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1. 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

2. 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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3. 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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4. 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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5. 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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6. 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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7. 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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8. 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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9. 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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10. 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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11. 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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12. 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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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. 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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23. 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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24. 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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25. 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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26. The ERN1 transcription factor gene is a target of the CCaMK/CYCLOPS complex and controls rhizobial infection in Lotus japonicus

Author: Cerri, Marion, Wang, Quanhui, Stolz, Paul, Folgmann, Jessica, Frances, Lisa, Katzer, Katja, Li, Xiaolin, Heckmann, Anne, Wang, Trevor, Downie, J. Allan, Klingl, Andreas, de Carvalho-Niebel, Fernanda, Xie, Fang, Parniske, Martin, Genetics, Faculty of Biology, Ludwig-Maximilians University [Munich] (LMU), National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences [Changchun Branch] (CAS), University of Chinese Academy of Sciences, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Norwich Research Park, Institut of Food Research, Plant Development and Electron Microscopy, Faculty of Biology, NSFC : 31470344, French Laboratoire d'Excellence (Labex) TULIP : ANR-10-LABX-41, ANR-11-IDEX-0002-02, Agence Nationale de la Recherche (ANR) : ANR-14-CE35-0007-01 COME-IN, ANR-14-CE35-0007,COME-IN,Cell-specific reprogramming of legume roots for endosymbiotic infection(2014), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), European Project: 340904, Ludwig Maximilian University [Munich] (LMU), Chinese Academy of Sciences [Beijing] (CAS), John Innes Centre [Norwich], National Natural Science Foundation of China (NSFC) : 31470344, European Research Council (ERC) : 340904, Biotechnology and Biological Sciences Research Council (BBSRC) : BB/F010591/1, Biotechnology and Biological Sciences Research Council (BBSRC) : BBS/E/J/00000150, Ludwig Maximilians University of Munich, and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV]Life Sciences [q-bio], CCaMK, Plant Roots, Rhizobium infection, Gene Expression Regulation, Plant, Rhizobiaceae, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Plant Immunity, transcriptional regulation, Promoter Regions, Genetic, Genetic Association Studies, Disease Resistance, Plant Diseases, Plant Proteins, promoter analysis, root nodule symbiosis, fungi, lotus japonicus, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, ERN1, CYCLOPS, rhizobium japonicum, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, nitrogen fixation, Lotus, Transcription Factors
Abstract: International audience; Bacterial accommodation inside living plant cells is restricted to the nitrogen-fixing root nodule symbiosis. In many legumes, bacterial uptake is mediated via tubular structures called infection threads (ITs).To identify plant genes required for successful symbiotic infection, we screened an ethyl methanesulfonate mutagenized population of Lotus japonicus for mutants defective in IT formation and cloned the responsible gene, ERN1, encoding an AP2/ERF transcription factor. We performed phenotypic analysis of two independent L.japonicus mutant alleles and investigated the regulation of ERN1 via transactivation and DNA-protein interaction assays.In ern1 mutant roots, nodule primordia formed, but most remained uninfected and bacterial entry via ITs into the root epidermis was abolished. Infected cortical nodule cells contained bacteroids, but transcellular ITs were rarely observed. A subset exhibited localized cell wall degradation and loss of cell integrity associated with bacteroid spread into neighbouring cells and the apoplast.Functional promoter studies revealed that CYCLOPS binds in a sequence-specific manner to a motif within the ERN1 promoter and in combination with CCaMK positively regulates ERN1 transcription. We conclude that the activation of ERN1 by CCaMK/CYCLOPS complex is an important step controlling IT-mediated bacterial progression into plant cells.
Published: 2017
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27. Pollen dispersal slows geographical range shift and accelerates ecological niche shift under climate change

Author: François Rousset, Robin Aguilée, Gaël Raoul, Ophélie Ronce, 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), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), 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, 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 de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, ANR EVORANGE (ANR-09-PEXT-01102), ANR MeCC (ANR-13-ADAPT-0006), ANR SEAD (ANR-13-ADAPT-0011), ANR MODEVOL (ANR-13-JS01-0009), Labex TULIP (ANR-10-LABX-41), CALMIP Grant 2013-153, ANR-13-JS01-0009,MODEVOL,Modèles mathématiques pour la biologie évolutive(2013), ANR-09-PEXT-0011,EVORANGE,Comment l'évolution affecte-t-elle la dynamique d'extinction et de changements d'aire dans le contexte des changements globaux ? Implications pour les projections écologiques(2009), ANR-13-ADAP-0006,MeCC,Mécanismes de l'adaptation au Changement Climatique: comment plasticité phénotypique, micro-évolution et migration affecteront-elles la phénologie des arbres forestiers ?(2013), ANR-13-ADAP-0011,SEAD,Comment l'autofécondation affecte-t-elle l'adaptation : Conséquences génétiques et démographiques(2013), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-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)
Subjects: 0106 biological sciences, 0301 basic medicine, Climate Change, Niche, Climate change, adaptation, Biology, medicine.disease_cause, Models, Biological, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Pollen, Seed Dispersal, Genetic model, medicine, Ecosystem, ComputingMilieux_MISCELLANEOUS, Population Density, 2. Zero hunger, Ecological niche, Extinction threshold, Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Geography, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], spatial heterogeneity, Genetic Variation, 15. Life on land, Adaptation, Physiological, Spatial heterogeneity, Phenotype, 030104 developmental biology, PNAS Plus, 13. Climate action, Biological dispersal, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, gene flow, extinction threshold, cline
Abstract: International audience; Species may survive climate change by migrating to track favorable climates and/or adapting to different climates. Several quantitative genetics models predict that species escaping extinction will change their geographical distribution while keeping the same ecological niche. We introduce pollen dispersal in these models, which affects gene flow but not directly colonization. We show that plant populations may escape extinction because of both spatial range and ecological niche shifts. Exact analytical formulas predict that increasing pollen dispersal distance slows the expected spatial range shift and accelerates the ecological niche shift. There is an optimal distance of pollen dispersal, which maximizes the sustainable rate of climate change. These conclusions hold in simulations relaxing several strong assumptions of our analytical model. Our results imply that, for plants with long distance of pollen dispersal, models assuming niche conservatism may not accurately predict their future distribution under climate change.
Published: 2016
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28. Functional assignment to positively selected sites in the core type III effector RipG7 from \textitR \textitalstonia solanacearum: RipG7 evolution, structure/function

Author: Chiu-Ping Cheng, Maria Anisimova, Chien-Hui Li, Fabien Lonjon, Stéphane Genin, Ilona Kars, Fabienne Vailleau, Andrey V. Kajava, Nemo Peeters, Philippe Remigi, Keke Wang, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science [ETH Zürich] (D-INFK), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Centre National de la Recherche Scientifique (CNRS), Centre de recherches de biochimie macromoléculaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-IFR122-Centre National de la Recherche Scientifique (CNRS), National Taiwan University [Taiwan] (NTU), 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), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), and LABEX 'TULIP' ANR-10-LABX-41 COST Action SUSTAIN FA1208 China Scholarship Council ANR-07-JCJC-0133
Subjects: 0301 basic medicine, virulence fonction, LRR, Soil Science, Virulence, ralstonia solanacearum, Plant Science, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Type three secretion system, 03 medical and health sciences, Phylogenetics, positive selection, Botany, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Genetics, Ralstonia solanacearum, biology, Effector, fungi, food and beverages, medicago truncatula, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Medicago truncatula, Plant disease, Complementation, 030104 developmental biology, Agronomy and Crop Science, type III effector
Abstract: article présenté lors du congrès Plant Biology 2015 ; Minneapolis (Etats-Unis) - (2015-07-26 - 2015-07-30); International audience; The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R. solanacearum are the type III secretion system (T3SS) and its associated type III effectors (T3Es), translocated into the host cells. Of the conserved T3Es among R. solanacearum strains, the Fbox protein RipG7 is required for R. solanacearum pathogenesis on Medicago truncatula. In this work, we describe the natural ripG7 variability existing in the R. solanacearum species complex. We show that eight representative ripG7 orthologues have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M. truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely a result of the variability in the leucine-rich repeat (LRR) domain of RipG7. We identified 11 sites under positive selection in the LRR domains of RipG7. By studying the functional impact of these 11 sites, we show the contribution of five positively selected sites for the function of RipG7CMR15 in M. truncatula colonization.This work reveals the genetic and functional variation of the essential core T3E RipG7 from R. solanacearum.This analysis is the first of its kind on an essential disease-controlling T3E, and sheds light on the co-evolutionary arms race between the bacterium and its hosts.
Published: 2016
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29. Adaptation to climate through flowering phenology: a case study in Medicago truncatula

Author: Maxime Bonhomme, Jean Marie Prosperi, Nevin D. Young, Peter Tiffin, Nathalie Chantret, Concetta Burgarella, Joëlle Ronfort, Institut de Recherche pour le Développement (IRD), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), 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), Department of Plant Biology, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Department of plant pathology, INRA (French National Institute of Agronomical Research) Department of Genetics and Plant Breeding, ARCAD, a flagship project of the Agropolis Foundation, NSF : 1237993, French laboratory of excellence project (LABEX) 'TULIP' : ANR-10-LABX-41, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Burgarella, Concetta, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, association genetics, Acclimatization, Climate, mixed model, Quantitative Trait Loci, climate adaptation, Flowers, flowering time, candidate genes, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, adaptation au climat, 03 medical and health sciences, Africa, Northern, Genetic variation, Genetics, Ecology, Evolution, Behavior and Systematics, Models, Genetic, floraison, Ecology, Phenology, fungi, food and beverages, medicago truncatula, 15. Life on land, biology.organism_classification, Phenotype, phénologie, Medicago truncatula, Agricultural sciences, Europe, Genetics, Population, 030104 developmental biology, 13. Climate action, Multigene Family, Trait, Adaptation, Sciences agricoles
Abstract: AGAP : équipe GEpop; International audience; Local climatic conditions likely constitute an important selective pressure on genes underlying important fitness-related traits such as flowering time and in many species flowering phenology and climatic gradients strongly covary. To test whether climate shapes genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large M. truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both climate variables and flowering phenotypes. Unlike genome-wide studies, candidate gene approaches are expected to enrich for the number of meaningful trait associations because they specifically target genes that are known to affect the trait of interest. We found that flowering time mediates adaptation to climatic conditions mainly by variation at genes located upstream in the flowering pathways, close to the environmental stimuli. Variables related to the annual precipitation regime reflected selective constraints on flowering time genes better than the other variables tested (temperature, altitude, latitude or longitude). By comparing phenotype and climate associations, we identified 12 flowering genes as the most promising candidates responsible for phenological adaptation to climate. Four of these genes were located in the known flowering time QTL region on chromosome 7. However, climate and flowering associations also highlighted largely distinct gene sets, suggesting different genetic architectures for adaptation to climate and flowering onset.
Published: 2016
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30. Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula

Author: Carine Satgé, Marie-Françoise Jardinaud, Karine Gallardo, Marie-Christine Auriac, Ludovic Cottret, Erika Sallet, Céline Noirot, Sandra Moreau, Pascal Gamas, Gaëlle Lefort, Céline Remblière, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), 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-Université Fédérale Toulouse Midi-Pyrénées, 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, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), and INRA SPE EPINOD project, ANR EPISYM project, Laboratoire d’Excellence (LABEX) TULIP (ANR-10- LABX-41)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Bisulfite sequencing, Plant Science, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], Epigenetics, [MATH]Mathematics [math], Symbiosis, Gene, Plant Proteins, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, DNA Methylation, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, DNA demethylation, DNA methylation, [SDE]Environmental Sciences, biology.protein, Demethylase, Root Nodules, Plant, Reprogramming, 010606 plant biology & botany, Rhizobium
Abstract: The legume–Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation. Bisulphite sequencing coupled to genomic capture enabled the identification of 474 regions that are differentially methylated during nodule development, including nodule-specific cysteine-rich peptide genes. Decreasing DME expression by RNA interference led to hypermethylation and concomitant downregulation of 400 genes, most of them associated with nodule differentiation. Massive reprogramming of gene expression through DNA demethylation is a new epigenetic mechanism controlling a key stage of indeterminate nodule organogenesis during symbiotic interactions. The legume–Rhizobium symbiosis allows nitrogen fixation. Development of nodules is a finely regulated developmental process that involves a DNA demethylase called DEMETER, linking epigenetic regulation and symbiosis.
Published: 2016
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31. The Symbiosis-Related ERN Transcription Factors Act in Concert to Coordinate Rhizobial Host Root Infection

Author: Audrey Kelner, Monique Erard, Marion R. Cerri, Joëlle Fournier, Jiangqi Wen, Patrick H. Middleton, David G. Barker, Kirankumar S. Mysore, Fernanda de Carvalho-Niebel, Giles E. D. Oldroyd, Marie-Christine Auriac, Lisa Frances, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of California [San Diego] (UC San Diego), University of California, The Samuel Roberts Noble Foundation, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), ANR-14-CE35-0007-01 COME-IN, LABEX TULIP (grant nos. ANR-10-LABX-41 and ANR-11-IDEX-0002-02), Ludwig Maximilian University [Munich] (LMU), John Innes Centre [Norwich], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, French Ministry of Education, National Science Foundation (NSF)/NSF - Directorate for Biological Sciences (BIO) : 1127155, ANR-14-CE35-0007,COME-IN,Cell-specific reprogramming of legume roots for endosymbiotic infection(2014), 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, Root nodule, Transcription, Genetic, Physiology, Organogenesis, [SDV]Life Sciences [q-bio], Mutant, Plant Science, Plant Roots, 01 natural sciences, Plant Epidermis, Gene Expression Regulation, Plant, Mycorrhizae, Promoter Regions, Genetic, ComputingMilieux_MISCELLANEOUS, Plant Proteins, integumentary system, biology, Articles, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Phenotype, Medicago truncatula, Cell biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDE]Environmental Sciences, Rhizobium, Root Nodules, Plant, Protein Binding, Signal Transduction, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Rhizobia, 03 medical and health sciences, Symbiosis, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, otorhinolaryngologic diseases, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Transcription factor, Alleles, Plant Diseases, Base Sequence, biology.organism_classification, 030104 developmental biology, Mutation, sense organs, Transcription Factors, 010606 plant biology & botany
Abstract: International audience; Legumes improve their mineral nutrition through nitrogen-fixing root nodule symbioses with soil rhizobia. Rhizobial infection of legumes is regulated by a number of transcription factors, including ERF Required for Nodulation1 (ERN1). Medicago truncatula plants defective in ERN1 are unable to nodulate, but still exhibit early symbiotic responses including rhizobial infection. ERN1 has a close homolog, ERN2, which shows partially overlapping expression patterns. Here we show that ern2 mutants exhibit a later nodulation phenotype than ern1, being able to form nodules but with signs of premature senescence. Molecular characterization of the ern2-1 mutation reveals a key role for a conserved threonine for both DNA binding and transcriptional activity. In contrast to either single mutant, the double ern1-1 ern2-1 line is completely unable to initiate infection or nodule development. The strong ern1-1 ern2-1 phenotype demonstrates functional redundancy between these two transcriptional regulators and reveals the essential role of ERN1/ERN2 to coordinately induce rhizobial infection and nodule organogenesis. While ERN1/ERN2 act in concert in the root epidermis, only ERN1 can efficiently allow the development of mature nodules in the cortex, probably through an independent pathway. Together, these findings reveal the key roles that ERN1/ERN2 play at the very earliest stages of root nodule development.
Published: 2016
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32. Mitogenomics of Hesperelaea, an extinct genus of Oleaceae

Author: Cynthia Hong-Wa, Céline Van de Paer, Guillaume Besnard, Céline Jeziorski, 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), Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Formation Agronomique (ENFA), Claude E Phillips Herbarium, University of Delaware [Newark], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées, Regional Council Midi-Pyrenees [AAP 13053637, 2014-EDB-UT3-DOCT], LABEX TULIP [ANR-10-LABX-0041], 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, and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: 0301 basic medicine, Mitochondrial DNA, RNA, Mitochondrial, Oleaceae, [SDV]Life Sciences [q-bio], Lamiales, Sequence assembly, Genomics, Extinction, Biological, Genome, DNA sequencing, Mitochondrial Proteins, 03 medical and health sciences, Phylogenetics, Genetics, De novo assembly, Hesperelaea palmeri, ComputingMilieux_MISCELLANEOUS, Phylogeny, Plant Proteins, biology, Olive, General Medicine, biology.organism_classification, 030104 developmental biology, RNA, Plant, [SDE]Environmental Sciences, Genome, Mitochondrial, RNA, Herbarium specimen
Abstract: The recent developments in high-throughput DNA sequencing allowed major advances in organelle genomics. Assembly of mitochondrial genomes (hereafter mitogenomes) in higher plants however remains a challenge due to their large size and the presence of plastid-derived regions and repetitive sequences. In this study, we reconstructed the first mitogenome of Oleaceae using a herbarium specimen of the extinct genus Hesperelaea collected in 1875. Paired-end reads produced with the HiSeq technology (shotgun) in a previous study were re-used. With an approach combining reference-guided and de novo assembly, we obtained a circular molecule of 658,522 bp with a mean coverage depth of 35 ×. We found one large repeat (ca. 8 kb) and annotated 46 protein-coding genes, 3 rRNA genes and 19 tRNA genes. A phylogeny of Lamiales mitogenomes confirms Oleaceae as sister to a group comprising Lamiaceae, Phyrmaceae and Gesneriaceae. The Hesperelaea mitogenome has lower rates of synonymous and non-synonymous substitution compared to Nicotiana tabacum than other available mitogenomes of Lamiales. To conclude, we show that mitogenome reconstruction in higher plants is possible with shotgun data, even from poorly preserved DNA extracted from old specimens. This approach offers new perspectives to reconstruct plant phylogenies from mitochondrial markers, and to develop functional mitogenomics in Oleaceae.
Published: 2016
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33. Identification and functional characterization of two HOOKLESS genes in tomato (Solanum lycopersicum)

Author: Mingchun Liu, Salma Chaabouni, Islam El-Sharkawy, Julien Pirrello, Jean-Paul Roustan, 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 Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées, Association Université Populaire de Toulouse, Partenaires INRAE, and 'Laboratoire d'Excellence' (LABEX) TULIP [ANR-10-LABX-41]
Subjects: 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, Genes, Plant, Real-Time Polymerase Chain Reaction, Apical hook, Tomato, Hypocotyl, 03 medical and health sciences, Ethylene, Solanum lycopersicum, Auxin, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Gene, Plant Proteins, chemistry.chemical_classification, HOOKLESS, biology, Indoleacetic Acids, Genetic Complementation Test, fungi, food and beverages, Meristem, Ethylenes, biology.organism_classification, Cell biology, Complementation, 030104 developmental biology, Phenotype, chemistry, Mutation, Solanum, Agronomy and Crop Science
Abstract: International audience; The apical hook of dark-grown dicotyledonous plants results from asymmetric growth of the inner and outer sides of the upper part of the hypocotyl. This protective structure prevents damage of the shoot apical meristem and the young leaves as the seedling pushes through the soil. HOOKLESS (HLS1) of Arabidopsis was recognised as an ethylene response gene whose product is required for hook formation. We cloned two cDNAs from tomato, Sl-HLS1 and Sl-HLS2, and showed through the complementation of the Arabidopsis hls1 mutant that the encoded proteins are functional orthologs of At-HLS1. The genomic clones of Sl-HLS1 and Sl-HLS2 showed similar structure with two introns and three exons. While the data indicate complete functional redundancy between the two tomato HLS genes, only the expression of Sl-HLS2 is regulated by ethylene and auxin and the ethylene-induced expression of Sl-HLS2 is localised in the outer side of the hook while the auxin-responsive expression is not restricted to a specific side of the hook. 1-MCP, an inhibitor of ethylene signalling, inhibited auxin-enhanced accumulation of Sl-HLS2 mRNA in the apical hook suggesting that regulation of Sl-HLS2 by auxin is ethylene-dependent. The overexpression of tomato Sl-HLS1 and Sl-HLS2 in Arabidopsis confers hypersensitivity to ethylene. The data presented bring further insight into the complex ethylene-auxin interplay in hook formation.
Published: 2016
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34. In papyro comparison of TMM (edgeR), RLE (DESeq2), and MRN normalization methods for a simple two-conditions-without-replicates RNA-Seq experimental design

Author: Elie Maza, 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)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Laboratoire d'Excellence (LABEX) TULIP (ANR-10-LABX-41), European funded COST ACTION FA1106 'Qualityfruit.', Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), and Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Subjects: 0301 basic medicine, Normalization (statistics), lcsh:QH426-470, Génomique, Transcriptomique et Protéomique, expression génique, Computer science, Bioinformatics, In silico, Sequencing data, Biochimie, Biologie Moléculaire, RNA-Seq, DESeq2, RNA-seq data, Comparison of methods, génome de la tomate, normalisation, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, analyse du transcriptome, Genetics (clinical), Original Research, edgeR, comparaison de méthodes, DESeq2, edgeR, R package, lcsh:Genetics, Normalization, 030104 developmental biology, analyse différentielle, EdgeR, Molecular Medicine, Bio-informatique, Algorithm, 030217 neurology & neurosurgery
Abstract: International audience; In the past 5 years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN. Both TMM and DESeq2 are widely used for differential gene expression analysis. This paper introduces properties that show when these three methods will give exactly the same results. These properties are proven mathematically and illustrated by performing in silico calculations on a given RNA-Seq data set.
Published: 2016
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35. The genetics of intra- and interspecific competitive response and effect in a local population of an annual plant species

Author: Laurent Amsellem, Julien Richirt, Romain Villoutreix, Fabrice Roux, Etienne Baron, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), LABEX TULIP (ANR-10-LABX-41, ANR-11-IDEX-0002-02), University of Lille 1 – Région Nord-Pas-de-Calais, University of Lille 1, Région Nord-Pas-de-Calais grant (project Bio-impact : Impacts des changements globaux sur la distribution de la Biodiversité en Région Nord-Pas-de-Calais), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: genome-wide association mapping, Population, reaction norms, Biology, Intraspecific competition, food, Stellaria media, Genetic variation, education, fitness-related traits, gradient of natural selection, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Genetics, education.field_of_study, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, food and beverages, Phenotypic trait, Interspecific competition, 15. Life on land, Storage effect, ecological genomics, food.food, competition
Abstract: International audience; 1. While competition is recognized as a major factor responsible for plant community dynamics, the genetics of intra- and interspecific competitive ability of a target species (i.e. level of intra-population genetic variation, identity of phenotypic traits under selection and genetic bases) still deserves a deeper investigation at the local spatial scale by considering both numerous genotypes and several interacting species. 2. In this study, we tested whether the genetics of competitive response and effect in Arabidopsis thaliana was dependent on the competitive environment at both the intraspecific and interspecific levels. We used a mapping population of 48 accessions (i) that maximize the genetic diversity of a local population of A. thaliana and (ii) that have been genotyped for 168 503 single nucleotide polymorphisms. 3. In a common garden experiment, those 48 accessions were grown in six competitive environments: the absence of competition, intraspecific competition and interspecific competition with four species frequently associated with A. thaliana in natural plant communities (i.e. Poa annua, Stellaria media, Trifolium repens and Veronica arvensis). A suite of nine phenotypic traits, including a proxy of fitness, were scored on each target A. thaliana plant and the aboveground dry biomass of its corresponding competitor was estimated. 4. We first showed that crossing reaction norms of competitive response (A. thaliana performance) and effect (competitor biomass) might promote maintenance of genetic variation in a local population of A. thaliana and species coexistence at a fine spatial scale. By estimating genotypic gradients of selection, we then demonstrated that the optimal phenotypic strategies in response to competition depend on the identity of the competitor species. Finally, a genomewide association mapping approach highlighted that genomic regions associated with direct genetic effects were (i) dependent on the competitor species and (ii) different from genomic regions associated with interspecific indirect genetic effects. 5. While a first step, this study highlighted the power of adding ecology to genomics in A. thaliana to identify genetic bases underlying micro-geographic adaptation to competition. Nextgeneration sequencing technologies will undoubtedly facilitate the discovery of molecular and genetic mechanisms underlying competitive ability in other plant species, and thereby the prediction of evolutionary trajectories of plant communities.
Published: 2015
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36. Hormonal Control of Lateral Root and Nodule Development in Legumes

Author: Sandra Bensmihen, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and LABEX TULIP
Subjects: 0106 biological sciences, root development, [SDV]Life Sciences [q-bio], Review, Plant Science, lateral root, 01 natural sciences, Rhizobia, 03 medical and health sciences, Symbiosis, Auxin, Medicago truncatula, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Lateral root formation, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, miRNA, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, hormones, local/systemic regulation, fungi, Lateral root, food and beverages, biology.organism_classification, symbiosis, Horticulture, chemistry, QK1-989, peptides, Nitrogen fixation, Rhizobium, auxin, 010606 plant biology & botany
Abstract: Many plants can establish symbioses with nitrogen-fixing bacteria, some of which lead to nodulation, including legumes. Indeed, in the rhizobium/legume symbiosis, new root organs, called nodules, are formed by the plant in order to host the rhizobia in protective conditions, optimized for nitrogen fixation. In this way, these plants can benefit from the reduction of atmospheric dinitrogen into ammonia by the hosted bacteria, and in exchange the plant provides the rhizobia with a carbon source. Since this symbiosis is costly for the plant it is highly regulated. Both legume nodule and lateral root organogenesis involve divisions of the root inner tissues, and both developmental programs are tightly controlled by plant hormones. In fact, most of the major plant hormones, such as auxin, cytokinins, abscisic acid, and strigolactones, control both lateral root formation and nodule organogenesis, but often in an opposite manner. This suggests that the sensitivity of legume plants to some phytohormones could be linked to the antagonism that exists between the processes of nodulation and lateral root formation. Here, we will review the implication of some major phytohormones in lateral root formation in legumes, compare them with their roles in nodulation, and discuss specificities and divergences from non-legume eudicot plants such as Arabidopsis thaliana.
Published: 2015

37. The genome of Eucalyptus grandis

Author: Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)
Subjects: Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract: International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
Published: 2014
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38. Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing

Author: Mohamed Zouine, Anne-Laure Chateigner-Boutin, Pierre Frasse, Jean-Paul Roustan, Yongyao Fu, Corinne Audran, Hua Wang, Isabelle Mila, 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 Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire d'Excellence (LABEX) [TULIP ANR-10-LABX-41], Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Zouine, Mohammed, and Fu, Yongyao
Subjects: 0106 biological sciences, Plant Phylogenetics, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, RNA Stability, lcsh:Medicine, Plant Science, Plant Genetics, Plant hormone auxin, 01 natural sciences, Gene Splicing, Transactivation, Solanum lycopersicum, RNA interference, Gene Expression Regulation, Plant, Plant Genomics, Cluster Analysis, RNA Processing, Post-Transcriptional, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, lcsh:Science, Phylogeny, Flowering Plants, Plant Proteins, 2. Zero hunger, Genetics, Regulation of gene expression, Plant Growth and Development, 0303 health sciences, Multidisciplinary, food and beverages, Plants, Organ Specificity, Multigene Family, RNA Interference, Research Article, Transcriptional Activation, DNA transcription, Biotechnologies, Biology, Tomato ARF genes, Fruits, Molecular Genetics, 03 medical and health sciences, Open Reading Frames, Plant development, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulation, Gene, Post-transcriptional regulation, 030304 developmental biology, Gene Expression Profiling, Alternative splicing, lcsh:R, fungi, Computational Biology, Gene expression profiling, Alternative Splicing, Fruit, lcsh:Q, Gene expression, 5' Untranslated Regions, Biologie végétale, 010606 plant biology & botany, Transcriptional mediators
Abstract: International audience; Background: The phytohormone auxin is involved in a wide range of developmental processes and auxin signaling is known to modulate the expression of target genes via two types of transcriptional regulators, namely, Aux/IAA and Auxin Response Factors (ARF). ARFs play a major role in transcriptional activation or repression through direct binding to the promoter of auxin-responsive genes. The present study aims at gaining better insight on distinctive structural and functional features among ARF proteins. Results: Building on the most updated tomato (Solanum lycopersicon) reference genome sequence, a comprehensive set of ARF genes was identified, extending the total number of family members to 22. Upon correction of structural annotation inconsistencies, renaming the tomato ARF family members provided a consensus nomenclature for all ARF genes across plant species. In silico search predicted the presence of putative target site for small interfering RNAs within twelve Sl-ARFs while sequence analysis of the 59-leader sequences revealed the presence of potential small uORF regulatory elements. Functional characterization carried out by transactivation assay partitioned tomato ARFs into repressors and activators of auxin-dependent gene transcription. Expression studies identified tomato ARFs potentially involved in the fruit set process. Genome-wide expression profiling using RNA-seq revealed that at least one third of the gene family members display alternative splicing mode of regulation during the flower to fruit transition. Moreover, the regulation of several tomato ARF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signaling pathways of these two hormones. Conclusion: All together, the data bring new insight on the complexity of the expression control of Sl-ARF genes at the transcriptional and post-transcriptional levels supporting the hypothesis that these transcriptional mediators might represent one of the main components that enable auxin to regulate a wide range of physiological processes in a highly specific and coordinated manner.
Published: 2014
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39. The long-term maintenance of a resistance polymorphism through diffuse interactions

Author: Sumitha Nallu, Joy Bergelson, Fabrice Roux, Luke G. Barrett, Brody J. DeYoung, Joel M. Kniskern, Ullrich Dubiella, Roger W. Innes, Jing Ding, Liping Gao, Richard R. Hudson, Ruben O. Lastra, Talia L. Karasov, University of Chicago, Indiana University [Bloomington], Indiana University System, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique et Evolution des Populations Végétales, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Education GAANN fellowship, Dropkin Foundation, National Institutes of Health (NIH) Postbaccalaureate Research Education Program award, Laboratory of Excellence (Labex) TULIP [ANR-10-LABX-41, ANR-11-IDEX-0002-02], NIH-NIGMS [R01 GM046451, R01 GM057994, R01 GM083068], and NSF [MCB0603515]
Subjects: 0106 biological sciences, Arabidopsis, Virulence, Pseudomonas syringae, Biology, Genes, Plant, 01 natural sciences, Article, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Plant Immunity, Allele, Selection, Genetic, Pathogen, Gene, Alleles, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Polymorphism, Genetic, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Obligate, Models, Genetic, Effector, Arabidopsis Proteins, R gene, Host-Pathogen Interactions, 010606 plant biology & botany
Abstract: Long-term plant resistance polymorphism does not require obligate association but instead is maintained in the face of diffuse ecological interactions. Despite the prevalence of generalist pathogens, ancient balanced polymorphisms in resistance (R) genes are ubiquitous in plants such as Arabidopsis thaliana, although they rarely provide adequate defence in an agricultural context. The mechanisms involved in maintaining such polymorphisms are unknown. Here Joy Bergelson and colleagues identify a naturally interacting R gene (in A. thaliana) and effector (in A. thaliana's pathogen Pseudomonas syringae) pair. The protein product of this R gene, RPS5, recognizes AvrPphB2 protein in P. syringae and exhibits a balanced polymorphism that has been maintained for more than two million years. The presence of P. syringae carrying avrPphB seems insufficient to explain the RPS5 polymorphism. Rather, selection for RPS5 may involve multiple non-homologous effectors and multiple pathogen species, suggesting that this R gene polymorphism is maintained through complex and diffuse community-wide interactions. Plant resistance (R) genes are a crucial component in plant defence against pathogens1. Although R genes often fail to provide durable resistance in an agricultural context, they frequently persist as long-lived balanced polymorphisms in nature2,3,4. Standard theory explains the maintenance of such polymorphisms through a balance of the costs and benefits of resistance and virulence in a tightly coevolving host–pathogen pair5,6. However, many plant–pathogen interactions lack such specificity7. Whether, and how, balanced polymorphisms are maintained in diffusely interacting species8 is unknown. Here we identify a naturally interacting R gene and effector pair in Arabidopsis thaliana and its facultative plant pathogen, Pseudomonas syringae. The protein encoded by the R gene RPS5 recognizes an AvrPphB homologue (AvrPphB2) and exhibits a balanced polymorphism that has been maintained for over 2 million years (ref. 3). Consistent with the presence of an ancient balanced polymorphism, the R gene confers a benefit when plants are infected with P. syringae carrying avrPphB2 but also incurs a large cost in the absence of infection. RPS5 alleles are maintained at intermediate frequencies in populations globally, suggesting ubiquitous selection for resistance. However, the presence of P. syringae carrying avrPphB is probably insufficient to explain the RPS5 polymorphism. First, avrPphB homologues occur at very low frequencies in P. syringae populations on A. thaliana. Second, AvrPphB only rarely confers a virulence benefit to P. syringae on A. thaliana. Instead, we find evidence that selection for RPS5 involves multiple non-homologous effectors and multiple pathogen species. These results and an associated model suggest that the R gene polymorphism in A. thaliana may not be maintained through a tightly coupled interaction involving a single coevolved R gene and effector pair. More likely, the stable polymorphism is maintained through complex and diffuse community-wide interactions.
Published: 2014
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40. Opening the Ralstonia solanacearum type III effector tool box: insights into host cell subversion mechanisms

Author: Laurent Deslandes, Stéphane Genin, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), French Agence Nationale de la Recherche [ANR-10-JCJC-1706], and Laboratoire d'Excellence (LABEX) 'TULIP' [ANR-10-LABX-41, ANR-11-IDEX-0002-02]
Subjects: Genetics, 0303 health sciences, Ralstonia solanacearum, 030306 microbiology, Effector, Mutant, food and beverages, Plant Science, Plants, Biology, biology.organism_classification, Type three secretion system, Microbiology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, Bacterial Proteins, Proteasome, TAL effector, Plant protein, Gene, Plant Diseases, 030304 developmental biology
Abstract: Effectors delivered to host cells by the Type III secretion system are essential to Ralstonia solanacearum pathogenicity, as in several other plant pathogenic bacteria. The establishment of exhaustive effector repertoires in multiple R. solanacearum strains drew a first picture of the evolutionary dynamics of the pathogen effector suites. Effector repertoires are diversified, with a core of 20-30 effectors present in most of the strains and the obtention of mutants lacking one or more effector genes revealed the functional overlap among this effector network. Recent functional studies have provided insights into the ability of single effectors to manipulate the host proteasome, elicit cell death, trigger the expression of plant genes, and/or display biochemical activities on plant protein targets.
Published: 2014
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41. Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Author: Fabien Guérin, Armelle Darrasse, Stéphane Cociancich, Monique Royer, Emmanuelle Lauber, Valérie Verdier, Valérie Barbe, Sébastien Carrère, Laurana Serres-Giardi, Alejandra Munoz, Philippe Rott, Marie-Agnès Jacques, Mario L. Arrieta-Ortiz, Endrick Guy, Christian Vernière, Stéphanie Fouteau, Sophie Bonneau, Arnaud Indiana, Martial Briand, Stéphane Poussier, Karine Durand, Lionel Gagnevin, Boris Szurek, Olivier Pruvost, Marie-Anne Van Sluys, Matthieu Arlat, Isabelle Pieretti, Ralf Koebnik, Isabelle Robène-Soustrade, Chrystelle Brin, Charles Manceau, Tristan Boureau, Laurent D. Noël, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, PRES Université Nantes Angers Le Mans (UNAM), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), Universidad de Los Andes [Mérida, Venezuela] (ULA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), 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), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Institut de Recherche pour le Développement (IRD), Résistance des plantes aux bio-agresseurs (UMR RPB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre IRD de Montpellier, INRA-SPE, region Pays de la Loire, France, French Ministry of National Education and Research, French Guyana, LABEX TULIP [ANR 10 LABX 41], [ANR 2010 GENM-013 Xanthomix], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Universidad de Los Andes [Venezuela] (ULA), 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)-Institut National de la Recherche Agronomique (INRA), UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), 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)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: effecteur, Genome, F30 - Génétique et amélioration des plantes, Pseudogène, Insertion sequence, Adaptation physiologique, Phylogeny, Genetics, 0303 health sciences, Chemotaxis, Seed-borne pathogen, Bean, Fabaceae, Flagella, pathogène des semences, Seeds, Effector, séquence d'insertion, Research Article, Biotechnology, Xanthomonas, Séquence nucléotidique, Pseudogene, Biology, Phaseolus vulgaris, Evolution, Molecular, 03 medical and health sciences, Effecteur moléculaire, Secretion system, chimiotaxie, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Plant Diseases, 030304 developmental biology, H20 - Maladies des plantes, Comparative genomics, Whole genome sequencing, Génie génétique, Génome, Base Sequence, 030306 microbiology, Sequence Analysis, DNA, biology.organism_classification, Genetic Fitness, Mobile genetic elements, xanthomonas fuscans, Genome, Bacterial
Abstract: Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.
Published: 2013
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42. Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes

Author: Maza, Elie, Frasse, Pierre, Senin, Pavel, Bouzayen, Mondher, Zouine, Mohamed, 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, and Laboratoire d’Excellence, LabEx, TULIP [ANR-10-LABX-41]
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, Relative transcriptome size, Differential gene expression analysis, Computational methods, High throughput sequencing, Normalization methods, RNA-Seq data
Abstract: International audience; In recent years, RNA-Seq technologies became a powerful tool for transcriptome studies. However, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In particular, it is known that the choice of a normalization procedure leads to a great variability in results of differential gene expression analysis. The present study compares the most widespread normalization procedures and proposes a novel one aiming at removing an inherent bias of studied transcriptomes related to their relative size. Comparisons of the normalization procedures are performed on real and simulated data sets. Real RNA-Seq data sets analyses, performed with all the different normalization methods, show that only 50% of significantly differentially expressed genes are common. This result highlights the influence of the normalization step on the differential expression analysis. Real and simulated data sets analyses give similar results showing 3 different groups of procedures having the same behavior. The group including the novel method named "Median Ratio Normalization" (MR N) gives the lower number of false discoveries. Within this group the MR N method is less sensitive to the modification of parameters related to the relative size of transcriptomes such as the number of down- and upregulated genes and the gene expression levels. The newly proposed MR N method efficiently deals with intrinsic bias resulting from relative size of studied transcriptomes. Validation with real and simulated data sets confirmed that MR N is more consistent and robust than existing methods.
Published: 2013
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43. Phenotypes associated with down-regulation of Sl-IAA27 support functional diversity among Aux/IAA family members in tomato

Author: Corinne Audran-Delalande, Carole Bassa, Mondher Bouzayen, Isabelle Mila, INRA, Génomique et Biotechnologie des Fruit, Institut National de la Recherche Agronomique (INRA), Universite' de Toulouse, INP-ENSA Toulouse, Ge'nomique et Biotechnologie des Fruits, Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Laboratoire d' Excellence (LABEX) [TULIP] [ANR-10-LABX-41], French government, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: 0106 biological sciences, Transcription, Genetic, Physiology, Plant Science, Aux/IAA, tomato, Plant Roots, 01 natural sciences, Solanum lycopersicum, Gene Expression Regulation, Plant, Transcription (biology), RNA interference, Génétique des plantes, Auxin, chlorophyll, Pollination, Plant Proteins, chemistry.chemical_classification, Genetics, Regulation of gene expression, 0303 health sciences, food and beverages, General Medicine, Plants, Genetically Modified, Phenotype, Seeds, RNA Interference, Subcellular Fractions, Génomique, Transcriptomique et Protéomique, Molecular Sequence Data, Down-Regulation, Flowers, Biology, Genes, Plant, Tomato, 03 medical and health sciences, Botany, Gene family, Amino Acid Sequence, Transcription factor, Gene, 030304 developmental biology, Indoleacetic Acids, fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, fruit, chemistry, Fertilization, Fruit, Chl, auxin, 010606 plant biology & botany
Abstract: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The phytohormone auxin is known to regulate several aspects of plant development and Aux/IAA transcription factors play a pivotal role in auxin signaling. To further extend our understanding of the multiple functions of Aux/IAAs, the present study describes the functional characterization of Sl-IAA27, a member of the tomato Aux/IAA gene family. Sl-IAA27 displays a distinct behavior compared to most Aux/IAA regarding the regulation of its expression by auxin and the Sl-IAA27 encoded protein harbors a unique motif of unknown function also present in Sl-IAA9 and remarkably conserved in monocot and dicot species. Tomato transgenic plants under-expressing the Sl-IAA27 gene revealed multiple phenotypes related to vegetative and reproductive growth. Silencing of Sl-IAA27 results in higher auxin sensitivity, altered root development and reduced chlorophyll content in leaves. Both ovule and pollen display dramatic loss of fertility in Sl-IAA27 down-regulated lines and the internal anatomy of the flower and the fruit are modified with enlarged placenta in smaller fruits. In line with the reduced chlorophyll content in Sl-IAA27 RNAi leaves, genes involved in chlorophyll synthesis display lower expression at the level of transcript accumulation. Even though Sl-IAA27 is closely related to Sl-IAA9 in terms of sequence homology and the encoded proteins share common structural features, the data indicate that the two genes regulate tomato fruit initiation and development in a distinct manner.
Published: 2012
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44. Nitric oxide (NO): a key player in the senescence of Medicago truncatula root nodules

Author: Claude Bruand, Yvan Cam, Olivier Pierre, Eric Boncompagni, Eliane Meilhoc, Didier Hérouart, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UMR 2594, Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-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), Agence Nationale de la Recherche [BLAN 071_184783], Laboratoired' Excellence (LABEX) TULIP [ANR-10-LABX-41], Contrat Jeune Scientifique INRA, and National Institute for Applied Sciences (INSA-Toulouse, France)
Subjects: 0106 biological sciences, Root nodule, Physiology, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, nodule senescence, Biomass, 0303 health sciences, Sinorhizobium meliloti, Microscopy, Confocal, Medicago, biology, food and beverages, LEGUME SYMBIOSIS, Darkness, SINORHIZOBIUM-MELILOTI, ARABIDOPSIS, Medicago truncatula, symbiosis, Cell biology, Hydrazines, [SDE]Environmental Sciences, COMPLEXES, medicine.symptom, Root Nodules, Plant, Plant Shoots, Signal Transduction, Subcellular Fractions, Hemeproteins, Senescence, EXPRESSION, Recombinant Fusion Proteins, S-NITROSYLATION, Nitric Oxide, Rhizobia, PROGRAMMED CELL-DEATH, 03 medical and health sciences, Bacterial Proteins, Symbiosis, flavohaemoglobin, 1 HEMOGLOBIN GENE, Stress, Physiological, Nitrogenase, Botany, medicine, PLANT HEMOGLOBINS, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nitric oxide (NO), 030306 microbiology, Nodule (medicine), biology.organism_classification, 010606 plant biology & botany, RESPONSES
Abstract: International audience; Nitric oxide (NO) is a signalling and defence molecule involved in diverse plant developmental processes, as well as in the plant response to pathogens. NO has also been detected at different steps of the symbiosis between legumes and rhizobia. NO is required for an optimal establishment of the Medicago truncatulaSinorhizobium meliloti symbiotic interaction, but little is known about the role of NO in mature nodules. Here, we investigate the role of NO in the late steps of symbiosis. Genetic and pharmacological approaches were conducted to modulate the NO level inside root nodules, and their effects on nitrogen fixation and root nodule senescence were monitored. An increase in endogenous NO levels led to a decrease in nitrogen fixation and early nodule senescence, characterized by cytological modifications of the nodule structure and the early expression of a specific senescence marker. By contrast, a decrease in NO levels led to a delay in nodule senescence. Together, our results strongly suggest that NO is a signal in developmental as well as stress-induced nodule senescence. In addition, this work demonstrates the pivotal role of the bacterial NO detoxification response in the prevention of early nodule senescence, and hence the maintenance of efficient symbiosis.
Published: 2012
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