This study is set within the framework of the 'Laboratoires d’Excellences (LABEX)' TULIP (ANR-10-LABX-41). The funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Statistics and Probability, DNA Copy Number Variations, Retrotransposon, Biology, Biological dark matter, Genome, General Biochemistry, Genetics and Molecular Biology, Bernouilli equation, Evolution, Molecular, 03 medical and health sciences, Negative selection, 0302 clinical medicine, Copy-number variation, Genome Ecology, General Immunology and Microbiology, Transcriptional and Post-transcriptional Gene Silencing, Host (biology), Applied Mathematics, Eukaryota, food and beverages, General Medicine, Genomics, Sexual reproduction, Evolvability, Copy Number Variations, 030104 developmental biology, Retrotransposons, Evolutionary biology, Modeling and Simulation, DNA Transposable Elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: International audience; Transposable elements (TEs) are essential components of the eukaryotic genomes. While mostly deleterious, evidence is mounting that TEs provide the host with beneficial adaptations. How ’selfish’ or ’parasitic’ DNA persists until it helps species evolution is emerging as a major evolutionary puzzle, especially in asexual taxa where the lack of sex strongly impede the spread of TEs. Since occasional but unchecked TE proliferations would ultimately drive host lineages toward extinction, asexual genomes are typically predicted to be free of TEs, which contrasts with their persistence in asexual taxa. We designed innovative ’Eco-genomic’ models that account for both host demography and within-host molecular mechanisms of transposition and silencing to analyze their impact on TE dynamics in asexual genome populations. We unraveled that the spread of TEs can be limited to a stable level by density-dependent purifying selection when TE copies are over-dispersed among lineages and the host demographic turn-over is fast. We also showed that TE silencing can protect host populations in two ways; by preventing TEs with weak effects to accumulate or by favoring the elimination of TEs with large effects. Our predictions may explain TE persistence in known asexual taxa that typically show fast demography and where TE copy number variation between lineages is expected. Such TE persistence in asexual taxa potentially has important implications for their evolvability and the preservation of sexual reproduction.
Published: 2021
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18. Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Author: Phillips, Helen, R. P., Bach, Elizabeth M., Bartz, Marie L. C., Bennett, Joanne, Beugnon, Rémy, Briones, Maria J. I., Brown, George, Ferlian, Olga, Gongalsky, Konstantin B., Guerra, Carlos A., König-Ries, Birgitta, Holdsworth, Andrew R., Coors, Anja, Crotty, Felicity V., Crumsey, Jasmine M., Dávalos, Andrea, Diaz Cosin, Darío J., Loss, Scott R., Dobson, Annise M., Dominguez, Anahí, Esteban Duhour, Andrés, Schirrmann, Michael, Eekeren, Nick van, Holmstrup, Martin, Emmerling, Christoph, Falco, Liliana B., Fernández, Rosa, Fonte, Steven J., Fragoso, Carlos, Franco, André L. C., Marichal, Raphael, Fusilero, Abegail T., Moreno, Gerardo, Geraskina, Anna P., Gholami, Shaieste, Hopfensperger, Kristine N., González, Grizelle, Gundale, Michael J., Gutiérrez López, Mónica, Hackenberger, Branimir K., Hackenberger, Davorka K., Hernández, Luis M., Hirth, Jeff R., Morón-Ríos, Alejandro, Huerta Lwanga, Esperanza, Huhta, Veikko, Hurisso, Tunsisa T., Iannone III, Basil V., Iordache, Madalina, Ramirez, Kelly S., Irmler, Ulrich, Minamiya, Yukio, Ivask, Mari, Jesus Lidon, Juan B., Motohiro, Hasegawa, Johnson-Maynard, Jodi L., Joschko, Monika, Kaneko, Nobuhiro, Kanianska, Radoslava, Keith, Aidan M., Kernecker, Maria L., Scharenbroch, Bryant C., Koné, Armand W., Kooch, Yahya, Hendrik Moos, Jan, Muys, Bart, Kukkonen, Sanna T., Lalthanzara, H., Lammel, Daniel R., Lebedev, Iurii M., Le Cadre, Edith, Lincoln, Noa K., López-Hernández, Danilo, Neirynck, Johan, Krebs, Julia, Norgrove, Lindsey, Novo, Marta, Nuutinen, Visa, Choi, Amy, Nuzzo, Victoria, Schmidt, Olaf, Rahman, P. Mujeeb, Pansu, Johan, Paudel, Shishir, Pérès, Guénola, Pérez-Camacho, Lorenzo, Ponge, Jean-François, Orgiazzi, Alberto, Prietzel, Jörg, Wall, Diana H., Rapoport, Irina B., Imtiaz Rashid, Muhammad, Schröder, Boris, Rebollo, Salvador, Rodríguez, Miguel Á., Roth, Alexander M., Rousseau, Guillaume X., Rozen, Anna, Sayad, Ehsan, Schaik, Loes van, Brose, Ulrich, Seeber, Julia, Shashkov, Maxim P., Singh, Jaswinder, Smith, Sandy M., Steinwandter, Michael, Capowiez, Yvan, Szlavecz, Katalin, Russell, David, Talavera, José A., Trigo, Dolores, Decaëns, Thibaud, Tsukamoto, Jiro, Uribe-López, Sheila, Valença, Anne W. de, Virto, Iñigo, Wackett, Adrian A., Warren, Matthew W., Cavagnaro, Timothy R., Webster, Emily R., Wehr, Nathaniel H., Schwarz, Benjamin, Lavelle, Patrick, Wironen, Michael B., Wolters, Volkmar, Wu, Pengfei, Zenkova, Irina V. Z., Zhang, Weixin, Cameron, Erin K., Eisenhauer, Nico, Loreau, Michel, Mathieu, Jérôme, Mulder, Christian, Putten, Wim H. van der, Rillig, Matthias C., Matula, Radim, Thakur, Madhav P., Clause, Julia, Vries, Franciska T. de, Wardle, David A., Ammer, Sabine, Arai, Miwa, Ayuke, Fredrick O., Baker, Geoff H., Baretta, Dilmar, Barkusky, Dietmar, Hishi, Takuo, Beauséjour, Robin, Bedano, José C., Cluzeau, Daniel, Birkhofer, Klaus, Blanchart, Eric, Blossey, Bernd, Bolger, Thomas, Bradley, Robert L., Brossard, Michel, Burtis, James C., German Research Foundation, European Commission, Academy of Finland, Natural Sciences and Engineering Research Council of Canada, Federal Ministry of Education and Research (Germany), European Research Council, Labex TULIP, Agence Nationale de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Russian Foundation for Basic Research, Tarbiat Modares University, Aurora Organic Dairy, Slovak Research and Development Agency, Wageningen University and Research Centre, International Atomic Energy Agency, Fundação de Amparo à Pesquisa do Estado de São Paulo, Oklahoma State University, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Royal Canadian Geographical Society, Environmental Protection Agency (Ireland), University of Hawaii at Manoa, U.S. Navy, Department of Science and Technology (India), Department of Defense (US), Fundação de Amparo à Pesquisa e ao Desenvolvimento Científico e Tecnológico do Maranhão, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Ministry of Education, Youth and Sports (Czech Republic), Colorado Wheat Research Foundation, Zone Atelier Alpes, Austrian Science Fund, Rentenbank, Welsh Government, European Agricultural Fund for Rural Development, Finnish Ministry of Agriculture and Forestry, Science Foundation Ireland, University of Toronto, Haliburton Forest & Wildlife Reserve, Arts and Sciences, Northern Kentucky University, University of Innsbruck, Higher Education Commission (Pakistan), Kerala Forest Research Institute, Universidad Complutense de Madrid, Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Fondo para la Investigación Científica y Tecnológica (Argentina), Universidad Nacional de Luján, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fonds de Recherche du Québec, Institute for Environmental Science and Policy, University of Illinois, Casey Tree, College of Liberal Arts and Social Sciences, DePaul University, Comisión Interministerial de Ciencia y Tecnología, CICYT (España), Japan Society for the Promotion of Science, McKnight Foundation, Russian Academy of Sciences, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Ministère de l'Europe et des Affaires étrangères (France), Bavarian Ministry for Food, Agriculture and Forestry, Ministero dell'Istruzione, dell'Università e della Ricerca, Idaho Agricultural Experiment Station, Estonian Science Foundation, Ministry of the Environment, Conservation and Parks (Ontario), National Natural Science Foundation of China, and Australian Research Council
Abstract: Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change., H.R.P.P., B.K-R., and the sWorm workshops were supported by the sDiv [Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (DFG FZT 118)]. H.R.P.P., O.F. and N.E. acknowledge funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 677232 to NE). K.S.R. and W.H.v.d.P. were supported by ERC-ADV grant 323020 to W.H.v.d.P. Also supported by iDiv (DFG FZT118) Flexpool proposal 34600850 (C.A.G. and N.E.); the Academy of Finland (285882) and the Natural Sciences and Engineering Research Council of Canada (postdoctoral fellowship and RGPIN-2019-05758) (E.K.C.); German Federal Ministry of Education and Research (01LO0901A) (D.J.R.); ERC-AdG 694368 (M.R.); the TULIP Laboratory of Excellence (ANR-10-LABX-41) (M.L); and the BBSRC David Phillips Fellowship to F.T.d.V. (BB/L02456X/1). In addition, data collection was funded by the Russian Foundation for Basic Research (12-04-01538-а, 12-04-01734-a, 14-44-03666-r_center_a, 15-29-02724-ofi_m, 16-04-01878-a 19-05-00245, 19-04-00-609-a); Tarbiat Modares University; Aurora Organic Dairy; UGC(NERO) (F. 1-6/Acctt./NERO/2007-08/1485); Natural Sciences and Engineering Research Council (RGPIN-2017-05391); Slovak Research and Development Agency (APVV-0098-12); Science for Global Development through Wageningen University; Norman Borlaug LEAP Programme and International Atomic Energy Agency (IAEA); São Paulo Research Foundation - FAPESP (12/22510-8); Oklahoma Agricultural Experiment Station; INIA - Spanish Agency (SUM 2006-00012-00-0); Royal Canadian Geographical Society; Environmental Protection Agency (Ireland) (2005-S-LS-8); University of Hawai’i at Mānoa (HAW01127H; HAW01123M); European Union FP7 (FunDivEurope, 265171; ROUTES 265156); U.S. Department of the Navy, Commander Pacific Fleet (W9126G-13-2-0047); Science and Engineering Research Board (SB/SO/AS-030/2013) Department of Science and Technology, New Delhi, India; Strategic Environmental Research and Development Program (SERDP) of the U.S. Department of Defense (RC-1542); Maranhão State Research Foundation (FAPEMA 03135/13, 02471/17); Coordination for the Improvement of Higher Education Personnel (CAPES 3281/2013); Ministry of Education, Youth and Sports of the Czech Republic (LTT17033); Colorado Wheat Research Foundation; Zone Atelier Alpes, French National Research Agency (ANR-11-BSV7-020-01, ANR-09-STRA-02-01, ANR 06 BIODIV 009-01); Austrian Science Fund (P16027, T441); Landwirtschaftliche Rentenbank Frankfurt am Main; Welsh Government and the European Agricultural Fund for Rural Development (Project Ref. A AAB 62 03 qA731606); SÉPAQ, Ministry of Agriculture and Forestry of Finland; Science Foundation Ireland (EEB0061); University of Toronto (Faculty of Forestry); National Science and Engineering Research Council of Canada; Haliburton Forest & Wildlife Reserve; NKU College of Arts & Sciences Grant; Österreichische Forschungsförderungsgesellschaft (837393 and 837426); Mountain Agriculture Research Unit of the University of Innsbruck; Higher Education Commission of Pakistan; Kerala Forest Research Institute, Peechi, Kerala; UNEP/GEF/TSBF-CIAT Project on Conservation and Sustainable Management of Belowground Biodiversity; Ministry of Agriculture and Forestry of Finland; Complutense University of Madrid/European Union FP7 project BioBio (FPU UCM 613520); GRDC; AWI; LWRRDC; DRDC; CONICET (National Scientific and Technical Research Council) and FONCyT (National Agency of Scientific and Technological Promotion) (PICT, PAE, PIP), Universidad Nacional de Luján y FONCyT (PICT 2293 (2006)); Fonds de recherche sur la nature et les technologies du Québec (131894); Deutsche Forschungsgemeinschaft (SCHR1000/3-1, SCHR1000/6-1, 6-2 (FOR 1598), WO 670/7-1, WO 670/7-2, & SCHA 1719/1-2), CONACYT (FONDOS MIXTOS TABASCO/PROYECTO11316); NSF (DGE-0549245, DGE-0549245, DEB-BE-0909452, NSF1241932, LTER Program DEB-97–14835); Institute for Environmental Science and Policy at the University of Illinois at Chicago; Dean’s Scholar Program at UIC; Garden Club of America Zone VI Fellowship in Urban Forestry from the Casey Tree Endowment Fund; J.E. Weaver Competitive Grant from the Nebraska Chapter of The Nature Conservancy; The College of Liberal Arts and Sciences at Depaul University; Elmore Hadley Award for Research in Ecology and Evolution from the UIC Dept. of Biological Sciences, Spanish CICYT (AMB96-1161; REN2000-0783/GLO; REN2003-05553/GLO; REN2003-03989/GLO; CGL2007-60661/BOS); Yokohama National University; MEXT KAKENHI (25220104); Japan Society for the Promotion of Science KAKENHI (25281053, 17KT0074, 25252026); ADEME (0775C0035); Ministry of Science, Innovation and Universities of Spain (CGL2017-86926-P); Syngenta Philippines; UPSTREAM; LTSER (Val Mazia/Matschertal); Marie Sklodowska Curie Postdoctoral Fellowship (747607); National Science & Technology Base Resource Survey Project of China (2018FY100306); McKnight Foundation (14–168); Program of Fundamental Researches of Presidium of Russian Academy of Sciences (AААА-A18–118021490070–5); Brazilian National Council for Scientific and Technological Development (CNPq 310690/2017–0, 404191/2019–3, 307486/2013–3); French Ministry of Foreign and European Affairs; Bavarian Ministry for Food, Agriculture and Forestry (Project No B62); INRA AIDY project; MIUR PRIN 2008; Idaho Agricultural Experiment Station; Estonian Science Foundation; Ontario Ministry of the Environment, Canada; Russian Science Foundation (16-17-10284); National Natural Science Foundation of China (41371270); Australian Research Council (FT120100463); USDA Forest Service-IITF.
Published: 2021

19. Quantitative estimates of freshwater fish stocking practices by recreational angling clubs in France

Author: Carsten Riepe, Robert Arlinghaus, Rémy Lassus, Frédéric Santoul, Mathieu Buoro, Julien Cucherousset, Paul Millet, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Biology & Ecology of Fishes, Leibniz Institute of Freshwater Ecology & Inland Fisheries, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Division of Integrative Fisheries Management, Humbolt University, Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-13-EDIB-0002, Office Français pour la Biodiversité (OFB). Grant Number: SPECTRA, German Ministry of Education and Research. Grant Numbers: 01LC1320A, 033W046A, German Research Foundation (DFG). Grant Number: AR 712/4‐1, and Laboratoire d’Excellence (LABEX) TULIP. Grant Number: ANR‐10‐LABX‐41
Subjects: 0106 biological sciences, angling club, Fishing, Aquatic Science, 01 natural sciences, Stocking, Recreational fishing, 14. Life underwater, Recreation, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, biology, 010604 marine biology & hydrobiology, conservation, stock enhancement, 04 agricultural and veterinary sciences, biology.organism_classification, Fishery, Geography, fisheries management, recreational fisheries, 040102 fisheries, Freshwater fish, 0401 agriculture, forestry, and fisheries, Fisheries management, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Although freshwater fish stocking is widely used by managers, quantitative assessments of stocking practices are lacking in many countries. The general objective of the present study was to determine the quantity and characteristics of fish stocking in metropolitan France. Using a survey‐based approach, stocking practices for 2013 by recreational angling clubs in France were quantified, which represented the bulk of fish stocking undertaken in that year. Stocking was found to be practiced by 88.6% of angling clubs in France, representing, on average, 65% of their annual budget. Overall, 22 species were stocked, including 13 native and nine non‐native species, with strong variations among species in terms of life stages and body sizes used for stocking. Using Bayesian modelling, a total biomass of 2.029 t, representing approximately 90 million fishes, was estimated to be stocked in France in 2013. In terms of biomass, the most widely stocked species were rainbow trout Oncorhynchus mykiss (Walbaum), brown trout Salmo trutta L., roach Rutilus rutilus (L.), common carp Cyprinus carpio L. and northern pike Esox lucius L. A stocking volume of approximately 60 fishes or 1.5 kg of fish biomass per angler per year seems commonplace in industrialised countries for which data are available
Published: 2021
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20. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species: Intraspecific dispersal of C4 physiology

Author: Bianconi, Matheus E., Dunning, Luke T., Curran, Emma V., Hidalgo, Oriane, Powell, Robyn F., Mian, Sahr, Leitch, Ilia J., Lundgren, Marjorie R., Manzi, Sophie, Vorontsova, Maria S., Besnard, Guillaume, Osborne, Colin P., Olofsson, Jill K., Christin, Pascal-Antoine, European Research Council, Royal Society (UK), Agence Nationale de la Recherche (France), and Labex TULIP
Abstract: C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin., This study was funded by the European Research Council (grant no. ERC-2014-STG-638333), the Royal Society (grant no. RGF\EA\181050) and has benefited from ‘Investissements d'Avenir' grants managed by the Agence Nationale de la Recherche (CEBA, ref. ANR-10-LABX-25-01 and TULIP, ref. ANR-10-LABX-41). Edinburgh Genomics, which contributed to the sequencing, is partly supported through core grants from the NERC (grant no. R8/H10/ 56), MRC (grant no. MR/K001744/1) and BBSRC (grant no. BB/ J004243/1). P.A.C. is funded by a Royal Society University Research Fellowship (grant no. URF\R\180022)., 1. Introduction 2. Materials and methods (a) Sampling, sequencing and data filtering (b) Genome sizing and carbon isotope analyses (c) Assembly of organelle genomes and molecular dating (d) Phylogenetic analyses of the nuclear genome (e) Genetic structure (f) Genome composition 3. Results (a) Genome sizes (b) Time-calibrated organelle phylogenies (c) Nuclear phylogeny (d) Population structure and genome composition 4. Discussion (a) Limited seed dispersal in the region of origin (b) Widespread pollen flow and sweep of the C4 nuclear genome (c) Recurrent hybridization and polyploidization 5. Concluding remarks Data accessibility Authors' contributions Competing interests Funding Acknowledgements Footnotes
Published: 2020

21. Data describing the eco-physiological responses of twenty-four sunflower genotypes to water deficit

Author: Philippe Debaeke, Pierre Maury, Nicolas B. Langlade, Harold Duruflé, Nicolas Blanchet, Louise Gody, Pierre Casadebaig, Florie Gosseau, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, French National Research Agency : ANR SUNRISE ANR-11-BTBR-0005, MAS Seeds, ANRT, 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41, and Caussade Semences
Subjects: 0106 biological sciences, 0301 basic medicine, abiotic stress, Specific leaf area, Heterosis, [SDV]Life Sciences [q-bio], helianthus, phenotyping platform, drought stress, Biology, lcsh:Computer applications to medicine. Medical informatics, 01 natural sciences, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Agricultural and Biological Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Helianthus, lcsh:Science (General), Transpiration, Hybrid, 2. Zero hunger, Genetic diversity, Multidisciplinary, Abiotic stress, fungi, food and beverages, 15. Life on land, biology.organism_classification, Sunflower, 030104 developmental biology, Agronomy, [SDE]Environmental Sciences, lcsh:R858-859.7, 010606 plant biology & botany, lcsh:Q1-390
Abstract: This article presents experimental data describing the physiology and morphology of sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower and included both inbred lines and their hybrids.Drought stress was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen at INRA Toulouse (France). Here, we provide data including specific leaf area, osmotic potential and adjustment, carbon isotope discrimination, leaf transpiration, plant architecture: plant height, leaf number, stem diameter. We also provide leaf areas of individual organs through time and growth rate during the stress period, environmental data such as temperatures, wind and radiation during the experiment. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the physiological basis of heterosis. It is available on the following repository: https://doi.org/10.25794/phenotype/er6lPW7V Keywords: Helianthus, Abiotic stress, Phenotyping platform, Drought stress
Published: 2018
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22. Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia

Author: Maarten Koornneef, Angela M. Hancock, Fabrice Roux, Joachim Hermisson, Andrea Fulgione, Max Planck Institute for Plant Breeding Research (MPIPZ), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Mathematics and BioSciences Group, Faculty of Mathematics [Vienna], University of Vienna [Vienna]-University of Vienna [Vienna], Vienna Graduate School of Population Genetics (Austrian Science Fund, FWF) : DK W1225-B20, Deutsche Forschungsgemeinschaft Research Unit 'Natural selection in structured populations' : FOR 1078, HE 3266 3/2, European Research Council : CVI_ADAPT 638810, Max Planck Society Funding, LABEX TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, European Project: 304301,EC:FP7:PEOPLE,FP7-PEOPLE-2011-CIG,CLIMATE_ADAPTATION(2012), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, 0301 basic medicine, Arabidopsis thaliana, Population genetics, Admixture, madère, Biology, Relict, 010603 evolutionary biology, 01 natural sciences, Island, 03 medical and health sciences, genetique des populations, Propagule, Effective population size, Genetics, Contact zone, Groep Koornneef, Colonization, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, Demography, demography, population genetics, relict, admixture, island, Vegetal Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], eurasie, iles océan pacifique, 030104 developmental biology, Biological dispersal, Selective sweep, Biologie végétale, Founder effect
Abstract: International audience; The study of model organisms on islands may shed light on rare long-range dispersal events, uncover signatures of local evolutionary processes, and inform demographic inference on the mainland. Here, we sequenced the genomes of Arabidopsis thaliana samples from the oceanic island of Madeira. These samples include the most diverged worldwide, likely a result of long isolation on the island. We infer that colonization of Madeira happened between 70 and 85 ka, consistent with a propagule dispersalmodel (of size >= 10), or with an ecological window of opportunity. This represents a clear example of a natural long-range dispersal event in A. thaliana. Long-term effective population size on the island, rather than the founder effect, had the greatest impact on levels of diversity, and rates of coalescence. Our results uncover a selective sweep signature on the ancestral haplotype of a known translocation in Eurasia, as well as the possible importance of the low phosphorous availability in volcanic soils, and altitude, in shaping early adaptations to the island conditions. Madeiran genomes, sheltered from the complexities of continental demography, help illuminate ancient demographic events in Eurasia. Our data support a model in which two separate lineages of A. thaliana, one originating in Africa and the other from the Caucasus expanded and met in Iberia, resulting in a secondary contact zone there. Although previous studies inferred that the westward expansion of A. thaliana coincided with the spread of human agriculture, our results suggest that it happened much earlier (20-40 ka).
Published: 2018
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23. Direct and Indirect Visualization of Bacterial Effector Delivery into Diverse Plant Cell Types during Infection

Author: Tania Y. Toruño, Elizabeth Henry, Alain Jauneau, Laurent Deslandes, Gitta Coaker, Department of Plant Pathology, Cornell University, Institut Fédératif de Recherche 3450, Plateforme Imagerie TRI-Genotoul, Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), UPS, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), USDA National Institute of Food and Agriculture predoctoral fellowship : 2014-67011-21563, National Institutes of Health : RO1GM092772, ANR : ANR-15-CE20-0016-01, Laboratoire d'Excellence (LABEX) TULIP : ANR-10-LABX-41, région Occitanie/Pyrenees-Mediterranee (PRISM-Project), Cornell University [New York], Plateforme Imagerie, Université Toulouse III - Paul Sabatier (UT3), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, genetic structures, Virulence Factors, Green Fluorescent Proteins, Arabidopsis, Pseudomonas syringae, Ralstonia, Plant Science, Biology, In Brief, Microbiology, Type three secretion system, Green fluorescent protein, Epitopes, 03 medical and health sciences, Bacterial Proteins, Solanum lycopersicum, infection de la plante, Plant Cells, Tobacco, plant breeding, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, pathologie végétale, Pathogen, Plant Diseases, Ralstonia solanacearum, Vegetal Biology, défense cellulaire, Effector, Microbiology and Parasitology, fungi, food and beverages, Cell Biology, Plants, Genetically Modified, biology.organism_classification, Microbiologie et Parasitologie, eye diseases, Molecular Imaging, Plant Leaves, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Host-Pathogen Interactions, Breakthrough Reports, protection des cultures, Biologie végétale, amélioration des plantes
Abstract: To cause disease, diverse pathogens deliver effector proteins into host cells. Pathogen effectors can inhibit defense responses, alter host physiology, and represent important cellular probes to investigate plant biology. However, effector function and localization have primarily been investigated after overexpression in planta. Visualizing effector delivery during infection is challenging due to the plant cell wall, autofluorescence, and low effector abundance. Here, we used a GFP strand system to directly visualize bacterial effectors delivered into plant cells through the type III secretion system. GFP is a beta barrel that can be divided into 11 strands. We generated transgenic Arabidopsis thaliana plants expressing GFP1-10 (strands 1 to 10). Multiple bacterial effectors tagged with the complementary strand 11 epitope retained their biological function in Arabidopsis and tomato (Solanum lycopersicum). Infection of plants expressing GFP1-10 with bacteria delivering GFP11-tagged effectors enabled direct effector detection in planta. We investigated the temporal and spatial delivery of GFP11-tagged effectors during infection with the foliar pathogen Pseudomonas syringae and the vascular pathogen Ralstonia solanacearum. Thus, the GFP strand system can be broadly used to investigate effector biology in planta.
Published: 2017
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24. Legumes tolerance to rhizobia is not always observed and not always deserved

Author: Benjamin Gourion, Claire Benezech, Maëva Doudement, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR) : ANR-10-LABX-41, ANR-11-IDEX-0002-02, ANR-17-CE20-0013, and Labex TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Nitrogen, [SDV]Life Sciences [q-bio], Immunology, Niche, Biology, rhizobia, Microbiology, Rhizobia, 03 medical and health sciences, Symbiosis, Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Immunity, innate immunity, 030304 developmental biology, Mutualism (biology), Genetics, 0303 health sciences, Experimental evolution, Innate immune system, Host Microbial Interactions, 030306 microbiology, fungi, food and beverages, Fabaceae, legume, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, symbiosis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Root Nodules, Plant, Plant genes, Rhizobium
Abstract: International audience; Rhizobia display dual lifestyle. These bacteria are soil inhabitants but can also elicit the formation of a special niche on the root of legume plants, the nodules. In such organs, rhizobia can promote the growth of their host by providing them nitrogen they captured from atmosphere. All along the infection process, the plant innate immunity has to be controlled to maintain compatible interaction. However, nodulation does not always result in profit for the plant as compatible interactions include both nitrogen-fixing and non-fixing associations. In recent years, our knowledge on the mechanisms involved in the control of plant innate immunity during rhizobia-legume interactions has greatly improved notably by the identification of bacterial and plant genes activating or suppressing the plant defences. Surprisingly, results also demonstrated that in some cases, plant defence reactions result in abortion of the nodulation process despite that the rhizobial strain has all the genetic potential to establish mutualism. In such situation, experimental evolution approaches highlighted possible rapid switches of incompatible rhizobia either to mutualistic or parasitic behaviour. Here, we review this recent literature.
Published: 2020
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25. Disentangling local, metapopulation, and cross‐community sources of stabilization and asynchrony in metacommunities

Author: Jurek Kolasa, Claire de Mazancourt, Michel Loreau, Matthew P. Hammond, McMaster University Hamilton - Department of Biology, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), BIOSTASES - ERCANR LABEX TULIP, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 666971,H2020,ERC-2014-ADG,BIOSTASES(2015), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, Metacommunity, metacommunity, Multiple forms, Population, Beta diversity, Metapopulation, 010603 evolutionary biology, 01 natural sciences, Article, diversity, Diversity index, lcsh:QH540-549.5, partitioning, Ecosystem, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, Ecology, variability, 010604 marine biology & hydrobiology, diversity-stability, metapopulation, 15. Life on land, stability, Local community, diversity–stability, Geography, 13. Climate action, [SDE]Environmental Sciences, community, lcsh:Ecology, asynchrony, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Asynchronous fluctuations of populations are essential for maintaining stable levels of bio-mass and ecosystem function in landscapes. Yet, understanding the stabilization of metacommunities by asynchrony is complicated by the existence of multiple forms of asynchrony that are typically studied independently: Community ecologists, for instance, focus on asynchrony within and among local communities, while population ecologists emphasize asynchrony of populations in metapopulations. Still, other forms of asynchrony, such as that which underlies the spatial insurance effect, are not captured by any existing analytical frameworks. We therefore developed a framework that would in one analysis unmask the stabilizing roles of local communities and metapopulations and so unify these perspectives. Our framework shows that metacommunity stabilization arises from one local and two regional forms of asynchrony: (1) asynchrony among species of a local community, (2) asynchrony among populations of a metapopulation, and (3) cross-community asynchrony, which is between different species in different local communities and underlies spatial insurance. For each type of stabilization, we derived links to diversity indices and associated diversity-stability relationships. We deployed this framework in a set of rock pool invertebrate metacommunities in Discovery Bay, Jamaica, to partition sources of stabilization and test their dependence on diversity. Cross-community asynchrony was the dominant form of stabilization, accounting for >60% of total metacommunity stabilization despite being undetectable with existing frameworks. Environmental variation influenced types of stabilization through different mechanisms. pH and dissolved oxygen, for example, increased asynchrony by decorrelating local species, while salinity did so by changing the abundance structure of metapopulations. Lastly, all types of asynchrony depended strongly on different types of diversity (alpha, metapopulation, and beta diversity drove local, metapopulation, and cross-community asynchrony, respectively) to produce multiple diversity-stability relationships within metacommunities. Our new partition of metacommunity dynamics highlights how different elements-from local communities to metapopulations-combine to stabilize metacommunities and depend critically on contrasting environmental regimes and diversities. Understanding and balancing these sources of stability in dynamic landscapes is a looming challenge for the future. We suggest that synthetic frameworks which merge ecological perspectives will be essential for grasping and safeguarding the stability of natural systems.
Published: 2020
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26. Medicago-Sinorhizobium-Ralstonia Co-infection Reveals Legume Nodules as Pathogen Confined Infection Sites Developing Weak Defenses

Author: Pascal Ratet, Fabienne Vailleau, Fathi Berrabah, Jeoffrey George, Benjamin Gourion, Marine Milhes, Claire Benezech, Gaofei Jiang, Marie-Françoise Jardinaud, Alexandre Le Scornet, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique, Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR), Labex TULIP : ANR-10-LABX-41, ANR-11-IDEX-000202, ANR-17-CE20-0013, ANR-10-LABX-0040-SPS, ANR-11-IDEX-000302, Labex SPS : ANR-10-LABX-41, ANR-11-IDEX-000202, ANR-17-CE20-0013, ANR-10-LABX-0040-SPS, ANR-11-IDEX-000302, Departement Sante des Plantes et Environnement of the INRA, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Root nodule, cost of mutualism, [SDV]Life Sciences [q-bio], legumes, Sinorhizobium, rhizobia, symbiotic organ, General Biochemistry, Genetics and Molecular Biology, Microbiology, Rhizobia, 03 medical and health sciences, 0302 clinical medicine, Symbiosis, Medicago truncatula, medicine, Plant Immunity, Plant Diseases, Ralstonia solanacearum, Medicago, biology, food and beverages, Nodule (medicine), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, plant pathogen, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, nitrogen fixation, defense responses, medicine.symptom, General Agricultural and Biological Sciences, Root Nodules, Plant, 030217 neurology & neurosurgery, Sinorhizobium meliloti
Abstract: Summary Legumes have the capacity to develop root nodules hosting nitrogen-fixing bacteria, called rhizobia. For the plant, the benefit of the symbiosis is important in nitrogen-deprived conditions, but it requires hosting and feeding massive numbers of rhizobia. Recent studies suggest that innate immunity is reduced or suppressed within nodules [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ]; this likely maintains viable rhizobial populations. To evaluate the potential consequences and risks associated with an altered immuni`ty in the symbiotic organ, we developed a tripartite system with the model legume Medicago truncatula [ 11 , 12 ], its nodulating symbiont of the genus Sinorhizobium (syn. Ensifer) [ 13 , 14 ], and the pathogenic soil-borne bacterium Ralstonia solanacearum [ 15 , 16 , 17 , 18 ]. We show that nodules are frequent infection sites where pathogen multiplication is comparable to that in the root tips and independent of nodule ability to fix nitrogen. Transcriptomic analyses indicate that, despite the presence of the hosted rhizobia, nodules are able to develop weak defense reactions against pathogenic R. solanacearum. Nodule defense response displays specificity compared to that activated in roots. In agreement with nodule innate immunity, optimal R. solanacearum growth requires pathogen virulence factors. Finally, our data indicate that the high susceptibility of nodules is counterbalanced by the existence of a diffusion barrier preventing pathogen spreading from nodules to the rest of the plant.
Published: 2020
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27. Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources

Author: Bouchaib Khadari, Ahmed El Bakkali, Laila Essalouh, Christine Tollon, Christian Pinatel, Guillaume Besnard, Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Conservatoire Botanique National Méditerranéen de Porquerolles, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Institut national de la recherche agronomique [Maroc] (INRA Maroc), Etablissement Public Local (EPL), Maison des Agriculteurs, Association pour le Développement de l'Apiculture Provençale (ADAPI), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, OliveMed/Agropolis Fondation N° 1202-066 project through the Investissements d’avenir/Labex Agro ANR- 10-Labex-0001-01 managed by the French National Research Agency (ANR), LABEX TULIP (ANR-10-LABX-0041), CEBA (ANR-10-LABX-25-01)., ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Association pour le Developpement de l'Apiculture Provencale (ADAPI), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, Mediterranean climate, [SDV]Life Sciences [q-bio], Genetic resource management, ex situ collection of Porquerolles, Plant Science, lcsh:Plant culture, Biology, Diversification (marketing strategy), ressource génétique, 01 natural sciences, caractérisation moléculaire, [SHS]Humanities and Social Sciences, Crop, génotype méditerranéen, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Cultivar, Parentage analysis, olea europaea, ComputingMilieux_MISCELLANEOUS, Original Research, 2. Zero hunger, Genetic diversity, Vegetal Biology, Olea europaea L, food and beverages, 15. Life on land, Simple sequence repeat, Genetic structure, Core collection, 030104 developmental biology, Agronomy, [SDE]Environmental Sciences, Gene pool, germplasme, Biologie végétale, 010606 plant biology & botany
Abstract: International audience; Molecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification.
Published: 2019
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28. High prevalence of Schistosoma haematobium × Schistosoma bovis hybrids in schoolchildren in Côte d'Ivoire

Author: Olivier Rey, Jean-François Allienne, André Offianan Touré, H. Menan, William Yavo, Jürg Utzinger, Jean T. Coulibaly, Eliézer K. N’Goran, Giovanna Raso, Jérôme Boissier, Oliver Balmer, Etienne K. Angora, Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), Université Félix Houphouët-Boigny (UFHB), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Côte d'Ivoire, Réseau International des Instituts Pasteur (RIIP), Centre Suisse de Recherches Scientifiques en Cote d'Ivoire [Abidjan] (CSRS-CI), This work was financially supported by the Agence National de Recherche (ANR), which supports the Hybrid Swarm project (HySWARM) in Perpignan that is set within the frame of the ‘Laboratoire d'Excellence (LABEX)’ TULIP (ANR-10-LABX-41). Additional financial support was obtained by the Swiss National Science Foundation for EKA, JU and OB (grant no. 31003A_170113). EKA is a recipient of a Swiss Government Excellence Scholarship (ESKAS, grant no. 2017-0746) for which he is deeply grateful., Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), and Unité de Formation et de Recherche Biosciences
Subjects: 0301 basic medicine, Veterinary medicine, Côte d'Ivoire, 030231 tropical medicine, Schistosomiasis, law.invention, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, parasitic diseases, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, molecular analysis, Internal transcribed spacer, Polymerase chain reaction, Schistosoma, Hybrid, Schistosoma haematobium, hybrids, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Haplotype, Tropical disease, biology.organism_classification, medicine.disease, 3. Good health, Cote d'Ivoire, 030104 developmental biology, Infectious Diseases, Schistosoma bovis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Animal Science and Zoology, Parasitology
Abstract: Schistosomiasis is a neglected tropical disease, though it is highly prevalent in many parts of sub-Saharan Africa. While Schistosoma haematobium-bovis hybrids have been reported in West Africa, no data about Schistosoma hybrids in humans are available from Côte d'Ivoire. This study aimed to identify and quantify S. haematobium-bovis hybrids among schoolchildren in four localities of Côte d'Ivoire. Urine samples were collected and examined by filtration to detect Schistosoma eggs. Eggs were hatched and 503 miracidia were individually collected and stored on Whatman® FTA cards for molecular analysis. Individual miracidia were molecularly characterized by analysis of mitochondrial cox1 and nuclear internal transcribed spacer 2 (ITS 2) DNA regions. A mitochondrial cox1-based diagnostic polymerase chain reaction was performed on 459 miracidia, with 239 (52.1%) exhibiting the typical band for S. haematobium and 220 (47.9%) the S. bovis band. The cox1 and ITS 2 amplicons were Sanger sequenced from 40 randomly selected miracidia to confirm species and hybrids status. Among the 33 cox1 sequences analysed, we identified 15 S. haematobium sequences (45.5%) belonging to seven haplotypes and 18 S. bovis sequences (54.5%) belonging to 12 haplotypes. Of 40 ITS 2 sequences analysed, 31 (77.5%) were assigned to pure S. haematobium, four (10.0%) to pure S. bovis and five (12.5%) to S. haematobium-bovis hybrids. Our findings suggest that S. haematobium-bovis hybrids are common in Côte d'Ivoire. Hence, intense prospection of domestic and wild animals is warranted to determine whether zoonotic transmission occurs.
Published: 2019
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29. Brachypodium distachyon tar2l(hypo) mutant shows reduced root developmental response to symbiotic signal but increased arbuscular mycorrhiza

Author: Camille Ribeyre, Sandra Bensmihen, Benoit Lefebvre, Luis Buendia, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche : ANR-16-CE20-0025-01, Ministere de l'Enseignement Superieur et de la Recherche, LABEX TULIP : ANR-10-LABX-41, and INRA/SPE [LCAux]
Subjects: 0106 biological sciences, 0301 basic medicine, Short Communication, arbuscular mycorrhizal fungi, Plant Science, 01 natural sciences, 03 medical and health sciences, Symbiosis, Auxin, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, heterocyclic compounds, Lateral root formation, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, biology, Endosymbiosis, Auxin homeostasis, fungi, food and beverages, lipo-chitooligosaccharide, 15. Life on land, biology.organism_classification, Arbuscular mycorrhiza, 030104 developmental biology, chemistry, Brachypodium, Brachypodium distachyon, auxin, 010606 plant biology & botany
Abstract: International audience; Auxin is a major phytohormone that controls root development. A role for auxin is also emerging in the control of plant-microbe interactions, including for the establishment of root endosymbiosis between plants and arbuscular mycorrhizal fungi (AMF). Auxin perception is important both for root colonization by AMF and for arbuscule formation. AMF produce symbiotic signals called lipo-chitooligosaccharides (LCOs) that can modify auxin homeostasis and promote lateral root formation (LRF). Since Brachypodium distachyon (Brachypodium) has a different auxin sensitivity compared to other plant species, we wondered whether this would interfere with the effect of auxin in arbuscular mycorrhizal (AM) symbiosis. Here we tested whether tar2l(hypo) a Brachypodium mutant with an increase in endogenous auxin content is affected in LRF stimulation by LCOs and in AM symbiosis. We found that, in contrast to control plants, LCO treatment inhibited LRF of the tar2l(hypo) mutant. However, the level of AMF colonization and the abundance of arbuscules were increased in tar2l(hypo) compared to control plants, suggesting that auxin also plays a positive role in both AMF colonization and arbuscule formation in Brachypodium.
Published: 2019
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30. Pangenomic type III effector database of the plant pathogenic Ralstonia spp

Author: Fabienne Vailleau, C. Sabbagh, Alberto P. Macho, Stéphane Genin, Fabien Lonjon, Nemo Peeters, Sébastien Carrère, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Cell & Systems Biology, University of Toronto, Chinese Academy of Sciences (CAS), Municipality of Nabatieh, Association of Specialization and Scientific Orientation, Shanghai Center for Plant Stress Biology (Chinese Academy of Sciences), Chinese 1000 Talents Program, and Laboratoire d'Excellence (LABEX) TULIP : ANR-10-LABX-41
Subjects: 0106 biological sciences, Plant Immunity, lcsh:Medicine, computer.software_genre, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Type III effector, Ralstonia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, 030304 developmental biology, 0303 health sciences, Vegetal Biology, Database, biology, 030306 microbiology, Host (biology), Effector, General Neuroscience, Ralstonia solanacearum species complex, fungi, Bacterial wilt, lcsh:R, food and beverages, General Medicine, Gene Annotation, Genome project, biology.organism_classification, General Agricultural and Biological Sciences, computer, Biologie végétale, 010606 plant biology & botany
Abstract: BackgroundThe bacterial plant pathogenicRalstoniaspecies belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex” gathering three newly defined species. Like many other Gram negative plant pathogens,Ralstoniapathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).MethodsExpert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors.ResultsWe curated the T3E repertoires of 12 plant pathogenicRalstoniastrains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenicRalstoniastrains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.
Published: 2019
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31. Endosymbiotic Sinorhizobium meliloti modulate Medicago root susceptibility to secondary infection via ethylene

Author: Fabienne Maillet, Chrystel Gibelin-Viala, Jacques Batut, David Rengel, Catherine Masson-Boivin, Clare Gough, Fernando Sorroche, Christian Chervin, Anne-Marie Garnerone, Lan Zou, Mathilda Walch, Véréna Poinsot, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), ANR ‘Nice Crops’ project (ANR‐14‐CE18‐0008‐02), ANR AOI (ANR‐15‐CE20‐0004‐01), China Scholarship Council, ‘Laboratoire d'Excellence (LABEX)’ TULIP (ANR‐10‐LABX‐41)., European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National Polytechnique de Toulouse - INPT (FRANCE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, 0301 basic medicine, Agronomie, Physiology, Secondary infection, [SDV]Life Sciences [q-bio], Mutant, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Plant Science, Root hair, Models, Biological, Plant Root Nodulation, Plant Roots, 01 natural sciences, Plant Epidermis, Rhizobia, Microbiology, 03 medical and health sciences, Ethylene, Bacterial Proteins, Symbiosis, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, Plant Diseases, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Volatile Organic Compounds, Sinorhizobium meliloti, Medicago, biology, Légume, food and beverages, Ethylenes, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Rhizobium, Infection, 010606 plant biology & botany
Abstract: International audience; A complex network of pathways coordinates nodulation and epidermal root hair infection in the symbiotic interaction between rhizobia and legume plants. Whereas nodule formation was known to be autoregulated, it was so far unclear whether a similar control is exerted on the infection process. We assessed the capacity of Medicago plants nodulated by Sinorhizobium meliloti to modulate root susceptibility to secondary bacterial infection or to purified Nod factors in split-root and volatile assays using bacterial and plant mutant combinations. Ethylene implication in this process emerged from gas production measurements, use of a chemical inhibitor of ethylene biosynthesis and of a Medicago mutant affected in ethylene signal transduction. We identified a feedback mechanism that we named AOI (for Autoregulation Of Infection) by which endosymbiotic bacteria control secondary infection thread formation by their rhizospheric peers. AOI involves activation of a cyclic adenosine 30,50-monophosphate (cAMP) cascade in endosymbiotic bacteria, which decreases both root infectiveness and root susceptibility to bacterial Nod factors. These latter two effects are mediated by ethylene. AOI is a novel component of the complex regulatory network controlling the interaction between Sinorhizobium meliloti and its host plants that emphasizes the implication of endosymbiotic bacteria in fine-tuning the interaction.
Published: 2019
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32. Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen‐fixing rhizobial symbiosis

Author: Arry Morel, J. Allan Downie, Nemo Peeters, Sebastian Pfeilmeier, Lena Stransfeld, Cyril Zipfel, Matthew Smoker, Jacob G. Malone, Sonali Roy, Jeoffrey George, University of Zurich, Zipfel, Cyril, The Sainsbury Laboratory [Norwich] (TSL), John Innes Centre [Norwich], Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Universität Zürich [Zürich] = University of Zurich (UZH), School of Biological Sciences, University of East Anglia [Norwich] (UEA), Norwich Research Park, BBSRC Institute Strategic Program Grant : BB/J004553/1, Gatsby Charitable Foundation, Laboratoire d'Excellence (LABEX) TULIP : ANR-10-LABX-41, and John Innes Foundation
Subjects: 0106 biological sciences, 0301 basic medicine, Root nodule, PAMPs, Arabidopsis, Plant Science, 580 Plants (Botany), 01 natural sciences, Plant Root Nodulation, Plant Roots, immunity, PRRs, symbiosis, disease resistance, biotechnology, 10126 Department of Plant and Microbial Biology, Gene Expression Regulation, Plant, 1110 Plant Science, Arabidopsis thaliana, Research Articles, Sinorhizobium meliloti, Vegetal Biology, biology, food and beverages, Plants, Genetically Modified, Medicago truncatula, Receptors, Pattern Recognition, 1305 Biotechnology, Rhizobium, Research Article, Plant disease resistance, Microbiology, Rhizobia, 03 medical and health sciences, Nitrogen Fixation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Immunity, 1102 Agronomy and Crop Science, 10211 Zurich-Basel Plant Science Center, Plant Diseases, Arabidopsis Proteins, fungi, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 030104 developmental biology, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract: Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad‐spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen‐associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae‐specific PRR ELONGATION FACTOR‐THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF‐Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF‐Tu‐derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR‐Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling., Plant Biotechnology Journal, 17 (3), ISSN:1467-7644, ISSN:1467-7652
Published: 2019
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33. The RIN ‐regulated Small Auxin‐Up RNA SAUR 69 is involved in the unripe‐to‐ripe phase transition of tomato fruit via enhancement of the sensitivity to ethylene

Author: Maria Aurineide Rodrigues, Isabelle Mila, Julien Pirrello, Jun-Hye Shin, Teva Vernoux, Mingchun Liu, Mondher Bouzayen, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Sichuan University [Chengdu] (SCU), Universidade de São Paulo = University of São Paulo (USP), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Labex TULIP (the Fellowship of Young Scientists for the Future), European Project: 679796,H2020,H2020-SFS-2015-2,TomGEM(2016), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), and École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, 0301 basic medicine, Ethylene, Transcription, Genetic, Physiology, Mutant, Arabidopsis, Down-Regulation, Plant Science, 01 natural sciences, Plant Roots, 03 medical and health sciences, chemistry.chemical_compound, Solanum lycopersicum, Auxin, Gene Expression Regulation, Plant, ComputingMilieux_MISCELLANEOUS, Plant Proteins, chemistry.chemical_classification, Sl-SAUR69, Tomato (Solanum lycopersicum), biology, Indoleacetic Acids, fungi, food and beverages, Ripening, Biological Transport, RIN, Ethylenes, Proton Pumps, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Plants, Genetically Modified, Cell biology, Up-Regulation, 030104 developmental biology, Onset of fruit ripening, chemistry, RNA, Plant, Fruit, Ectopic expression, Polar auxin transport, Climacteric, Developmental transition, 010606 plant biology & botany, Signal Transduction
Abstract: International audience; Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to the initiation of the ripening process remain elusive, although the presumed role of active hormone interplay has often been postulated. To unravel the putative role of auxin in the unripe-to-ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl-SAUR69, previously identified as a RIN target gene, using reverse genetics approaches. Auxin signalling undergoes dramatic decline at the onset of ripening in wild-type fruit, but not in the nonripening rin mutant. Sl-SAUR69 exhibits reduced expression in rin and its up-regulation results in premature initiation of ripening, whereas its down-regulation extends the time to ripening. Overexpression of Sl-SAUR69 reduces proton pump activity and polar auxin transport, and ectopic expression in Arabidopsis alters auxin transporter abundance, further arguing for its active role in the regulation of auxin transport. The data support a model in which Sl-SAUR69 represses auxin transport, thus generating auxin minima, which results in enhanced ethylene sensitivity. This defines a regulation loop, fed by ethylene and auxin as the main hormonal signals and by RIN and Sl-SAUR69 as modulators of the balance between the two hormones.
Published: 2019
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34. Adaptation to plant communities across the genome of Arabidopsis thaliana

Author: Claudia Bartoli, Baptiste Mayjonade, Nina-Coralie Hautekèete, Fabrice Roux, Léa Frachon, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Napoli Federico II, University of Zürich [Zürich] (UZH), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, AGROCAMPUS OUEST [Le Rheu], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Zurich, Wright, Stephen, Roux, Fabrice, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes, International Society for Molecular Plant-Microbe Interactions (IS-MPMI). INT., Dipartimento di Biologia, Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Lille, Region Midi-Pyrenees (CLIMARES project), LABEX TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, University of Naples Federico II = Università degli studi di Napoli Federico II, Universität Zürich [Zürich] = University of Zurich (UZH), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: 0106 biological sciences, Evolution, plant-plant interactions, Adaptation, Biological, Arabidopsis, Context (language use), Biology, 580 Plants (Botany), 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 1311 Genetics, Behavior and Systematics, Interaction network, 1312 Molecular Biology, Genetics, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 10211 Zurich-Basel Plant Science Center, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Ecosystem, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Local adaptation, 2. Zero hunger, Abiotic component, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Community, Ecology, fungi, food and beverages, Plant community, 15. Life on land, biology.organism_classification, 10121 Department of Systematic and Evolutionary Botany, 1105 Ecology, Evolution, Behavior and Systematics, Evolutionary biology, Genome-Environment Association, France, Adaptation, Genome, Plant, local adaptation, community ecology
Abstract: Associate Editor: Stephen Wright; International audience; Despite the importance of plant-plant interactions on plant community dynamics and crop yield, our understanding of the adaptive genetics underlying these interactions is still limited and deserves to be investigated in the context of complex and diffuse interactions occurring in plant assemblages. Here, based on 145 natural populations of Arabidopsis thaliana located in south-west of France and characterized for plant communities, we conducted a Genome-Environment Association analysis to finely map adaptive genomic regions of A. thaliana associated with plant community descriptors. To control for correlated abiotic environment effects, we also characterized the populations for a set of biologically meaningful climate and soil variables. A nonnegligible fraction of top single nucleotide polymorphisms was associated with both plant community descriptors and abiotic variables, highlighting the importance of considering the actual abiotic drivers of plant communities to disentangle genetic variants for biotic adaptation from genetic variants for abiotic adaptation. The adaptive loci associated with species abundance were highly dependent on the identity of the neighboring species suggesting a high degree of biotic specialization of A. thaliana to members of its plant interaction network. Moreover, the identification of adaptive loci associated with a-diversity and composition of plant communities supports the ability of A. thaliana to interact simultaneously with multiple plant neighbors, which in turn can help to understand the role of community-wide selection. Altogether, our study highlights that dissecting the genetic basis underlying plant-plant interactions at a regional scale while controlling for abiotic confounding factors can help understanding the adaptive mechanisms modulating natural plant assemblages.
Published: 2019
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35. Legume Nodules: Massive Infection in the Absence of Defense Induction

Author: Pascal Ratet, Benjamin Gourion, Fathi Berrabah, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), rench National Research Agency under an Investments for the Future program : ANR-10-LABX-0040-SPS, ANR-11-IDEX-0003-02, Labex TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, ANR-17-CE20-0013, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), and ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017)
Subjects: 0106 biological sciences, 0301 basic medicine, Root nodule, Physiology, [SDV]Life Sciences [q-bio], Plant Immunity, Biology, 01 natural sciences, Microbiology, Rhizobia, 03 medical and health sciences, Symbiosis, Immunity, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, fungi, food and beverages, Nodule (medicine), Fabaceae, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Biological Evolution, 030104 developmental biology, bacteria, Rhizobium, medicine.symptom, Root Nodules, Plant, Agronomy and Crop Science, Bacteria, 010606 plant biology & botany
Abstract: Plants of the legume family host massive intracellular bacterial populations in the tissues of specialized organs, the nodules. In these organs, the bacteria, named rhizobia, can fix atmospheric nitrogen and transfer it to the plant. This special metabolic skill provides to the legumes an advantage when they grow on nitrogen-scarce substrates. While packed with rhizobia, the nodule cells remain alive, metabolically active, and do not develop defense reactions. Here, we review our knowledge on the control of plant immunity during the rhizobia-legume symbiosis. We present the results of an evolutionary process that selected both divergence of microbial-associated molecular motifs and active suppressors of immunity on the rhizobial side and, on the legume side, active mechanisms that contribute to suppression of immunity.
Published: 2019
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36. The m 6 A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

Author: Michèle Laudié, Moaine El Baidouri, Jacinthe Azevedo, Sylvie Lahmy, Christel Llauro, Tao Xu, Aurore Attina, Dominique Pontier, Claire Picart, François Roudier, Thierry Lagrange, Marie-Christine Carpentier, Christophe Hirtz, Lisha Shen, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire des organismes photosynthétiques (UMR8186), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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)-Centre National de la Recherche Scientifique (CNRS), Sciences pour l'environnement (SPE), Centre National de la Recherche Scientifique (CNRS)-Université Pascal Paoli (UPP), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Institute of Research in Biotherapy, Laboratory of Biochemistry and Clinical Proteomics, French National Research Agency (ANR)Centre National de la Recherche Scientifique (CNRS)Universite de Perpignan Via Domitia National University of SingaporeTemasek Life Sciences Laboratory ENS de Lyon 'Laboratoires d'Excellences (LABEX)' TULIP, ANR-11-BSV6-0010,TRANSLATOR,la voie de signalisation TOR et la traduction chez les plantes(2011), ANR-10-LABX-0032,LaSIPS,ANR-10-LABX-0040-LaSIPS(2010), Université Pascal Paoli (UPP)-Centre National de la Recherche Scientifique (CNRS), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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 de Strasbourg (UNISTRA), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), 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), and Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)
Subjects: 0106 biological sciences, Regulation of gene expression, 0303 health sciences, Ecology, Polyadenylation, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Plant Science, Cleavage and polyadenylation specificity factor, Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 01 natural sciences, Biochemistry, Genetics and Molecular Biology (miscellaneous), Chromatin, Cell biology, Gene expression profiling, Transcriptome, 03 medical and health sciences, Transcription (biology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.
Published: 2019
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37. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development

Author: Gaudioso-Pedraza, R, Beck, M, Frances, L, Kirk, P, Ripodas, C, Niebel, A, Oldroyd, GED, Benitez-Alfonso, Y, de Carvalho-Niebel, F, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), Leeds University : 110 French Laboratoire d'Excellence (Labex) TULIP post-doctoral grant 'Young Scientists for the Future', AgreenSkills fellowship : 2013609398, BBSRC DTP : BB/M011151/1, Royal Society, EPSRC : EF/M027740/1, Leverhulme Trust : RPG-2016-136, ANR COME-IN grant : ANR-14-CE35-0007-01, TULIP grant : ANR-10-LABX-41, and European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula beta-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing beta-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.
Published: 2018
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38. A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale

Author: Léa Frachon, Claudia Bartoli, Sébastien Carrère, Olivier Bouchez, Adeline Chaubet, Mathieu Gautier, Dominique Roby, Fabrice Roux, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Génétique Animale (DEPT GA), Institut National de la Recherche Agronomique (INRA), Region Midi-Pyrenees (CLIMARES project), LABEX TULIP : ANR-10-LABX-41, ANR-1-IDEX-0002-02, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0301 basic medicine, cartographie génomique, arabidopsis thaliana, bayesian hierarchical model, climate change, genome-environment association analysis, local adaptation, pool-Seq, spatial grain, Climate change, Plant Science, Biology, lcsh:Plant culture, genome–environment association analysis, 03 medical and health sciences, lcsh:SB1-1110, ComputingMilieux_MISCELLANEOUS, Local adaptation, Ecological niche, Genetic diversity, Global warming, 15. Life on land, 030104 developmental biology, 13. Climate action, Evolutionary biology, Genetic marker, Spatial ecology, adaptation au changement climatique, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome-environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.
Published: 2018
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39. Evolutionary History of Plant LysM Receptor Proteins Related to Root Endosymbiosis

Author: Clare Gough, Ludovic Cottret, Benoit Lefebvre, Jean-Jacques Bono, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41, ANR 'NICE CROPS' : ANR-14-CE18-0008-02, and ANR 'WHEATSYM' : ANR-16-CE20-0025-01
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, Vegetal Biology, LYR3, [SDV]Life Sciences [q-bio], fungi, LysM domain, kinase domain, NFP, nodulation, arbuscular mycorrhization, lipochitooligosaccharide, food and beverages, lipo-chitooligosaccharide, Plant Science, lcsh:Plant culture, LYK3, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Perspective, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Biologie végétale, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; LysM receptor-like kinases (LysM-RLKs), which are specific to plants, can control establishment of both the arbuscular mycorrhizal (AM) and the rhizobium-legume (RL) symbioses in response to signal molecules produced, respectively, by the fungal and bacterial symbiotic partners. While most studies on these proteins have been performed in legume species, there are also important findings that demonstrate the roles of LysM-RLKs in controlling symbiosis in non-legume plants. Phylogenomic studies, which have revealed the presence or absence of certain LysM-RLKs among different plant species, have provided insight into the evolutionary mechanisms underlying both the acquisition and the loss of symbiotic properties. The role of a key nodulation LysM-RLK, NFP/NFR5, in legume plants has thus probably been co-opted from an ancestral role in the AM symbiosis, and has been lost in most plant species that have lost the ability to establish the AM or the RL symbiosis. Another LysM-RLK, LYK3/NFR1, that controls the RL symbiosis probably became neo-functionalised following two rounds of gene duplication. Evidence suggests that a third LysM-RLK, LYR3/LYS12, is also implicated in perceiving microbial symbiotic signals, and this protein could have roles in symbiosis and/or plant immunity in different plant species. By focusing on these three LysM-RLKs that are widespread in plants we review their evolutionary history and what this can tell us about the evolution of both the RL and the AM symbioses.
Published: 2018
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40. Parallels between experimental and natural evolution of legume symbionts

Author: Eduardo P. C. Rocha, Camille Clerissi, Stéphane Cruveiller, Clémence Genthon, Mingxing Tang, Lionel Moulin, Catherine Masson-Boivin, Matthew A. Parker, Marie Touchon, Delphine Capela, Céline Lopez-Roques, Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique des génomes - Genetics of Genomes (UMR 3525), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), Binghamton University [SUNY], State University of New York (SUNY), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), French National Research Agency : ANR-12-ADAP-0014-01, ANR-16-CE20-0011-01, the 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41, France Genomique National infrastructure - 'Investissement d'avenir' program : ANR-10-INBS-09, ANR-12-ADAP-0014,SHAPE,Design de nouveaux rhizobia par évolution expérimentale: vers une compréhension de l'adaptation des bactéries à l'environnement plante(2012), ANR-16-CE20-0011,REPLAY,Rejouer l'évolution des rhizobia: vers un cadre conceptuel et pratique pour le design de nouveaux symbiotes fixateurs(2016), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique des génomes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Genome evolution, Symbiogenesis, Science, [SDV]Life Sciences [q-bio], 030106 microbiology, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, Article, Rhizobia, Population genomics, 03 medical and health sciences, Negative selection, lcsh:Science, 030304 developmental biology, Comparative genomics, 0303 health sciences, Experimental evolution, Multidisciplinary, biology, 030306 microbiology, Cupriavidus taiwanensis, General Chemistry, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Horizontal gene transfer, lcsh:Q, Adaptation, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis., It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.
Published: 2018
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41. In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana

Author: Léa Frachon, Carine Huard-Chauveau, Matthieu Barret, Claudia Bartoli, Sébastien Carrère, Baptiste Mayjonade, Dominique Roby, Catherine Zanchetta, Olivier Bouchez, Mylene Rigal, Fabrice Roux, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Region Midi-Pyrenees (CLIMARES project), LABEX TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, Metaprogramme MEM (INRA, Metabar programme), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire des Interactions Plantes Micro organismes, Université Fédérale Toulouse Midi-Pyrénées, Centre INRA de Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, 0106 biological sciences, In situ, [SDV]Life Sciences [q-bio], Arabidopsis, Biological pest control, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Microbiology, Plant Roots, 01 natural sciences, Article, 03 medical and health sciences, Arabidopsis thaliana, Pathogen, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Plant Diseases, 030304 developmental biology, 0303 health sciences, Microbial pathogenesis, Bacteria, biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Microbiota, Species diversity, biology.organism_classification, Plant Leaves, 030104 developmental biology, Potential biomarkers, Host invasion, France, Microbiota composition, 010606 plant biology & botany
Abstract: A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root and leaf associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in South-West of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota OTUs. This result suggests that the potential biomarkers controlling pathogen’s invasion are highly dynamic.
Published: 2018
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42. Whole-genome landscape of Medicago truncatula symbiotic genes

Author: David Latrasse, Christine Lelandais-Brière, William Marande, Hélène Bergès, Frédéric Debellé, Stéphane Muños, Julia Buitink, Sébastien Carrère, Andreas Niebel, Mohamed Zouine, Pascal Gamas, Jonathan Kreplak, Moussa Benhamed, Olivier Bouchez, Sandra Moreau, Marie-Françoise Jardinaud, Stéphane Cauet, Thomas Blein, Jérôme Gouzy, Carine Satgé, Erika Sallet, Yann Pecrix, Céline Lopez-Roques, Margot Zahm, Baptiste Mayjonade, Aurélie Bérard, Florian Frugier, S. Evan Staton, Martin Crespi, Abdelhafid Bendahmane, Céline Chantry-Darmon, Magali Perez, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of British Columbia, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ANR grants EPISYM (grant no. ANR-15-CE20-0002), NODCCAAT (no. ANR-15-CE20-0012), REGULEG (no. ANR-15-CE20-0001), the ‘Laboratoire d’Excellence (LABEX)’ TULIP (no. ANR-10-LABX-41), the LABEX Saclay Plant Sciences (SPS, no. ANR-10-LABX-40) and the European Research Council (no. ERC-SEXYPARTH), and we made use of data previously generated in the ANR SYMbiMICS (ANR-08-GENO-106) and the INRA SPE EPINOD projects. The sequencing platform was supported by France Génomique National infrastructure (grant no. ANR-10-INBS-09) and by the GET-PACBIO programme (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020)., Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-15-CE20-0002,EPISYM,Régulations épigénétiques dans le développement de nodules symbiotiques racinaires chez les légumineuses(2015), ANR-15-CE20-0012,NODCCAAT,Comprendre le mode d'action du facteur de transcription NF-YA1 spécifique de l'intearction symbiotique rhizobium-légumineuses chez Medicago truncatula(2015), ANR-15-CE20-0001,REGULEG,Identification des régulateurs participant à la plasticité d'adaptation des graines de légumineuses aux changements environnementaux(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0044,CEMAM,Center of Excellence in Multifunctional Architectured Materials(2010), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Laboratoire des Interactions Plantes Micro organismes, Université Fédérale Toulouse Midi-Pyrénées, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), UR Etude du Polymorphisme des Génomes végétaux, Centre National de Génotypage (CNG), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], RNA, Untranslated, [SDV]Life Sciences [q-bio], Symbiose, Sequence assembly, Genomics, Plant Science, Computational biology, 01 natural sciences, Genome, DNA sequencing, Epigenesis, Genetic, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Genome-wide analysis of gene expression, Gene Expression Regulation, Plant, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Rhizobial symbiosis, Whole genome sequencing, Symbiote, Génome, biology, phytogénétique, DNA Methylation, biology.organism_classification, 030104 developmental biology, RNA, Plant, Multigene Family, Next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Root Nodules, Plant, Genome, Plant, 010606 plant biology & botany
Abstract: This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PSQE00000000.; Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
Published: 2018
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43. Melanin-based coloration and host–parasite interactions under global change

Author: Lisa Jacquin, Julien Gasparini, Simon Blanchet, Andrew P. Hendry, A. Boniface, Jessica Côte, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), McGill University = Université McGill [Montréal, Canada], Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Sorbonne Universités (COMUE), Agence de l’Eau Adour-Garonne AEAG at Toulouse University [PHYPAT-RECAC16P0068], McGill University (QCBS international award), NSERC, Toulouse University (Fyssen fellowship and Idex starting grant) [IDEX-V5RJACQ], AEAG grant [PHYPAT-RECAC16P0068-RECAC17P0154], CNRS EC2CO grant (ECODYN national program), LABEX TULIP [ANR-11-IDEX-0002-02], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, genetic structures, Climate Change, [SDV]Life Sciences [q-bio], Color, Context (language use), Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Melanin, 03 medical and health sciences, melanin pigments, evolution, Parasite hosting, Animals, sexual selection, Review Articles, General Environmental Science, Melanins, Natural selection, animal coloration, General Immunology and Microbiology, Host (biology), Pigmentation, Animal coloration, General Medicine, immunity, disease risk, behaviour, host-parasite interactions, 030104 developmental biology, Evolutionary biology, Sexual selection, Vertebrates, Disease risk, sense organs, ecology, General Agricultural and Biological Sciences
Abstract: International audience; The role of parasites in shaping melanin-based colour polymorphism, and the consequences of colour polymorphism for disease resistance, remain debated. Here we review recent evidence of the links between melanin-based coloration and the behavioural and immunological defences of vertebrates against their parasites. First we propose that (1) differences between colour morphs can result in variable exposure to parasites, either directly (certain colours might be more or less attractive to parasites) or indirectly (variations in behaviour and encounter probability). Once infected, we propose that (2) immune variation between differently coloured individuals might result in different abilities to cope with parasite infection. We then discuss (3) how these different abilities could translate into variable sexual and natural selection in environments varying in parasite pressure. Finally, we address (4) the potential role of parasites in the maintenance of melanin-based colour polymorphism, especially in the context of global change and multiple stressors in human altered environments. Because global change will probably affect both coloration and the spread of parasitic diseases in the decades to come, future studies should take into account melanin-based coloration to better predict the evolutionary responses of animals to changing disease risk in human-altered environments.
Published: 2018
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44. The Ralstonia solanacearum type-III effector RipAY targets plant redox regulators to suppress immune responses

Author: Sang, Yuying, Wang, Yaru, Ni, Hong, Cazalé, Anne-Claire, She, Yi-Min, Peeters, Nemo, Macho, Alberto P., Chinese Academy of Sciences (CAS), Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Shanghai Center for Plant Stress Biology (Chinese Academy of Sciences), National Natural Science Foundation of China : 31571973, Chinese 1000 Talents Program, and LABEX TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02
Subjects: Cell Nucleus, Virulence, Green Fluorescent Proteins, fungi, Arabidopsis, food and beverages, Original Articles, thioredoxin, biochemical phenomena, metabolism, and nutrition, Thioredoxins, Bacterial Proteins, Plant Cells, redox, Tobacco, Ralstonia solanacearum, Type III Secretion Systems, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cysteine, glutathione, plant immunity, Oxidation-Reduction, gamma-Glutamylcyclotransferase, type III effector, ralstonia
Abstract: International audience; The subversion of plant cellular functions is essential for bacterial pathogens to proliferate in host plants and cause disease. Most bacterial plant pathogens employ a type III secretion system to inject type III effector (T3E) proteins inside plant cells, where they contribute to the pathogen-induced alteration of plant physiology. In this work, we found that the Ralstonia solanacearum T3E RipAY suppresses plant immune responses triggered by bacterial elicitors and by the phytohormone salicylic acid. Further biochemical analysis indicated that RipAY associates in planta with thioredoxins from Nicotiana benthamiana and Arabidopsis. Interestingly, RipAY displays γ-glutamyl cyclotransferase (GGCT) activity to degrade glutathione in plant cells, which is required for the reported suppression of immune responses. Given the importance of thioredoxins and glutathione as major redox regulators in eukaryotic cells, RipAY activity may constitute a novel and powerful virulence strategy employed by R. solanacearum to suppress immune responses and potentially alter general redox signalling in host cells.
Published: 2018
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45. LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization

Author: Benoit Lefebvre, Luis Buendia, Ariane Girardin, Tongming Wang, Ludovic Cottret, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ANR 'WHEATSYM' : ANR-16-CE20-0025-01, 'Laboratoire d'Excellence (LABEX)' TULIP, ANR-10-LABX-41 Region Occitanie, INRA Department of Plant Health and Environment (SPE), Chinese Scholarship Council (CSC), and French 'Ministere de l'Enseignement Superieur et de la Recherche'
Subjects: 0106 biological sciences, 0301 basic medicine, Protein family, [SDV]Life Sciences [q-bio], Plant Science, Review, Biology, lcsh:Plant culture, 01 natural sciences, defense, symbiosis, MAMP, symbiotic signal, receptor ligand interaction, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, Extracellular, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Receptor, Genetics, Phylogenetic tree, Kinase, fungi, food and beverages, 3. Good health, 030104 developmental biology, chemistry, [SDE]Environmental Sciences, Peptidoglycan, 010606 plant biology & botany
Abstract: International audience; Members of plant specific families of receptor-like kinases (RLKs) and receptor-like proteins (RLPs), containing 3 extracellular LysMs have been shown to directly bind and/or to be involved in perception of lipo-chitooligosaccharides (LCO), chitooligosaccharides (CO), and peptidoglycan (PGN), three types of GlcNAc-containing molecules produced by microorganisms. These receptors are involved in microorganism perception by plants and can activate different plant responses leading either to symbiosis establishment or to defense responses against pathogens. LysM-RLK/Ps belong to multigenic families. Here, we provide a phylogeny of these families in eight plant species, including dicotyledons and monocotyledons, and we discuss known or putative biological roles of the members in each of the identified phylogenetic groups. We also report and discuss known biochemical properties of the LysM-RLK/Ps.
Published: 2018
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46. A novel tomato F-box protein, SlEBF3, is involved in tuning ethylene signaling during plant development and climacteric fruit ripening

Author: Julien Pirrello, Yao Chen, Heng Deng, Yongsheng Liu, Mondher Bouzayen, Ximena Chirinos, Sihua Zhu, Nan Li, Mingchun Liu, Sichuan University [Chengdu] (SCU), Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, National Key R&D Program of China (2016YFD0400100), National Natural Science Foundation of China (31772372), Labex TULIP (ANR-10- LABX-41), European Project: 679796,H2020,H2020-SFS-2015-2,TomGEM(2016), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, F-box protein, Ethylene, Ethylene signaling, Plant Science, 01 natural sciences, 03 medical and health sciences, Bimolecular fluorescence complementation, chemistry.chemical_compound, Abscission, Arabidopsis, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Post-transcriptional regulation, Tomato (Solanum lycopersicum), biology, food and beverages, Ripening, Cell Biology, biology.organism_classification, Fruit ripening, Cell biology, 030104 developmental biology, chemistry, biology.protein, Feedback loop, Climacteric, 010606 plant biology & botany
Abstract: International audience; Ethylene is instrumental to climacteric fruit ripening and EIN3 BINDING F‐BOX (EBF) proteins have been assigned a central role in mediating ethylene responses by regulating EIN3/EIL degradation in Arabidopsis. However, the role and mode of action of tomato EBFs in ethylene‐dependent processes like fruit ripening remains unclear. Two novel EBF genes, SlEBF3 and SlEBF4, were identified in the tomato genome, and SlEBF3 displayed a ripening‐associated expression pattern suggesting its potential involvement in controlling ethylene response during fruit ripening. SlEBF3 downregulated tomato lines failed to show obvious ripening‐related phenotypes likely due to functional redundancy among SlEBF family members. By contrast, SlEBF3 overexpression lines exhibited pleiotropic ethylene‐related alterations, including inhibition of fruit ripening, attenuated triple‐response and delayed petal abscission. Yeast‐two‐hybrid system and bimolecular fluorescence complementation approaches indicated that SlEBF3 interacts with all known tomato SlEIL proteins and, consistently, total SlEIL protein levels were decreased in SlEBF3 overexpression fruits, supporting the idea that the reduced ethylene sensitivity and defects in fruit ripening are due to the SlEBF3‐mediated degradation of EIL proteins. Moreover, SlEBF3 expression is regulated by EIL1 via a feedback loop, which supposes its role in tuning ethylene signaling and responses. Overall, the study reveals the role of a novel EBF tomato gene in climacteric ripening, thus providing a new target for modulating fleshy fruit ripening.
Published: 2018
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47. Strain-Specific Symbiotic Genes: A New Level of Control in the Intracellular Accommodation of Rhizobia Within Legume Nodule Cells

Author: Benjamin Gourion, Benoit Alunni, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Labex TULIP grant : ANR-10-LABX-41, ANR-11-IDEX-0002-02, Labex Saclay Plant Science grant : ANR-10-LABX-0040-SPS, Agence Nationale de la Recherche grant : ANR-17-CE20-0011-02, ANR-17-CE20-0013, ANR-17-CE20-0011,SymbiontCellCyc,Rôle du cycle cellulaire bactérien dans la fixation symbiotique d'azote chez les Légumineuses(2017), and ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017)
Subjects: 0106 biological sciences, 0301 basic medicine, Nodule (geology), MICROBIO, Physiology, [SDV]Life Sciences [q-bio], Intracellular Space, PBI, Biology, engineering.material, Genes, Plant, 01 natural sciences, Microbiology, Rhizobia, 03 medical and health sciences, Species Specificity, Plant Immunity, Symbiosis, Gene, Legume, Strain (chemistry), Fabaceae, General Medicine, biology.organism_classification, 030104 developmental biology, engineering, Root Nodules, Plant, Agronomy and Crop Science, Intracellular, 010606 plant biology & botany, Rhizobium
Abstract: This is a short commentary on the article by Wang et al. published in MPMI Vol. 31, No. 2, pages 240-248.
Published: 2018
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48. Development of a GAL4-VP16/UAS trans-activation system for tissue specific expression in Medicago truncatula

Author: Andreas Niebel, Charles Rosenberg, Mélanie Sicard, Sandra Bensmihen, Amélie Sevin-Pujol, Clare Gough, Marie-Christine Auriac, Agnes Lepage, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Bensmihen, Sandra, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41
Subjects: 0301 basic medicine, Golden Gate Cloning, Gene Expression, lcsh:Medicine, Plant Science, Biochemistry, Medicago, Arabidopsis thaliana, Cloning, Molecular, Promoter Regions, Genetic, lcsh:Science, Flowering Plants, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Vegetal Biology, Plant Anatomy, Eukaryota, food and beverages, Fabaceae, medicago truncatula, Plants, Legumes, Medicago truncatula, Experimental Organism Systems, Research Article, Transcriptional Activation, Brassica, Computational biology, Biology, Research and Analysis Methods, Genes, Plant, 03 medical and health sciences, Model Organisms, Plant and Algal Models, Gene Types, DNA-binding proteins, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulation, Molecular Biology Techniques, Molecular Biology, Gene, Transcription factor, Cloning, Reporter gene, Endodermis, lcsh:R, fungi, arabidopsis thaliana, Organisms, Biology and Life Sciences, Proteins, Promoter, biology.organism_classification, Regulatory Proteins, 030104 developmental biology, Trans-Activators, lcsh:Q, Pericycle, Biologie végétale, Transcription Factors, Reporter Genes
Abstract: International audience; Promoters with tissue-specific activity are very useful to address cell-autonomous and non cell autonomous functions of candidate genes. Although this strategy is widely used in Arabidopsis thaliana, its use to study tissue-specific regulation of root symbiotic interactions in legumes has only started recently. Moreover, using tissue specific promoter activity to drive a GAL4-VP16 chimeric transcription factor that can bind short upstream activation sequences (UAS) is an efficient way to target and enhance the expression of any gene of interest. Here, we developed a collection of promoters with different root cell layers specific activities in Medicago truncatula and tested their abilities to drive the expression of a chimeric GAL4-VP16 transcription factor in a trans-activation UAS: P-Glucuronidase (GUS) reporter gene system. By developing a binary vector devoted to modular Golden Gate cloning together with a collection of adapted tissue specific promoters and coding sequences we could test the activity of four of these promoters in trans-activation GAL4/UAS systems and compare them to "classical" promoter GUS fusions. Roots showing high levels of tissue specific expression of the GUS activity could be obtained with this trans-activation system. We therefore provide the legume community with new tools for efficient modular Golden Gate cloning, tissue specific expression and a trans-activation system. This study provides the ground work for future development of stable transgenic lines in Medicago truncatula.
Published: 2017
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49. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits

Author: Mondher Bouzayen, Mingchun Liu, Pierre Frasse, Guojian Hu, Jean-Pierre-Amans Routaboul, Elie Maza, James J. Giovannoni, Wei Deng, Benoît van der Rest, Zhengguo Li, Julia Vrebalov, Mohamed Zouine, Isabelle Mila, Baowen Huang, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), Genetic Engineering Research Center (GERC), Chongqing University (CHINA), Cornell University, Cornell University (USA), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Génomique et Biotechnologie des Fruits ( GBF ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, Institut National de la Recherche Agronomique ( INRA ), Genetic Engineering Research Center ( GERC ), Institut National Polytechnique de Toulouse - INPT (FRANCE), Génomique et Biotechnologie des Fruits - GBF (Castanet-Tolosan, France), Genetic Engineering Research Center - GERC (Chongqing, China), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Cornell University [New York], Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, USDA-ARS Robert W. Holley Center, United States Department of Agriculture, Boyce Thompson Institute, Labex TULIP (ANR-10-LABX-41), National Key Research and Development Program (2016YFD0400101), National Natural Science Foundation of China (31572175), ERASMUS MUNDUS program, Boyce Thompson Institute [Ithaca], Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and European Project: 679796,H2020,H2020-SFS-2015-2,TomGEM(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, fleshy fruit, Biodiversité et Ecologie, Ingénierie des aliments, Gene Expression, Plant Science, 01 natural sciences, Sepal, tomate, Solanum lycopersicum, RNA interference, MADS, Ovule, surexpression génique, MADS-box, Plant Proteins, 2. Zero hunger, Vegetal Biology, Cell wall, Fruit development, food and beverages, Ripening, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Phenotype, Cell biology, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], développement du fruit, Fleshy tissue, paroi cellulaire, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, gene overexpression, fruit charnu, MADS Domain Proteins, Flowers, Biology, Tomato, 03 medical and health sciences, transcription factors, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Gene Expression Profiling, 030104 developmental biology, Fruit, Ectopic expression, facteur de transcription, Biologie végétale, 010606 plant biology & botany
Abstract: International audience; MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3 , both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling high-lighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development.
Published: 2017
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50. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time

Author: Etienne Baron, Olivier Bouchez, Renaud Vitalis, Laurent Amsellem, Sébastien Carrère, Cyril Libourel, Fabrice Roux, Cédric Glorieux, Joy Bergelson, Marie Vidal, Léa Frachon, Romain Villoutreix, Carine Huard-Chauveau, Miguel Navascués, Valérie Le Corre, Dominique Roby, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Département de Génétique Animale [Toulouse], Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Ecology and Evolution [Chicago], University of Chicago, This work was funded by the Region Midi-Pyrenees (CLIMARES project), the INRA Sante des Plantes et Environnement department (RESURRECTION project), the INRA-ACCAF metaprogram (SELFADAPT project), the LABEX TULIP (ANR-10-LABX-41, ANR-11-IDEX-0002-02) and the National Institute of Health., ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), GeT PlaGe, Genotoul, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet Tolosan, France, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire des interactions plantes micro-organismes ( LIPMO ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 ( Evo-Eco-Paléo ), Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Biologie Computationnelle ( IBC ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut National de la Recherche Agronomique ( INRA ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, and Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, Population, Adaptation, Biological, Arabidopsis, Genome-wide association study, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic variation, Genetic Pleiotropy, Association mapping, education, Gene, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, fungi, food and beverages, Biological Evolution, Genetic architecture, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], 030104 developmental biology, Evolutionary biology, Genome-Wide Association Study
Abstract: International audience; Rapid phenotypic evolution of quantitative traits can occur within years, but its underlying genetic architecture remains uncharacterized. Here we test the theoretical prediction that genes with intermediate pleiotropy drive adaptive evolution in nature. Through a resurrection experiment, we grew Arabidopsis thaliana accessions collected across an 8-year period in six micro-habitats representative of that local population. We then used genome-wide association mapping to identify the single-nucleotide polymorphisms (SNPs) associated with evolved and unevolved traits in each micro-habitat. Finally, we performed a selection scan by testing for temporal differentiation in these SNPs. Phenotypic evolution was consistent across micro-habitats, but its associated genetic bases were largely distinct. Adaptive evolutionary change was most strongly driven by a small number of quantitative trait loci (QTLs) with intermediate degrees of pleiotropy; this pleiotropy was synergistic with the per-trait effect size of the SNPs, increasing with the degree of pleiotropy. In addition, weak selection was detected for frequent micro-habitat-specific QTLs that shape single traits. In this population, A. thaliana probably responded to local warming and increased competition, in part mediated by central regulators of flowering time. This genetic architecture, which includes both synergistic pleiotropic QTLs and distinct QTLs within particular micro-habitats, enables rapid phenotypic evolution while still maintaining genetic variation in wild populations.
Published: 2017
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