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Start Over Author "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)"
311 results on '"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)"'

1. Traits of a mussel transmissible cancer are reminiscent of a parasitic life style

Author

Burioli, E., Hammel, M., Bierne, N., Thomas, F., Houssin, M., Destoumieux-Garzón, D., Charrière, G., Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), 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 Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), LABÉO, Pôle d’analyses et de recherche de Normandie (LABÉO), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and ANR-18-CE35-0009,TRANSCAN,ECOLOGIE ET EVOLUTION DES CANCERS TRANSMISSIBLES(2018)

Subjects
0106 biological sciences, Cell biology, Hemocytes, Cell Survival, Mytilus edulis, Science, Diseases, [SDV.CAN]Life Sciences [q-bio]/Cancer, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Hemolymph, Neoplasms, Animals, Parasites, Seawater, 14. Life underwater, Cancer, Cell Proliferation, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Multidisciplinary, Ecology, 3. Good health, Phenotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine
Abstract

Some cancers have evolved the ability to spread from host to host by transmission of cancerous cells. These rare biological entities can be considered parasites with a host-related genome. Still, we know little about their specific adaptation to a parasitic lifestyle. MtrBTN2 is one of the few lineages of transmissible cancers known in the animal kingdom. Reported worldwide, MtrBTN2 infects marine mussels. We isolated MtrBTN2 cells circulating in the hemolymph of cancerous mussels and investigated their phenotypic traits. We found that MtrBTN2 cells had remarkable survival capacities in seawater, much higher than normal hemocytes. With almost 100% cell survival over three days, they increase significantly their chances to infect neighboring hosts. MtrBTN2 also triggered an aggressive cancerous process: proliferation in mussels was ~ 17 times higher than normal hemocytes (mean doubling time of ~ 3 days), thereby favoring a rapid increase of intra-host population size. MtrBTN2 appears to induce host castration, thereby favoring resources re-allocation to the parasites and increasing the host carrying capacity. Altogether, our results highlight a series of traits of MtrBTN2 consistent with a marine parasitic lifestyle that may have contributed to the success of its persistence and dissemination in different mussel populations across the globe.

Published
2021

2. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar

Author

Jose Caius, Sophie Lanciano, Régis Fichot, Sylvie Citerne, Véronique Brunaud, Jörg Tost, Vincent Segura, Steven H. Strauss, Ludivine Soubigou-Taconnat, Stéphane Maury, Alain Delaunay, Isabelle Le Jan, Marie-Claude Lesage-Descauses, Franck Brignolas, Anne-Laure Le Gac, Marie Mirouze, Christoph Grunau, Cristian Chaparro, Hervé Cochard, Christian Daviaud, Mamadou Dia Sow, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, adaptation, développement des plantes (UMR DIADE), 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]), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-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 Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), 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 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), 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 de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Oregon State University (OSU), Ministere de la Recherche et Enseignement Superieur, INRAEPI EFPA-2014, RTP3E CNRS grants for mobility, ANR-17-CE32-0009,EPITREE,Impacts évolutif et fonctionnel de variations épigénétiques chez des arbres forestiers.(2017), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-13-JSV6-0002,EXTRACHROM,Contrôle épigénétique des formes extrachromosomiques des éléments transposables chez les plantes.(2013), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), 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), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 Ministère de la Recherche et Enseignement SupérieurINRAE PI EFPA-2014RTP3E CNRS grantsIJPB's Plant Observatory technological platformsInfinity English SIRET 82950710200012

Subjects
0106 biological sciences, Transposable element, Physiology, Meristem, hormone, drought, Plant Science, Biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, shoot apical meristem, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], mobilome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Epigenetics, Gene, 030304 developmental biology, 0303 health sciences, DNA methylation, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], epigenetics, fungi, 15. Life on land, ddm1, Droughts, Chromatin, Cell biology, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Populus, Differentially methylated regions, poplar, RNA Interference, 010606 plant biology & botany
Abstract

Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via down regulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula 9 Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit.We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways ; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.

Published
2021

3. Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni

Author

Chrystelle Lasica, Hélène Moné, Cristian Chaparro, Christoph Grunau, Agnieszka Zelisko-Schmidt, Ronaldo de Carvalho Augusto, Gabriel Mouahid, Anne-Clémence Veillard, 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 de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), diagenode, Modat, Anne, 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), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0303 health sciences, limited biological material, biology, Human blood, library input, 030231 tropical medicine, ChIPmentation, Medicine (miscellaneous), Computational biology, Schistosoma mansoni, biology.organism_classification, Biological materials, General Biochemistry, Genetics and Molecular Biology, ChIP-seq, 03 medical and health sciences, 0302 clinical medicine, Human parasite, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Chromatin immunoprecipitation, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030304 developmental biology, N-ChIP
Abstract

In living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic information and as such have been increasingly studied since about the year 2000. One of the principal techniques to gather information about the association between DNA and modified histones is chromatin immunoprecipitation (ChIP), also combined with massive sequencing (ChIP-Seq). Automated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq in many model species, using in general roughly 106 cells per experiment. Such high cell numbers are sometimes difficult to produce. Using the human parasite Schistosoma mansoni, whose production requires sacrificing animals and should therefore be kept to a minimum, we show here that automated ChIPmentation is suitable for limited biological material. We define the operational limit as ≥20,000 Schistosoma cells. We also present a streamlined protocol for the preparation of ChIP input libraries.

Published
2022

4. Spatial epidemiological modelling of infection by Vibrio aestuarianus shows that connectivity and temperature control oyster mortality

Author

LUPO, Coralie, Dutta, Bhagat Lal, Petton, Sébastien, Ezanno, Pauline, Tourbiez, Delphine, Travers, Marie-Agnès, Pernet, Fabrice, Bacher, Cédric, Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Dynamiques de l'Environnement Côtier (DYNECO), ANR-12-AGRO-0001,GIGASSAT,Adaptation des écosystèmes ostréicoles au changement global(2012), ANR-15-CE35-0004,ENVICOPAS,Impact des changements environnementaux sur les organismes pathogènes dans les écosystèmes côtiers(2015), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), 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), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and Dynamiques des Écosystèmes Côtiers (DYNECO)

Subjects
Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Oyster disease, Crassostrea gigas, Hydrodynamics, Vibrio aestuarianus, Aquaculture. Fisheries. Angling, food and beverages, SH1-691, Sensitivity analysis, Basic reproduction number, QH540-549.5
Abstract

International audience; Vibrio aestuarianus infection in oyster populations causes massive mortality, resulting in losses for oyster farmers. Such dynamics result from host-pathogen interactions and contagion through water-borne transmission. To assess the spatiotemporal spread of V. aestuarianus infection and associated oyster mortality at a bay scale, we built a mathematical model informed by experimental infection data at 2 temperatures and spatially dependent marine connectivity of oyster farms. We applied the model to a real system and tested the importance of each factor using a number of modelling scenarios. Results suggest that introducing V. aestuarianus in a fully susceptible adult oyster population in the bay would lead to the mortality of all farmed oysters over 6 to 12 mo, depending on the location in which infection was initiated. The effect of temperature was captured by the basic reproduction number (R0), which was >1 at high seawater temperatures, as opposed to values

Published
2020

5. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses

Author

Yannick Gueguen, J. de Lorgeril, Samuel Dupont, C. Salmeron, G. Tanguy, Caroline Montagnani, J.Y. Bou Khalil, Jean-Christophe Auguet, Jean-Michel Escoubas, Bruno Petton, B. La Scola, Eve Toulza, A. Lokmer, Christelle Desnues, Guillaume Mitta, David Pecqueur, Erwan Corre, Laure Guillou, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), The present study was supported by: the DHOF program of the UMR5244/IHPE (http://ihpe.univ-perp.fr/en/ihpe-transversal-holobiont/), the Ifremer project HémoMicrobiote, EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future (ANR-10-INBS-02), the ANR projects DECIPHER (ANR-14-CE19–0023) and ENVICOPAS (ANR-15-CE35–0004), the EU funded project VIVALDI (H2020 program, n°678589), by Ifremer, CNRS, Université de Montpellier, Université de Perpignan via Domitia, by the IHU Méditerranée Infection, Marseille, France, by the French Government under the «Investissements d’avenir» program (reference: Méditerranée Infection 10-IAHU-03) and by the Région Provence-Alpes-Côte d’Azur and by the European funding FEDER PRIMI. This study is set within the framework of the 'Laboratoires d’Excellences (LABEX)' TULIP (ANR-10-LABX-41)., ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), ANR-15-CE35-0004,ENVICOPAS,Impact des changements environnementaux sur les organismes pathogènes dans les écosystèmes côtiers(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Éco-Anthropologie (EAE), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Parasitologie fonctionnelle et évolutive (PFE), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Radiopathologie et Thérapies Expérimentales [IRSN, Fontenay-aux-Roses] (PRP-HOM - SRBE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, animal structures, Early-life microbiota, lcsh:QR1-502, Zoology, medicine.disease_cause, Within-host ecosystem, lcsh:Microbiology, 03 medical and health sciences, biology.animal, medicine, Trans-kingdom interactions, Human virome, Microbiome, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ecological niche, 0303 health sciences, lcsh:Veterinary medicine, biology, 030306 microbiology, Host (biology), Oyster genetic background, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Protist, General Medicine, Pacific oyster, biology.organism_classification, Transplantation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Crassostrea gigas, lcsh:SF600-1100, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acln, Hemolymph microbiota dynamics, Research Article
Abstract

Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.

Published
2020

6. Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific oyster mortality syndrome

Author

Jean-Michel Escoubas, Philippe Haffner, Bruno Petton, Franck Lagarde, Yannick Gueguen, Aude Lucasson, Valérie Perez, Pierre-Louis Stenger, Jean-François Allienne, Caroline Montagnani, Julien de Lorgeril, M. Leroy, Guillaume Mitta, Jeremie Vidal-Dupiol, Lionel Degremont, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), 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 national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), The present study was supported by the ANR project DECIPHER (ANR-14-CE19–0023), by the ANR project DECICOMP and by Ifremer, CNRS, Université de Montpellier and Université de Perpignan via Domitia., ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), 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 de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut 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 de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, animal structures, Invertebrate immunity, lcsh:QH426-470, lcsh:Biotechnology, Resistance, Transcriptome, 03 medical and health sciences, Antiviral molecular pathways, Stress, Physiological, biology.animal, lcsh:TP248.13-248.65, Genotype, Genetics, Animals, Pacific oyster, RNA-Seq, 14. Life underwater, Crassostrea, Gene, Panzootic, 030304 developmental biology, 0303 health sciences, biology, OsHV-1, Acl, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Oyster disease, food and beverages, 04 agricultural and veterinary sciences, biology.organism_classification, Phenotype, lcsh:Genetics, Genes, 040102 fisheries, 0401 agriculture, forestry, and fisheries, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biotechnology, Research Article
Abstract

Background As a major threat to the oyster industry, Pacific Oyster Mortality Syndrome (POMS) is a polymicrobial disease affecting the main oyster species farmed across the world. POMS affects oyster juveniles and became panzootic this last decade, but POMS resistance in some oyster genotypes has emerged. While we know some genetic loci associated with resistance, the underlying mechanisms remained uncharacterized. So, we developed a comparative transcriptomic approach using basal gene expression profiles between different oyster biparental families with contrasted phenotypes when confronted to POMS (resistant or susceptible). Results We showed that POMS resistant oysters show differential expression of genes involved in stress responses, protein modifications, maintenance of DNA integrity and repair, and immune and antiviral pathways. We found similarities and clear differences among different molecular pathways in the different resistant families. These results suggest that the resistance process is polygenic and partially varies according to the oyster genotype. Conclusions We found differences in basal expression levels of genes related to TLR-NFκB, JAK-STAT and STING-RLR pathways. These differences could explain the best antiviral response, as well as the robustness of resistant oysters when confronted to POMS. As some of these genes represent valuable candidates for selective breeding, we propose future studies should further examine their function.

Published
2020

7. Getting out of crises: Environmental, social-ecological and evolutionary research is needed to avoid future risks of pandemics

Author

Destoumieux-Garzón, Delphine, Matthies-Wiesler, Franziska, Bierne, Nicolas, Binot, Aurélie, Boissier, Jérôme, Devouge, Anaïs, Garric, Jeanne, Gruetzmacher, Kim, Grunau, Christoph, Guégan, Jean-François, Hurtrez-Boussès, Sylvie, Huss, Anke, Morand, Serge, Palmer, Clare, Sarigiannis, Denis, Vermeulen, Roel, Barouki, Robert, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Helmholtz-Zentrum München (HZM), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Riverly (Riverly), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde [Berlin], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Universiteit Utrecht, Texas A&M University [College Station], Aristotle University of Thessaloniki, Istituto Universitario di Studi Superiori (IUSS), European Commission : 825417, Laboratoires d'Excellence (LABEX) : ANR-10-LABX-41, National Institutes of Health-National Science Foundation Ecology of Infectious Disease Program Grant : NSF-1911457, IRD, INRAE, French School of Public Health (EHESP), University of Montpellier, Thailand International Cooperation Agency (TICA) project 'Animal Innovative Health', ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-17-CE35-0003,FutureHealthSEA,Scénarios de la santé en Asie du Sud-Est: changements d'utilisation des terres, changement climatique et maladies infectieuses(2017), Morand, Serge, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, Scénarios de la santé en Asie du Sud-Est: changements d'utilisation des terres, changement climatique et maladies infectieuses - - FutureHealthSEA2017 - ANR-17-CE35-0003 - AAPG2017 - VALID, 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), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Montpellier (UM), Utrecht University [Utrecht], University School for Advanced Study IUSS, ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and RiverLy - Fonctionnement des hydrosystèmes (RiverLy)

Subjects
Naturebased solutions, Biodiversity Loss, Climate Change, Ecology, Emerging Infectious Disease, Evolution, Nature-based Solutions, Ecological health, Ecology (disciplines), Social ecology, EcoHealth, Social Environment, Article, 03 medical and health sciences, 0302 clinical medicine, Multidisciplinary approach, Environmental Science(all), Political science, 11. Sustainability, media_common.cataloged_instance, Animals, Humans, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Climate change, GE1-350, European union, Pandemics, Ecosystem, 030304 developmental biology, General Environmental Science, media_common, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, SARS-CoV-2, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Nature-based solutions, COVID-19, Emerging infectious disease, 3. Good health, Environmental sciences, One Health, 13. Climate action, 030220 oncology & carcinogenesis, Biodiversity loss
Abstract

International audience; The implementation of One Health/EcoHealth/Planetary Health approaches has been identified as key (i) to address the strong interconnections between risk for pandemics, climate change and biodiversity loss and (ii) to develop and implement solutions to these interlinked crises. As a response to the multiple calls from scientists on that subject, we have here proposed seven long-term research questions regarding COVID-19 and emerging infectious diseases (EIDs) that are based on effective integration of environmental, ecological, evolutionary, and social sciences to better anticipate and mitigate EIDs. Research needs cover the social ecology of infectious disease agents, their evolution, the determinants of susceptibility of humans and animals to infections, and the human and ecological factors accelerating infectious disease emergence. For comprehensive investigation, they include the development of nature-based solutions to interlinked global planetary crises, addressing ethical and philosophical questions regarding the relationship of humans to nature and regarding transformative changes to safeguard the environment and human health. In support of this research, we propose the implementation of innovative multidisciplinary facilities embedded in social ecosystems locally: ecological health observatories and living laboratories. This work was carried out in the frame of the European Community project HERA (www. HERAresearchEU.eu), which aims to set priorities for an environment, climate and health research agenda in the European Union by adopting a systemic approach in the face of global environmental change

Published
2022

8. A fine‐scale analysis reveals microgeographic hotspots maximizing infection rate between a parasite and its fish host

Author

Géraldine Loot, Geoffrey Marselli, Orlane Scelsi, Olivier Rey, Simon Blanchet, Camille Poesy, Eglantine Mathieu-Bégné, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), 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), 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), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR-11-JSV7-0010,INCLIMPAR,Les effets du changement climatique sur les parasites : une étude prédictive intégrée(2011), 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 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), and 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)

Subjects
0106 biological sciences, 0303 health sciences, Host (biology), microhabitat, aggregation, Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, Infection rate, Scale analysis (statistics), 03 medical and health sciences, host-parasite interactions, Parasite hosting, %22">Fish , [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 14. Life underwater, freshwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, encounter filter, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; For parasites, finding their hosts in vast and heterogeneous environments is a task that can be complex. Some parasite species rely on elaborate strategies to increase encounter rate with their hosts (e.g. behavioural modification of host), but others do not. For these parasites, a key issue is to reveal the processes that enable them to successfully find their hosts and complete their life cycles. Here, we tested the hypothesis that infective larvae of the freshwater ectoparasite Tracheliastes polycolpus are not homogeneously distributed along the river and preferentially occur in very specific microhabitats that maximize encounter rate, and hence infection rate, with their host fish. To do this, we combined an in situ experiment (caging) with an empirical survey carried out on the same sites to identify potential 'hotspots' of infection at the microgeographic scale and their environmental characteristics. Experimental and empirical results demonstrated that infections were not evenly distributed among microhabitats, and that infections were spatially aggregated in hotspots at a very fine spatial grain. We further found that certain combinations of environmental variables were consistently and nonlinearly associated with higher infection rate for both caged and wild-caught fish. Microhabitats characterized by very low or high stream velocities, associated with medium or very small substrate, respectively, and a deep water column were strongly and repeatedly associated with higher infection rates. These microhabitats could concentrate parasites and/or promote physical contact with the hosts. We conclude that the characteristics of some microhabitats could facilitate contact between hosts and parasites and explain how some parasites manage to find their hosts in complex environments.

Published
2022

9. Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture

Author

Isabelle Arzul, Luigi Vezzulli, K. Mathias Wegner, Alberto Pallavicini, Christine Paillard, Yannick Gueguen, David Bass, Paillard, Christine, Gueguen, Yannick, Wegner, K Mathia, Bass, David, Pallavicini, Alberto, Vezzulli, Luigi, Arzul, Isabelle, 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 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), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Alfred Wegener Institute for Polar and Marine Research (AWI), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Life Sciences, Università degli studi di Trieste, National Institute of Oceanography and Applied Geophysics (OGS), Dipartimento di Scienze della Terra dell'Ambiente e della Vita (DISTAV), Universita degli studi di Genova, Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), 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), Università degli studi di Trieste = University of Trieste, Università degli studi di Genova = University of Genoa (UniGe), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), and ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017)

Subjects
Functional role, Biomedical Engineering, Bioengineering, Context (language use), [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Disease, Aquaculture, Biology, Animals, Host-Pathogen Interactions, Bivalvia, Microbiota, 03 medical and health sciences, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Ecology, Host (biology), business.industry, Animal, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Host-Pathogen Interaction, 13. Climate action, [SDE]Environmental Sciences, Disease prevention, business, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; In bivalves, no clear-cut functional role of microbiota has yet been identified, although many publications suggest that they could be involved in nutrition or immunity of their host. In the context of climate change, integrative approaches at the crossroads of disciplines have been developed to explore the environment-host-pathogen microbiota system. Here, we attempt to synthesize work on (1) the current methodologies to analyse bivalve microbiota, (2) the comparison of microbiota between species, between host compartments and their surrounding habitat, (3) how the bivalve microbiota are governed by environmental factors and host genetics and (4) how host-associated microorganisms act as a buffer against pathogens and/or promote recovery, and could thereby play a role in the prevention of disease or mortalities.

Published
2022

10. Morphological and genomic characterisation of the Schistosoma hybrid infecting humans in Europe reveals admixture between Schistosoma haematobium and Schistosoma bovis

Author

Julien Kincaid-Smith, Alan Tracey, Ronaldo de Carvalho Augusto, Ingo Bulla, Nancy Holroyd, Anne Rognon, Olivier Rey, Cristian Chaparro, Ana Oleaga, Santiago Mas-Coma, Jean-François Allienne, Christoph Grunau, Matthew Berriman, Jérôme Boissier, Eve Toulza, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), 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), Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Universität Greifswald - University of Greifswald, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Parasitology Laboratory, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Universitat de València (UV), Departamento de Parasitologia, Universitat de València (UV)-Facultad de farmacia, CG and RA were supported by the Wellcome Trust [grant number 107475/Z/15/Z], and Deutsche Forschungsgemeinschaft Fellowship BU 2685/5-1. MB was supported by the Wellcome Trust [grant number 098051]. SMC was funded by Health Research Project No. PI16/00520, Plan Estatal de Investigacion Cientifica y Tecnica y de Innovacion, ISCIII-MINECO, Madrid, Spain, Red de Investigacion de Centros de Enfermedades Tropicales - RICET (Project No. RD16/0027/0023 of the PN de I+D+I, ISCIII-RETICS), Ministry of Health and Consumption, Madrid, Spain. JB, ET, OR were funded by the French National Research Agency ANR project HySWARM ANR-18-CE35-0001., ANR-18-CE35-0001,HySWARM,Hybrid Swarm: rôle de l'hybridation dans les capacités invasives, l'épidémiologie et le diagnostic de la schistosomiase(2018), Ministerio de Economía y Competitividad (España), Oleaga, Ana, 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Oleaga, Ana [0000-0002-8019-7354]

Subjects
Male, Physiology, Introgression, Eggs, RC955-962, Snails, Disease Vectors, 0302 clinical medicine, Medical Conditions, Reproductive Physiology, Arctic medicine. Tropical medicine, Invertebrate Genomics, Medicine and Health Sciences, Body Size, Schistosomiasis, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Eukaryota, Genomics, 3. Good health, Europe, Infectious Diseases, Schistosoma bovis, Schistosoma haematobium, Schistosoma, Female, Public aspects of medicine, RA1-1270, Schistosomes, Research Article, Evolutionary Processes, Bulinus, 030231 tropical medicine, 03 medical and health sciences, Helminths, Parasitic disease, parasitic diseases, Genetics, Parasitic Diseases, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030304 developmental biology, Evolutionary Biology, Genome, Helminth, [SDV.GEN]Life Sciences [q-bio]/Genetics, Chimera, Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, Paleontology, Invertebrates, Animal Genomics, Earth Sciences, Hybridization, Genetic, Paleogenetics, Zoology
Abstract

Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature of these dioecious parasites is their ability to produce viable and fertile hybrid offspring. Originally only present in the tropics, schistosomiasis is now also endemic in southern Europe. Based on the analysis of two genetic markers the European schistosomes had previously been identified as hybrids between the livestock- and the human-infective species Schistosoma bovis and Schistosoma haematobium, respectively. Here, using PacBio long-read sequencing technology we performed genome assembly improvement and annotation of S. bovis, one of the parental species for which no satisfactory genome assembly was available. We then describe the whole genome introgression levels of the hybrid schistosomes, their morphometric parameters (eggs and adult worms) and their compatibility with two European snail strains used as vectors (Bulinus truncatus and Planorbarius metidjensis). Schistosome-snail compatibility is a key parameter for the parasites life cycle progression, and thus the capability of the parasite to establish in a given area. Our results show that this Schistosoma hybrid is strongly introgressed genetically, composed of 77% S. haematobium and 23% S. bovis origin. This genomic admixture suggests an ancient hybridization event and subsequent backcrosses with the human-specific species, S. haematobium, before its introduction in Corsica. We also show that egg morphology (commonly used as a species diagnostic) does not allow for accurate hybrid identification while genetic tests do., PLoS Neglected Tropical Diseases, 15 (12), ISSN:1935-2727, ISSN:1935-2735

Published
2021

11. Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris: possible influence of the rearing water and more

Author

Dominique Ansquer, Jean-René Mailliez, Carolane Giraud, Nolwenn Callac, Nazha Selmaoui-Folcher, Viviane Boulo, Dominique Pham, Maxime Beauvais, Nelly Wabete, Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Institut de sciences exactes et appliquées (ISEA), Université de la Nouvelle-Calédonie (UNC), Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), and 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)

Subjects
Thalassolituus, Eggs, Zoology, Marine Biology, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Marinobacterium, Aquaculture, Nauplii, Fisheries and Fish Science, 14. Life underwater, Alteromonas, Molecular Biology, visual_art.artwork, 030304 developmental biology, Rearing water, 0303 health sciences, Lineage transmission, Active microbiota, 030306 microbiology, business.industry, General Neuroscience, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Subjects Aquaculture, General Medicine, Zoology Active microbiota, Marinobacter, biology.organism_classification, Vibrio, Shrimp, visual_art, Candidatus, Medicine, General Agricultural and Biological Sciences, business, Shrimps
Abstract

Background Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. Method In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. Results We found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.

Published
2021

12. Are cercarial emergence rhythms of the diurnal and nocturnal chronotypes of the parasite Schistosoma mansoni circadian ?

Author

Lasica, Chrystelle, Mouahid, Gabriel, F., Chevalier, Le Clec’h, Winka, Chaparro, Cristian, Grunau, Christoph, Savassi, Boris A.E.S., Al Yafae, Salem, Anderson, Timothy J., Moné, Hélène, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Texas Biomedical Research Institute [San Antonio, TX], Directorate General of Health Services, Dhofar Governorate, and Ministry of Health [Mozambique]

Subjects
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

13. First morphogenetic analysis of parasite eggs from Schistosomiasis haematobium infected sub-Saharan migrants in Spain and proposal for a new standardised study methodology

Author

M. Isabel Cabeza-Barrera, Alejandra de Elias-Escribano, M. Carmen Oliver-Chiva, Jérôme Boissier, Patricio Artigas, Santiago Mas-Coma, Joaquín Salas-Coronas, M. Adela Valero, M. Dolores Bargues, Marta Reguera-Gomez, Universitat de València (UV), Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
Sub saharan, Range (biology), Veterinary (miscellaneous), Eggs, 030231 tropical medicine, Population, Zoology, Schistosomiasis, bovis, S. haematobium S. bovis, 030308 mycology & parasitology, haematobium S, Standardised methodology, 03 medical and health sciences, Schistosomiasis haematobia, 0302 clinical medicine, Intergenic region, Phenotypic analysis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, Parasite hosting, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, S. mansoni, education, Africa South of the Sahara, Schistosoma, Ovum, Transients and Migrants, 0303 health sciences, education.field_of_study, biology, Tropical disease, Sub-Saharan migrants, mansoni, biology.organism_classification, medicine.disease, 3. Good health, Infectious Diseases, Spain, Insect Science, Schistosoma haematobium, Parasitology
Abstract

International audience; Schistosomiasis is a Neglected Tropical Disease caused by trematode species of the genus Schistosoma. Both, autochthonous and imported cases of urogenital schistosomiasis have been described in Europe. The present study focuses on eggs, considered pure S. haematobium by genetic characterisation (intergenic ITS region of the rDNA and cox1 mtDNA). A phenotypic characterisation of S. haematobium eggs was made by morphometric comparison with experimental populations of S. bovis and S. mansoni, to help in the diagnosis of S. haematobium populations infecting sub-Saharan migrants in Spain. Analyses were made by Computer Image Analysis System (CIAS) applied on the basis of new standardised measurements and geometric morphometric tools. The principal component analysis (PCA), including seventeen non-redundant measurements, showed three phenotypic patterns in eggs of S. haematobium, S. bovis and S. mansoni. PCA showed that the S. bovis population presented a large egg size range with a pronouncedly larger maximum size. Similarly, S. bovis shows bigger spine values than S. haematobium. Mahalanobis distances between each pair of groups were calculated for each discriminant analysis performed. In general, S. mansoni and S. bovis present larger distances between them than with S. haematobium, i.e. they present the greatest differences. Regarding the spine, S. haematobium and S. mansoni are the most distant species. Results show the usefulness of this methodology for the phenotypic differentiation between eggs from these Schistosoma species, capable of discerning morphologically close eggs, as is the case of the haematobium group. Schistosoma egg phenotyping approaches may be applied to assess not only hybrid forms but also potential influences of a variety of other factors

Published
2021

14. 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

15. Tetrodotoxins in French Bivalve Mollusks—Analytical Methodology, Environmental Dynamics and Screening of Bacterial Strain Collections

Author

Jean-Luc Rolland, Damien Réveillon, Julien Chevé, Eric Abadie, Dominique Hervio-Heath, Philipp Hess, Marie-Pierre Halm-Lemeille, Estelle Schaefer, Véronique Savar, Marie-Agnès Travers, Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire Environnement Ressource Bretagne Nord (LERBN), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire Environnement Ressources de Normandie (LERN), 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), Santé, Génétique et Microbiologie des Mollusques (SGMM), 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), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biodiversité et Environnement de la Martinique (BIODIENV), Dynamiques de l'Environnement Côtier (DYNECO), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), 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), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and Biodiversité et Environnement (BIODIVENV)

Subjects
Veterinary medicine, seafood contamination, Health, Toxicology and Mutagenesis, Ruditapes, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, Tetrodotoxin, Toxicology, 01 natural sciences, Article, Matrix (chemical analysis), 03 medical and health sciences, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Tandem Mass Spectrometry, [SDV.IDA]Life Sciences [q-bio]/Food engineering, emerging toxins, Animals, 14. Life underwater, Solid phase extraction, Crassostrea, TTXs, Shellfish, 030304 developmental biology, coastal contamination, REMI, 0303 health sciences, biology, 010401 analytical chemistry, Extraction (chemistry), Solid Phase Extraction, biology.organism_classification, 0104 chemical sciences, Bivalvia, Food Microbiology, REPHY, Medicine, France, Bay, Bacteria, coastal and seafood contamination, Chromatography, Liquid
Abstract

International audience; Tetrodotoxins (TTXs) are potentially lethal paralytic toxins that have been identified in European shellfish over recent years. Risk assessment has suggested comparatively low levels (44 µg TTX-equivalent/kg) but stresses the lack of data on occurrence. Both bacteria and dinoflagellates were suggested as possible biogenic sources, either from an endogenous or exogenous origin. We thus investigated TTXs in (i) 98 shellfish samples and (ii) 122 bacterial strains, isolated from French environments. We optimized a method based on mass spectrometry, using a single extraction step followed by ultrafiltration without Solid Phase Extraction and matrix-matched calibration for both shellfish and bacterial matrix. Limits of detection and quantification were 6.3 and 12.5 µg/kg for shellfish and 5.0 and 10 µg/kg for bacterial matrix, respectively. Even though bacterial matrix resulted in signal enhancement, no TTX analog was detected in any strain. Bivalves (either Crassostrea gigas or Ruditapes philippinarum) were surveyed in six French production areas over 2.5–3 month periods (2018–2019). Concentrations of TTX ranged from ‘not detected’ to a maximum of 32 µg/kg (Bay of Brest, 17 June 2019), with events lasting 2 weeks at maximum. While these results are in line with previous studies, they provide new data of TTX occurrence and confirm that the link between bacteria, bivalves and TTX is complex.

Published
2021
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16. Population genomics of Pocillopora corals: insights from RAD-sequencing

Author

François Bonhomme, Marine Pratlong, Eve Toulza, Pauline Gélin, Didier Aurelle, Hélène Magalon, Guillaume Mitta, Michel R. Claereboudt, Pierre Pontarotti, Anne Haguenauer, Nicolas Oury, Mehdi Adjeroud, Lauric Reynes, Pascal Romans, Camille Noûs, Jeremie Vidal-Dupiol, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), Université de La Réunion (UR), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Sultan Qaboos University (SQU), Laboratoire Cogitamus, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-12-ADAP-0016,ADACNI,Processus adaptatifs chez les cnidaires: étude intégrative de la réponse au stress thermique et au changement climatique, des gènes aux populations(2012), ANR-10-LABX-0046,EGID,EGID Diabetes Pole(2010), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mitochondrial DNA, Lineage (evolution), [SDV]Life Sciences [q-bio], Population, Biology, RAD sequencing, 010603 evolutionary biology, 01 natural sciences, Population genomics, 03 medical and health sciences, genetic structure, 14. Life underwater, Pocillopora, education, coral, 030304 developmental biology, 0303 health sciences, education.field_of_study, Genetic diversity, species limits, biology.organism_classification, Genetic marker, Evolutionary biology, Genetic structure
Abstract

Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.

Published
2021

17. Satellite-like W Elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni

Author

Stitz, Maria, Chaparro, Cristian, Lu, Zhigang, Olzog, V Janett, Weinberg, Christina E, Blom, Jochen, Goesmann, Alexander, Grunau, Christoph, Grevelding, Christoph G, Betran, Esther, Institute of Parasitology, BFS, Justus Liebig University Giessen, Germany, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Institute of Biochemistry, Medical Faculty, University of Leipzig, Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany, Institute for Bioinformatics and Systems Biology, and Justus-Liebig-University [Gießen, Germany]

Subjects
AcademicSubjects/SCI01140, Male, Genome evolution, Heterochromatin, DNA, Satellite, genome evolution, Genome, noncoding RNA, Schistosoma mansoni, 03 medical and health sciences, ribozyme, 0302 clinical medicine, Genetics, Animals, Repeated sequence, Biology, Ecology, Evolution, Behavior and Systematics, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, 0303 health sciences, Sex Chromosomes, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], mobile genetic element, AcademicSubjects/SCI01130, Chromosome, biology.organism_classification, 3. Good health, W-element, Evolutionary biology, Female, Mobile genetic elements, 030217 neurology & neurosurgery, Heterogametic sex, Research Article
Abstract

A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.

Published
2021

18. Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge

Author

Adriana S. A. Pereira, Claudia J. de Dood, Rafaela de Paula Freitas, Murilo S. Amaral, Ronaldo de Carvalho Augusto, Patricia A. Miyasato, Jorge Kalil, Vânia Gomes de Moura Mattaraia, Christoph Grunau, R. Alan Wilson, Simone de Oliveira Castro, Paul L. A. M. Corstjens, Daisy Woellner Santos, Elisa M. Tjon Kon Fat, Sergio Verjovski-Almeida, Eliana Nakano, Govert J. van Dam, Ana Carolina Tahira, João V M Malvezzi, Instituto Butantan [São Paulo], Universidade de São Paulo = University of São Paulo (USP), Leiden University Medical Center (LUMC), Universiteit Leiden, 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 de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of York [York, UK], École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Modat, Anne, Universidade de São Paulo (USP), and 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)

Subjects
Male, General Physics and Astronomy, Vacuole, Epigenesis, Genetic, Histones, 0302 clinical medicine, Histone post-translational modifications, Lymphocytes, Genes, Helminth, 0303 health sciences, Multidisciplinary, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Schistosoma mansoni, Acquired immune system, 3. Good health, Rhesus macaque, Lytic cycle, Larva, Female, Antibody, Parasitic infection, Science, 030231 tropical medicine, Antibodies, Helminth, General Biochemistry, Genetics and Molecular Biology, Article, Antibodies, Host-Parasite Interactions, 03 medical and health sciences, Antigen, Immunity, parasitic diseases, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Animals, Parasite Egg Count, 030304 developmental biology, General Chemistry, biology.organism_classification, Macaca mulatta, Schistosomiasis mansoni, Disease Models, Animal, Antigens, Helminth, Reinfection, Immunology, biology.protein, Parasite host response, Granulocytes
Abstract

The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut-derived antigen, we show that from week 10 onwards an established infection with Schistosoma mansoni is cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrates that protection is strong in all animals and complete in some. Antibody profiles suggest that antigens mediating protection are the released products of developing schistosomula. In culture they are killed by addition of rhesus plasma, collected from week 8 post-infection onwards, and even more efficiently with post-challenge plasma. Furthermore, cultured schistosomula lose chromatin activating marks at the transcription start site of genes related to worm development and show decreased expression of genes related to lysosomes and lytic vacuoles involved with autophagy. Overall, our results indicate that enhanced antibody responses against the challenge migrating larvae mediate the naturally acquired protective immunity and will inform the route to an effective vaccine., To date there is only one single drug with modest efficacy and no vaccine available to protect from schistosomiasis. Here, Amaral et al. characterize the self-cure process of rhesus macaques following primary infection and secondary challenge with Schistosoma mansoni to inform future vaccine development studies.

Published
2021

19. Prevalence and polymorphism of a mussel transmissible cancer in Europe

Author

Guillaume M. Charrière, Maryline Houssin, Maurine Hammel, John J. Welch, Christine Arbiol, Michael J. Metzger, Ismaël Bernard, Nicolas Bierne, Delphine Destoumieux-Garzón, E. A. V. Burioli, Antonio Villalba, Jean-Francois Pepin, Abdellah Benabdelmouna, Alexis Simon, Jean-Baptiste Lamy, 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 Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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), Center for Applied Medical Research [Plamplona] (CIMA), Universidad de Navarra [Pamplona] (UNAV), Universidad de Alcala, Spain, University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), LABÉO, Pôle d’analyses et de recherche de Normandie (LABÉO), Laboratoire Environnement Ressources des Pertuis Charentais (LERPC), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Santé, Génétique et Microbiologie des Mollusques (SGMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), SAS Eurêka Mer, University of Cambridge [UK] (CAM), Pacific Northwest Research Institute (PNRI), ANR-18-CE35-0009,TRANSCAN,ECOLOGIE ET EVOLUTION DES CANCERS TRANSMISSIBLES(2018), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), 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), CBET research group, Dept. of Zoology and Animal Cell Biology, Research Centre for Experimental Marine Biology and Biotechnology PiE and Science and Technology Faculty, University of the Basque Country (UPV/EHU), Sarriena z/g, E-48940 Leioa, Basque Country, Spain, Laboratoire Environnement Ressources des Pertuis Charentais (LER/PC), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Hammel, Maurine [0000-0001-9937-5678], Simon, Alexis [0000-0002-6176-5045], Burioli, Erika AV [0000-0003-2666-9258], Pépin, Jean-François [0000-0001-8548-8938], Lamy, Jean-Baptiste [0000-0002-6078-0905], Bernard, Ismael [0000-0002-3666-7419], Charrière, Guillaume M [0000-0002-4796-1488], Destoumieux-Garzon, Delphine [0000-0002-8793-9138], Bierne, Nicolas [0000-0003-1856-3197], and Apollo - University of Cambridge Repository

Subjects
0106 biological sciences, Mytilus edulis, genetic chimerism, Single-nucleotide polymorphism, Biology, 010603 evolutionary biology, 01 natural sciences, Genetic analysis, Article, 03 medical and health sciences, Rare Diseases, Dogs, Polymorphism (computer science), Neoplasms, Genotype, disseminated neoplasia, Genetics, Prevalence, 2.1 Biological and endogenous factors, Animals, genetic polymorphism, Aetiology, Allele, Genotyping, Ecology, Evolution, Behavior and Systematics, Cancer, 030304 developmental biology, Mytilus, Evolutionary Biology, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Sciences, biology.organism_classification, Null allele, Mytilus sp, 3. Good health, Europe, mussels, Mytilus sp. mussels, transmissible cancer
Abstract

Transmissible cancers are parasitic malignant cell lineages that have acquired the ability to infect new hosts from the same species, or sometimes related species. First described in dogs and Tasmanian devils, transmissible cancers were later discovered in some marine bivalves affected by a leukaemia-like disease. In Mytilus mussels, two lineages of bivalve transmissible neoplasia (BTN) have been described to date (MtrBTN1 and MtrBTN2), both of which emerged in a Mytilus trossulus founder individual. Here, we performed extensive screening of genetic chimerism, a hallmark of transmissible cancer, by genotyping 106single nucleotide polymorphisms of 5,907 European Mytilus mussels. Genetic analysis allowed us to simultaneously obtain the genotype of hosts - Mytilus edulis, M.galloprovincialis or hybrids - and the genotype of tumours of heavily infected individuals. In addition, a subset of 222 individuals were systematically genotyped and analysed by histology to screen for possible nontransmissible cancers. We detected MtrBTN2 at low prevalence in M. edulis, and also in M.galloprovincialis and hybrids although at a much lower prevalence. No MtrBTN1 or new BTN were found, but eight individuals with nontransmissible neoplasia were observed at a single polluted site on the same sampling date. We observed a diversity of MtrBTN2genotypes that appeared more introgressed or more ancestral than MtrBTN1 and reference healthy M.trossulus individuals. The observed polymorphism is probably due to somatic null alleles caused by structural variations or point mutations in primer-binding sites leading to enhanced detection of the host alleles. Despite low prevalence, two sublineages divergent by 10% fixed somatic null alleles and one nonsynonymous mtCOI (mitochondrial cytochrome oxidase I) substitution are cospreading in the same geographical area, suggesting a complex diversification of MtrBTN2since its emergence and host species shift.

Published
2021

20. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

Author

Morga, Benjamin, Jacquot, Maude, Pelletier, Camille, Chevignon, Germain, Dégremont, Lionel, Biétry, Antoine, Pepin, Jean-François, Heurtebise, Serge, Escoubas, Jean-Michel, Bean, Tim, Rosani, Umberto, Bai, Chang-Ming, Renault, Tristan, Lamy, Jean-Baptiste, Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie des Mollusques Marins - Ifremer (SG2M-LGPMM), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (Cefas), University of Padua [Italy], Yellow Sea Fisheries Research Institute, and Chinese Academy of Fishery Sciences

Subjects
Microbiology (medical), shellfish farming, OsHV-1, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], measurably evolution, marine virus, Microbiology, ComputingMilieux_MISCELLANEOUS, Original Research, diversity
Abstract

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.

Published
2021
Full Text
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21. Réussir l'épreuve écrite de sciences et technologie. Nouveau concours 2022

Author

Bächtold, Manuel, Boyer, Antonin, Mouahid, Gabriel, Roca, Pascale, Laboratoire Interdisciplinaire de Recherche en Didactique, Éducation et Formation (LIRDEF), Université de Montpellier (UM)-Université Paul-Valéry - Montpellier 3 (UPVM), Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

22. Limited dispersal and in situ diversification drive the evolutionary history of Rasborinae fishes in Sundaland

Author

Hadi Dahruddin, Tedjo Sukmono, Juliette Pouzadoux, Daisy Wowor, Erwan Delrieu-Trottin, Fabien L. Condamine, Arni Sholihah, Jean-François Agnèse, Lukas Rüber, Yuli Sulistya Fitriana, Marie-Ka Tilak, Nicolas Hubert, 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 Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut Teknologi Bandung (ITB), Indonesian Government, Museum für Naturkunde [Berlin], Universitas Indonesia (UI ), Indonesian Institute of Sciences (LIPI), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Naturhistorisches Museum [Bern], Institute of Ecology and Evolution [Bern, Switzerland], University of Bern, This study was supported by IRD through annual allocations (2012–2020) and incentive funds (2012–2013), the Ministry of Foreign Affairs and International Development through a BIO-Asia grant (BIOSHOT 2016-2017) managed by Campus France, the 'Institut Français d’Indonésie' through a 'Science et impacts' grant (2016-5758) and the European Commission through a grant from the Southeast Asia –Europe Joint Funding Scheme for Research and Innovation Programme (FRESHBIO, 307943/00). AS benefited from a PhD scholarship from the Indonesian Endowment Fund for Education (LPDP). The Indonesian ministry of research and technology approved this study., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and 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)

Subjects
0106 biological sciences, In situ, dispersal pathways, Pleistocene climatic fluctuations, 0303 health sciences, cryptic diversity, Ecology, historical biogeography, mitogenomes, phylogenetic reconstructions, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, sea levels, diversification models, ancestral areas estimation, 03 medical and health sciences, Geography, Biological dispersal, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Sea level, 030304 developmental biology
Abstract

Aim Sea-level changes have long been put forward to explain the colonization of Southeast Asian islands by freshwater aquatic organisms. We examined the relative impact of Sundaland geology since the Oligocene and of Pleistocene Eustatic Fluctuations on the mitochondrial lineage diversification of a species-rich subfamily of freshwater fishes widely distributed in Southeast Asia. We specifically tested if the expansion of exposed lands and increased island connectivity during Pleistocene low sea levels (the paleoriver hypothesis) induced bursts of diversification. Location Sundaland. Taxon Rasborinae (Actinopterygii, Cypriniformes, Danionidae). Methods We aggregated 1,017 cytochrome oxidase I sequences and 79 mitogenomes to delineate Molecular Operational Taxonomic Units (MOTUs) and further reconstruct a time-calibrated phylogeny of Rasborinae. Ancestral area estimations were conducted using both island and paleoriver partitioning to examine the impact of island connectivity during Pleistocene sea-level changes on dispersal. Temporal trends of diversification are explored through statistical selection of best-fit models. Results The origin of Sundaland mitochondrial lineages is dated at c. 33 Ma and four major clades are identified, which diversified between c. 31 and 22 Ma. The Island of Borneo and North Sunda paleoriver are identified as the source of Sundaland Rasborinae. Geographical patterns of lineage divergence indicate that most divergence events occurred within islands and diversification under constant birth rate models are the most likely for all clades. Conclusions The geographical and historical context of diversification of mitochondrial lineages in Rasborinae provides little support for the paleoriver hypothesis. The onset of isolation of Borneo from mainland Asia triggered the initial diversification of the group (c. 31–22 Ma). The late colonization of Java and Sumatra occurred through several independent dispersal events, poorly explained by Pleistocene sea-level changes and frequently followed by in situ diversification.

Published
2021

23. Is the cercarial emission rhythm of the parasite Schistosoma mansoni circadian ?

Author

Lasica, Chrystelle, Mouahid, Gabriel, F.D., chevalier, Le Clec’h, Winka, Chaparro, Cristian, Grunau, Christoph, Anderson, Timothy J., Moné, Hélène, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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 Texas Biomedical Research Institute [San Antonio, TX]

Subjects
ComputerSystemsOrganization_COMPUTERSYSTEMIMPLEMENTATION, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MathematicsofComputing_GENERAL, ComputingMilieux_MISCELLANEOUS, GeneralLiterature_MISCELLANEOUS, MathematicsofComputing_DISCRETEMATHEMATICS
Abstract

Best poster (teaser) prize. The prize was awarded by the EEID 2021 Scientific Committee.; International audience

Published
2021

24. Genetic analysis of praziquantel response in schistosome parasites implicates a Transient Receptor Potential channel

Author

Aidan M. Emery, Tim J. Anderson, Amadou Garba Djirmay, Amanda Strickland, Frédéric D. Chevalier, Marina McDew-White, Hélène Moné, Robbie Diaz, Khalid M. Al Mashikhi, Bonnie L. Webster, Joanne P. Webster, Ana Mattos, Salem Al Yafae, Claudia M. Rohr, Jonathan S. Marchant, Gabriel Mouahid, Mohamed A. Idris, Safari Kinung’hi, Fiona Allan, David Rollinson, Winka Le Clec’h, Philip T. LoVerde, Texas Biomedical Research Institute [San Antonio, TX], University of Texas Health Science Center at San Antonio [San Antonio], Medical College of Wisconsin [Milwaukee] (MCW), National Institute for Medical Research [Tanzania] (NIMR), The Natural History Museum [London] (NHM), Parasites and Vectors Division, London Centre for Neglected Tropical Disease Research, Natural History Museum, Wolfson Wellcome Biomedical Laboratories, The Natural History Museum, CEEED Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, Réseau International Schistosomiases Environnemental Aménagement et Lutte, World Health Organization [Geneva], Directorate General of Health Services, Sultan Qaboos University (SQU), Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
030231 tropical medicine, Nonsense mutation, Population, Schistosomiasis, Biology, Pharmacology, Genetic analysis, Praziquantel, 03 medical and health sciences, Transient receptor potential channel, Transient Receptor Potential Channels, 0302 clinical medicine, parasitic diseases, medicine, Animals, Parasites, Allele, education, 030304 developmental biology, Anthelmintics, 0303 health sciences, education.field_of_study, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, medicine.disease, biology.organism_classification, Schistosomiasis mansoni, 3. Good health, Schistosoma mansoni, Genome-Wide Association Study, medicine.drug
Abstract

Mass treatment with praziquantel (PZQ) monotherapy is the mainstay for schistosomiasis treatment. This drug shows imperfect cure rates in the field and parasites showing reduced PZQ response can be selected in the laboratory, but the extent of resistance in Schistosoma mansoni populations is unknown. We examined the genetic basis of variation in PZQ response in a S. mansoni population (SmLE-PZQ-R) selected with PZQ in the laboratory: 35% of these worms survive high dose (73 µg/mL) PZQ treatment. We used genome wide association to map loci underlying PZQ response. The major chr. 3 peak contains a transient receptor potential (Sm.TRPMPZQ) channel (Smp_246790), activated by nanomolar concentrations of PZQ. PZQ response shows recessive inheritance and marker-assisted selection of parasites at a single Sm.TRPMPZQ SNP enriched populations of PZQ-resistant (PZQ-ER) and sensitive (PZQ-ES) parasites showing >377 fold difference in PZQ response. The PZQ-ER parasites survived treatment in rodents better than PZQ-ES. Resistant parasites show 2.25-fold lower expression of Sm.TRPMPZQ than sensitive parasites. Specific chemical blockers of Sm.TRPMPZQ enhanced PZQ resistance, while Sm.TRPMPZQ activators increased sensitivity. A single SNP in Sm.TRPMPZQ differentiated PZQ-ER and PZQ-ES lines, but mutagenesis showed this was not involved in PZQ-response, suggesting linked regulatory changes. We surveyed Sm.TRPMPZQ sequence variation in 259 parasites from the New and Old World revealing one nonsense mutation that results in a truncated protein with no PZQ-binding site. Our results demonstrate that Sm.TRPMPZQ underlies variation in PZQ response in S. mansoni and provides an approach for monitoring emerging PZQ-resistance alleles in schistosome elimination programs.One Sentence SummaryA transient receptor potential channel determines variation in praziquantel-response in Schistosoma mansoni.

Published
2021

25. Molecular approaches reveal weak sibship aggregation and a high dispersal propensity in a non‐native fish parasite

Author

Prunier, J��r��me, Saint-P��, Keoni, Blanchet, Simon, Loot, G��raldine, Rey, Olivier, 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), 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, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), ANR-11-JSV7-0010,INCLIMPAR,Les effets du changement climatique sur les parasites : une étude prédictive intégrée(2011), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and 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)

Subjects
Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Populations and Evolution (q-bio.PE), transmission, full‐sibs, Parasite dispersal, Tracheliastes polycolpus, parasite dispersal, Full-sibs, full&#8208, FOS: Biological sciences, sibs, genetic structure, parentage analysis, Parentage analysis, Quantitative Biology - Populations and Evolution, Tracheliastespolycolpus, QH540-549.5, Original Research
Abstract

Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity are important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer these parameters from wildlife parasites given the difficulty in tracking these organisms. Molecular‐based inferences constitute a promising approach that has yet rarely been applied in the wild. Here, we combined several population genetic analyses including sibship reconstruction to document the genetic structure, patterns of sibship aggregation, and the dispersal dynamics of a non‐native parasite of fish, the freshwater copepod ectoparasite Tracheliastes polycolpus. We collected parasites according to a hierarchical sampling design, with the sampling of all parasites from all host individuals captured in eight sites spread along an upstream–downstream river gradient. Individual multilocus genotypes were obtained from 14 microsatellite markers, and used to assign parasites to full‐sib families and to investigate the genetic structure of T. polycolpus among both hosts and sampling sites. The distribution of full‐sibs obtained among the sampling sites was used to estimate individual dispersal distances within families. Our results showed that T. polycolpus sibs tend to be aggregated within sites but not within host individuals. We detected important upstream‐to‐downstream dispersal events of T. polycolpus between sites (modal distance: 25.4 km; 95% CI [22.9, 27.7]), becoming scarcer as the geographic distance from their family core location increases. Such a dispersal pattern likely contributes to the strong isolation‐by‐distance observed at the river scale. We also detected some downstream‐to‐upstream dispersal events (modal distance: 2.6 km; 95% CI [2.2–23.3]) that likely result from movements of infected hosts. Within each site, the dispersal of free‐living infective larvae among hosts likely contributes to increasing genetic diversity on hosts, possibly fostering the evolutionary potential of T. polycolpus., Knowledge about parasite dispersal is still scarce, although it may greatly influence key ecological and evolutionary processes such as virulence and local adaptation. We here focused on the freshwater ectoparasite Tracheliastes polycolpus and its principal fish host Leuciscus burdigalensis in a French river network. Using genetic assignment approaches, we found that dispersal in T. polycolpus at the metapopulation level is mostly driven by waterflow during its free‐living infectious stage (downstream movements of ~25.4 km) and, to a lesser extent, by movements of its hosts during its adult parasitic stage (upstream movements of ~2.6 km). Furthermore, T. polycolpus sibs do not tend to aggregate on the same fish, thus fostering genetic variation within hosts.

Published
2021

26. Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome

Author

Céline Cosseau, Jérôme Boissier, Christoph Grunau, Beatriz Vicoso, Ronaldo de Carvalho Augusto, Nathalie Arancibia, David Roquis, Marion Picard, Ingo Bulla, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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 Institute of Science and Technology [Austria] (IST Austria)

Subjects
chromatin landscape, Gene dosage, Chromosomes, Female heterogamety, Chromatin remodeling, Epigenesis, Genetic, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Dosage Compensation, Genetic, Genetics, Animals, Dosage compensation, Epigenetics, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Z chromosome, female heterogamety, biology, histone modifications, Histone modifications, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Schistosoma mansoni, Chromatin, Histone, dosage compensation, biology.protein, Female, Chromatin landscape, 030217 neurology & neurosurgery, Heterogametic sex, Research Article
Abstract

Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.

Published
2019

27. Litopenaeus vannamei stylicins are constitutively produced by hemocytes and intestinal cells and are differentially modulated upon infections

Author

Rafael Diego Rosa, Evelyne Bachère, Cairé Barreto, Gabriel Machado Matos, Paulina Schmitt, Luciane Maria Perazzolo, Natanael Dantas Farias, Jean-Luc Rolland, Nicolas Argenta, Marcelo Falchetti, Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Pontificia Universidad Católica de Valparaíso (PUCV), Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
0301 basic medicine, Hemocytes, Invertebrate immunity, Litopenaeus, Crustacean, Peptide, Aquatic Science, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Microbiology, 03 medical and health sciences, White spot syndrome virus 1, Penaeidae, Molecular diversity, Gene expression, Animals, Environmental Chemistry, Amino Acid Sequence, 14. Life underwater, Gene, Vibrio, chemistry.chemical_classification, Base Sequence, Penaeid shrimp, biology, fungi, Midgut, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, Shrimp, Intestines, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Gene Expression Regulation, chemistry, Host-Pathogen Interactions, 040102 fisheries, Host defense peptide, 0401 agriculture, forestry, and fisheries, Peptides, Antimicrobial peptide
Abstract

International audience; Stylicins are anionic antimicrobial host defense peptides (AAMPs) composed of a proline-rich Nterminal region and a C-terminal portion containing 13 conserved cysteine residues. Here, we have increased our knowledge about these unexplored crustacean AAMPs by the characterization of novel stylicin members in the most cultivated penaeid shrimp, Litopenaeus vannamei. We showed that the L. vannamei stylicin family is composed of two members (Lvan-Stylicin1 and Lvan-Stylicin2) encoded by different loci which vary in gene copy number. Unlike the other three gene-encoded antimicrobial peptide families from penaeid shrimp, the expression of Lvan-Stylicins is not restricted to hemocytes. Indeed, they are also produced by the columnar epithelial cells lining the midgut and its anterior caecum. Interestingly, Lvan-Stylicins are simultaneously transcribed at different transcriptional levels in a single shrimp and are differentially modulated in hemocytes after infections. While the expression of both genes showed to be responsive to damage-associated molecular patterns, only Lvan-Stylicin2 was induced after a Vibrio infection. Besides, Lvan-Stylicins also showed a distinct pattern of gene expression in the three portions of the midgut (anterior, middle and posterior) and during shrimp development. We provide here the first evidence of the diversity of the stylicin antimicrobial peptide family in terms of sequence and gene expression distribution and regulation.

Published
2019

28. Changes in planktonic microbial components in interaction with juvenile oysters during a mortality episode in the Thau lagoon (France)

Author

Behzad Mostajir, Marion Richard, Charles Vanhuysse, Serge Mortreux, Béatrice Bec, Valerie Derolez, Jocelyne Oheix, Jean Luc Rolland, Patrick Le Gall, Vincent Ouisse, Sébastien Mas, Franck Lagarde, David Parin, Annie Fiandrino, Myriam D. Callier, Gregory Messiaen, Camila Chantalat, Martine Fortune, E. Hatey, Anaïs Degut, Dominique Munaron, Emmanuelle Roque D'Orbcastel, Laboratoire d'Informatique Médicale et Ingénierie des Connaissances en e-Santé (LIMICS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris 13 (UP13), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Centre d'Ecologie marine expérimentale (MEDIMEER), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Environnement Ressources (LER-LR), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Institut Français de Recherche pour l'Exploitation de la Mer, Station expérimentale de Palavas les Flots, Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Université Paris 13 (UP13)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Environnement Ressources Languedoc Roussillon (LERLR), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), and Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL)

Subjects
Spat, Oyster, animal structures, [SDV]Life Sciences [q-bio], Zoology, Aquatic Science, 03 medical and health sciences, Heterotrophic flagellates, Aquaculture, biology.animal, Juvenile, 14. Life underwater, Mortality, Picoplankton, ComputingMilieux_MISCELLANEOUS, Shellfish, 030304 developmental biology, 0303 health sciences, Ciliates, biology, business.industry, Balanion, fungi, food and beverages, Pelagic zone, 04 agricultural and veterinary sciences, Pacific oyster, equipment and supplies, biology.organism_classification, Magallana gigas, Uronema, OsHV-1 mu Var, Crassostrea gigas, [SDE]Environmental Sciences, 040102 fisheries, bacteria, 0401 agriculture, forestry, and fisheries, Crassostrea, business
Abstract

Oysters modify the planktonic microbial community structure by their filtration and NH4 excretion activities. While many studies have been conducted on this subject with adult oysters, none had been carried out in situ with juveniles. Pacific oyster juveniles (Magallana gigas, previously Crassostrea gigas) died massively all over the world since 2008 in relation with OsHV-1 infection. During mortality episodes, sick and dead oysters are not separated from healthy live ones, and left to decay in the surrounding environment, with unknown consequences for the nutrient cycle and planktonic microbial components (PMC). The present study aimed to elucidate for the first time the interactions between oyster juveniles and PMC during a mortality episode. Innovative 425-L pelagic chambers were deployed weekly in situ around oyster lanterns along a stocking-density gradient in the Thau Mediterranean lagoon (France) before, during and after an oyster mortality episode, from April to May 2015. This study reveals (i) significant changes of planktonic microbial community structure during mortality episodes, with a proliferation of picoplankton (

Published
2019

29. Hypomethylated poplars show higher tolerance to water deficit and highlight a dual role for DNA methylation in shoot meristem: regulation of stress response and genome integrity

Author

Jose Caius, Sophie Lanciano, Stéphane Maury, M-C Lesage-Descauses, Sylvie Citerne, Hervé Cochard, Christian Daviaud, Steven H. Strauss, Christoph Grunau, Mamadou Dia Sow, Alain Delaunay, Franck Brignolas, A-L Le Gac, Régis Fichot, Cristian Chaparro, Ludivine Soubigou-Taconnat, Jörg Tost, Véronique Brunaud, Marie Mirouze, I. le Jan, Vincent Segura, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, adaptation, développement des plantes (UMR DIADE), 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]), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-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 Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), 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), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Forest Ecosystems and Society, Oregon State University (OSU), 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), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and 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)

Subjects
0106 biological sciences, Transposable element, 0303 health sciences, Phenotypic plasticity, DNA methylation, Epigenics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Biology, Meristem, transposable element, phytohormone, 01 natural sciences, Cell biology, Transcriptome, 03 medical and health sciences, RNA interference, Copy-number variation, Gene, 030304 developmental biology, 010606 plant biology & botany, Meristematic cells : drought
Abstract

As fixed and long living organisms subjected to repeated environmental stresses, trees have developed mechanisms such as phenotypic plasticity that help them to cope with fluctuating environmental conditions. Here, we tested the role DNA methylation as a hub of integration, linking plasticity and physiological response to water deficit in the shoot apical meristem of the model tree poplar (Populus). Using a reverse genetic approach, we compared hypomethylated RNAi-ddm1lines to wild-type trees for drought tolerance. An integrative analysis was realized with phytohormone balance, methylomes, transcriptomes and mobilomes.Hypomethylated lines were more tolerant when subjected to moderate water deficit and were intrinsically more tolerant to drought-induced cavitation. The alteration of theDDM1machinery induced variation in DNA methylation in a cytosine context dependent manner, both in genes and transposable elements. Hypomethylated lines subjected to water deficit showed altered expression of genes involved in phytohormone pathways, such as salicylic acid and modified hormonal balance. Several transposable elements showed stress- and/or line-specific patterns of reactivation, and we could detect copy number variations for two of them in stressedddm1lines.Overall, our data highlight two major roles for DNA methylation in the shoot apical meristem: control of stress response and plasticity through transduction of hormone signaling and maintenance of genome integrity through the control of transposable elements.

Published
2021

30. Effects of temperature and p CO 2 on the respiration, biomineralization and photophysiology of the giant clam Tridacna maxima

Author

Claire E. Lazareth, Claude Soyez, Chloé Brahmi, Nabila Gaertner-Mazouni, Jeremie Vidal-Dupiol, Gilles Le Moullac, Benoit Beliaeff, Leila Chapron, Université de la Polynésie Française (UPF), 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'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), and 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)

Subjects
0106 biological sciences, photosynthetic yield, Effects of global warming on oceans, Thermal stress, ocean acidification, Photosynthesis, 010603 evolutionary biology, 01 natural sciences, Acclimatization, chemistry.chemical_compound, Respiration, 14. Life underwater, Growth rate, symbionts, biology, Chemistry, 010604 marine biology & hydrobiology, giant clam, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Giant clam, biology.organism_classification, 13. Climate action, Environmental chemistry, Carbon dioxide, Seawater, respiration
Abstract

Such as many other reef organisms, giant clams are today confronted to global change effects and can suffer mass bleaching or mortality events mainly related to abnormally high seawater temperatures. Despite its strong ecological and socio-economical importance, its responses to the two most alarming threats linked to global change (i.e., ocean warming and acidification) still need to be explored. We investigated physiological responses of 4-years-oldTridacna maximaspecimens to realistic levels of temperature and partial pressure of carbon dioxide (pCO2) (+1.5°C and +800μatm of CO2) predicted for 2100 in French Polynesian lagoons during the warmer season. During a 65-days crossed-factor experiment, individuals were exposed to two temperatures (29.2°C; 30.7°C) and twopCO2(430µatm; 1212µatm) conditions. Impact of each parameter and their potential synergetic effect were evaluated on respiration, biomineralization and photophysiology. Kinetics of thermal and acidification stress were evaluated by performing measurements at different times of exposure (29, 41, 53, 65 days). At 30.7°C, the holobiont O2production, symbiont photosynthetic yield, and density were negatively impacted. HighpCO2had a significant negative effect on shell growth rate, symbiont photosynthetic yield and density. Shell microstructural modifications were observed from 41 days in all temperature andpCO2conditions. No significant synergetic effect was found. Today thermal conditions (29.2°C) appeared to be sufficiently stressful to induce a host acclimatization process. All these observations indicate that temperature andpCO2are both forcing variables affectingT. maximaphysiology and jeopardize its survival under environmental conditions predicted for the end of this century.

Published
2021

31. Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta

Author

Guillaume Mitta, Marine Pratlong, Jeremie Vidal-Dupiol, Pierre Pontarotti, Cristian Chaparro, Christoph Grunau, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), 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), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0303 health sciences, geography, geography.geographical_feature_category, Coral, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Sequence assembly, Coral reef, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Deep sequencing, 03 medical and health sciences, Annotation, Evolutionary biology, Marine ecosystem, 14. Life underwater, Gene, 030304 developmental biology
Abstract

Coral reefs are the most divers marine ecosystem. However, under the pressure of global changes and anthropogenic disturbances corals and coral reefs are declining worldwide. In order to better predict and understand the future of these organisms all the tools of modern biology are needed today. However, many NGS based approaches are not feasible in corals because of the lack of reference genomes. Therefore we have sequenced, de novo assembled, and annotated, the draft genome of one of the most studied coral species, Pocillopora acuta (ex damicornis). The sequencing strategy was based on four libraries with complementary insert size and sequencing depth (180pb, 100x; 3Kb, 25x; 8kb, 12x and 20 kb, 12x). The de novo assembly was performed with Platanus (352 Mb; 25,553 scaffolds; N50 171,375 bp). 36,140 genes were annotated by RNA-seq data and 64,558 by AUGUSTUS (Hidden-Markov model). Gene functions were predicted through Blast and orthology based approaches. This new genomic resource will enable the development of a large array of genome wide studies but also shows that the de novo assembly of a coral genome is now technically feasible and economically realistic.

Published
2021

32. Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis

Author

Anaïs Portet, David Duval, Richard Galinier, Camille Huot, Ana Lokmer, Eve Toulza, Benjamin Gourbal, Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Galinier, Richard [0000-0002-4180-9303], Gourbal, Benjamin [0000-0003-2097-2563], and Apollo - University of Cambridge Repository

Subjects
Microbiology (medical), QH301-705.5, Biomphalaria snail, Biomphalaria, Schistosomiasis, Snail, Microbiology, immune response, 03 medical and health sciences, Schistosoma infection, Virology, biology.animal, parasitic diseases, microbiota, medicine, Biomphalaria glabrata, Biology (General), Immune response, bacteria, 030304 developmental biology, Schistosoma, 0303 health sciences, biology, Bacteria, 030306 microbiology, Microbiota, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Intermediate host, food and beverages, dysbiosis, medicine.disease, biology.organism_classification, 3. Good health, stomatognathic diseases, Dysbiosis, Schistosoma mansoni
Abstract

Host-parasite interaction can result in a strong alteration of the host-associated microbiota. This dysbiosis can affect the fitness of the host, can modify pathogen interaction and the outcome of diseases. Biomphalaria glabrata is the snail intermediate host of the trematode Schistosoma mansoni, the agent of human schistosomiasis, causing hundreds of thousands of deaths every year. Here, we present the first study of the snail bacterial microbiota in response to Schistosoma infection. We examined the interplay between B. glabrata, S. mansoni and host microbiota. Snails were infected and the microbiota composition was analysed by 16S rDNA amplicon sequencing approach. We demonstrated that the microbial composition of water did not affect the microbiota composition. Then, we characterised the Biomphalaria bacterial microbiota at the individual scale in both naive and infected snails. Sympatric and allopatric strains of parasites were used for infections and re-infections to analyse the modification or dysbiosis of snail microbiota in different host-parasite co-evolutionary contexts. Concomitantly, using RNAseq, we investigated the link between bacterial microbiota dysbiosis and snail anti-microbial peptide immune response. This work paves the way for a better understanding of snail/schistosome interaction and should have critical consequences in terms of snail control strategies for fighting schistosomiasis disease in the field.

Published
2021

33. No pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: From mating interactions to differential gene expression

Author

Jérôme Boissier, Stephen Mulero, Julien Kincaid-Smith, Marta Reguera-Gomez, Jean-François Allienne, Eglantine Mathieu-Bégné, Eve Toulza, Cristian Chaparro, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), CEEED Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain, and Université de Perpignan Via Domitia (UPVD)

Subjects
0301 basic medicine, Male, Introgression, RC955-962, Gene Expression, Biochemistry, Transmembrane Transport Proteins, 0302 clinical medicine, Medical Conditions, Cricetinae, Arctic medicine. Tropical medicine, Medicine and Health Sciences, Mating, Schistosoma haematobium, Genetics, Mammals, biology, Mosaicism, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Reproduction, Eukaryota, Reproductive isolation, Genomics, Infectious Diseases, Mate choice, Vertebrates, Hamsters, Schistosoma, Female, Public aspects of medicine, RA1-1270, Transcriptome Analysis, Research Article, Evolutionary Processes, Reproductive Isolation, Genetic Speciation, 030231 tropical medicine, Rodents, 03 medical and health sciences, Helminths, Parasitic Diseases, Animals, Gene, Evolutionary Biology, Host (biology), Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, Computational Biology, Proteins, biology.organism_classification, Genome Analysis, Invertebrates, Schistosoma Haematobium, 030104 developmental biology, Gene Expression Regulation, Amniotes, Zoology
Abstract

Species usually develop reproductive isolation mechanisms allowing them to avoid interbreeding. These preventive barriers can act before reproduction, “pre-zygotic barriers”, or after reproduction, “post-zygotic barriers”. Pre-zygotic barriers prevent unfavourable mating, while post-zygotic barriers determine the viability and selective success of the hybrid offspring. Hybridization in parasites and the underlying reproductive isolation mechanisms maintaining their genetic integrity have been overlooked. Using an integrated approach this work aims to quantify the relative importance of pre-zygotic barriers in Schistosoma haematobium x S. bovis crosses. These two co-endemic species cause schistosomiasis, one of the major debilitating parasitic diseases worldwide, and can hybridize naturally. Using mate choice experiments we first tested if a specific mate recognition system exists between both species. Second, using RNA-sequencing we analysed differential gene expression between homo- and hetero-specific pairing in male and female adult parasites. We show that homo- and hetero-specific pairing occurs randomly between these two species, and few genes in both sexes are affected by hetero-specific pairing. This suggests that i) mate choice is not a reproductive isolating factor, and that ii) no pre-zygotic barrier except spatial isolation “by the final vertebrate host” seems to limit interbreeding between these two species. Interestingly, among the few genes affected by the pairing status of the worms, some can be related to pathways affected during male and female interactions and may also present interesting candidates for species isolation mechanisms and hybridization in schistosome parasites., Author summary Understanding how species maintain their genetic integrity is a central question in evolutionary biology. While isolation mechanisms are well documented in free-living organisms, it is currently not the case for parasite species. Yet, occurrence of parasite hybrids is a critical global health concern since these hybrids are expected to be more harmful than parental species. We addressed the question of reproductive isolation mechanisms in parasitic species by conducting an integrative experimental study (from mate choice to gene expression) on two schistosome species (Schistosoma haematobium and S. bovis) that parasitize human and cattle, respectively. Importantly, their hybrid progeny has been involved in recent outbreaks, including outbreaks outside of endemic areas. We showed that rather than having a homo-specific mate choice, S. haematobium and S. bovis mate randomly. Also, male and female worms only express a few genes differentially when involved in a hetero-specific pair compared to a homo-specific pair. We consequently suggest that these two schistosome species lack strong reproduction isolation mechanisms, except those imposed by specificity to the final host species. Our results raise the concern that in the absence of post-zygotic barriers in sympatric zones hybridization might be more common than previously thought if these two species are able to encounter each other.

Published
2021

34. BioQuiz : Parasitologie « Une histoire d'éperon »

Author

Saint, Chloé, Damiani, Céline, Boissier, Jérôme, Totet, Anne, Le Govic, Yohann, Laboratoire de parasitologie et de mycologie médicales [CHU Amiens], CHU Amiens-Picardie, Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Université de Perpignan Via Domitia (UPVD), Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Abstract

International audience; Description Un jeune garçon de 15 ans est hospitalisé pour malaise et perte de connaissance à la suite d'une dispute avec sa famille d'accueil temporaire. Le bilan étiologique complet, comprenant notamment un scanner cérébral injecté et un électroencéphalogramme, est sans particularité. Au cours de l'hospitalisation, on découvre une hématurie macroscopique, associée à des douleurs scrotales. Le reste de l'examen clinique est normal. Le patient est, par ailleurs, apyrétique et en parfait état général. À l'interrogatoire, on apprend qu'il est originaire de Côte d'Ivoire, qu'il vit le reste de l'année dans un foyer pour mineurs en Seine-Saint-Denis (93), et que son dernier séjour dans son pays natal remonte à cinq ans. Le bilan sanguin montre une légère hyperéosinophilie (1,1 G/L ; N inférieur à 0,5 G/L) sans aucune autre anomalie. Un examen cytobactériologique des urines confirme l'hématurie, accompagnée d'une leucocyturie. La culture est négative. Une échographie vésicale est pratiquée, montrant un épaississement pseudo-polypoïde isoéchogène sur la paroi postérieure de la vessie. Un examen parasitologique des urines est alors réalisé. Outre la présence d'hématies, plusieurs éléments attirent l'attention du microscopiste (figures 1A et 1B). La barre représente 50 μm.

Published
2021

35. New insights into biomphalysin gene family diversification in the vector snail Biomphalaria glabrata

Author

Silvain Pinaud, Guillaume Tetreau, Pierre Poteaux, Richard Galinier, Cristian Chaparro, Damien Lassalle, Anaïs Portet, Elodie Simphor, Benjamin Gourbal, David Duval, Interactions Hôtes-Pathogènes-Environnements (IHPE), and 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)

Subjects
Pore Forming Cytotoxic Proteins, 0301 basic medicine, lcsh:Immunologic diseases. Allergy, invertebrate immunity, In silico, Immunology, biomphalysin, Snail, Disease Vectors, Genome, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, aerolysin, Species Specificity, Gene Duplication, biology.animal, Gene duplication, parasitic diseases, biomphalaria, Animals, Immunology and Allergy, Biomphalaria glabrata, Gene family, structure, Gene, Phylogeny, Original Research, Genetics, 030102 biochemistry & molecular biology, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, Schistosoma mansoni, biology.organism_classification, 030104 developmental biology, pore-forming toxin (PFT), Multigene Family, Horizontal gene transfer, lcsh:RC581-607
Abstract

Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - inBiomphalaria glabratasnail, the intermediate host of the trematodeSchistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. Anin silicostructural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.

Published
2021

36. la diversité génétique viral quelle est son rôle dans l'interaction du virus ostreid herpesvirus 1 et son hôte l’huître crassostrea gigas ?

Author

Delmotte, Jean, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Université Montpellier, and Jean-Michel Escoubas

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Host pathogene interaction, Viral diversity, Diversité génétique, Ostreid herpesvirus 1, Oyster, Interactions hôte pathogène, Huître, Genetic diversity
Abstract

The contemporary genetic diversity of viruses is the result of the continuous and dynamic interaction of past ecological and evolutionary processes with its host. For more than 30 years, mortality episodes have been impacting the oyster industry. These have complex etiologies but are often associated with a Herpesvirus: Ostreid Herpesvirus 1 (OsHV-1). Since 2008, unprecedented mortality events in Crassostra gigas species have been reported worldwide. The appearance of these excess mortalities coincides with the emergence of a new genotype of the virus: the OsHV-1 µVar. After several years of research to understand this pathosystem, it was recently demonstrated that a Herpesvirus: Ostreid herpesvirus 1 (OsHV-1) was the agent initiating pathogenesis and leading to host death. In parallel, the observation of other related variants of OsHV-1 virus have been associated with other mortality epidemics in other bivalve species. However, until recently, studies on the genetic diversity of the virus used a short fragment of the virus genome. There is therefore an urgent need to characterize this OsHV-1 genetic diversity at the whole genome level. This thesis manuscript provides us with the tools necessary for a complete characterization of the virus genome. We confirm that OsHV-1 viral populations are different according to their geographical location with potential genomic signatures between sites. Finally, thanks to the complete assembly of twenty-one genomes, we propose a scheme of virus dissemination through molecular epidemiology analysis using innovative bioinformatics tools. Our results suggest that the genetic diversity of the virus within the C. gigas species is relatively small. This observation seems to contrast with previous work suggesting a significant genetic diversity of the OsHV-1 virus. However, we show that it is necessary to better define the diversity within a particular species and within a given time frame in order to correctly interpret it. However, this diversity is not non-existent and we discuss what could be the driving force behind the observed diversity. This thesis work is thus a notable starting point for future research characterizing genetic diversity in order to understand its biological consequences. Thus it provides the theoretical and methodological framework for a better understanding of pathogenic host interactions.; La diversité génétique contemporaine des virus est le résultat de l'interaction continue et dynamique des processus écologiques et évolutifs passés avec son hôte. Depuis plus de 30 ans des épisodes de mortalités impactent l’industrie ostréicole. Celles-ci ont des étiologies complexes mais sont souvent associées à un Herpèsvirus : l’Ostreid Herpèsvirus 1 (OsHV-1). Depuis 2008 l’apparition d'événements de mortalité sans précédent chez l’espèce Crassostra gigas ont été signalés à l’échelle mondiale. L’apparition de ces surmortalités coïncident avec l'émergence d’un nouveau génotype du virus : l’OsHV-1 µVar. Après plusieurs années de recherche pour comprendre ce pathosystème, il a été démontré récemment qu’un Herpèsvirus : l’Ostreid herpesvirus 1 (OsHV-1) était l’agent initiant la pathogenèse et aboutissant à la mort de l’hôte. En parallèle, l’observation d’autres variants apparentés du virus OsHV-1 ont été associés à d'autres épidémies de mortalité pour d’autres espèces de bivalves. Or jusqu'à récemment, les études sur la diversité génétique du virus utilisent un court fragment du génome du virus. Il est donc urgent de caractériser cette diversité génétique d’OsHV-1 à l’échelle du génome entier. Dans ce manuscrit de thèse nous apportant les outils nécessaire à la caractérisation complète du génome du virus. Nous confirmons que les populations virales d’OsHV-1 sont différentes selon leurs localisation géographique avec de potentiels signatures génomiques entre les sites. Enfin, grâce à l’assemblage complet de vingt et un génomes nous proposons un schéma de dissémination du virus au travers d'analyses d’épidémiologie moléculaire à l’aide d’outils bioinformatique innovants. Nos résultats semblent indiquer que la diversité génétique du virus au sein de l’espèce C. gigas est relativement restreinte. Cette observation semble contraster avec les travaux antérieurs suggérant une diversité génétique importante du virus OsHV-1. Cependant, nous montrons qu’il est nécessaire de mieux définir la diversité au sein d’une espèce en particulier et dans un temps donnée pour interpréter correctement celle-ci. Cette diversité n’est cependant pas inexistante et nous discutons quelle pourrait être le moteur de la diversité observé. Ce travail de thèse est donc un point de départ notable pour les recherches futures caractérisant la diversité génétique pour appréhender ses conséquences biologiques. Ainsi il fournit le cadre théorique et méthodologique pour mieux comprendre les interactions hôtes pathogènes.

Published
2021

37. Application of a genus-specific LAMP assay for schistosome species to detect Schistosoma haematobium x Schistosoma bovis hybrids

Author

Begoña Febrer-Sendra, Beatriz Crego-Vicente, Etienne K. Angora, Pedro Fernández-Soto, Jérôme Boissier, Juan García-Bernalt Diego, Ana Oleaga, Antonio Muro, Research Centre for Tropical Diseases at the University of Salamanca, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny (UFHB), Parasitology Laboratory, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Instituto de Salud Carlos III, European Commission, Oleaga, Ana [0000-0002-8019-7354], and Oleaga, Ana

Subjects
Schistosome hybrids, 030231 tropical medicine, lcsh:Medicine, Schistosomiasis, genus-specific LAMP, Article, Serology, 03 medical and health sciences, 0302 clinical medicine, Genus, Schistosoma haematobium, LAMP, parasitic diseases, molecular diagnosis, medicine, schistosome hybrids, species-specific LAMP, Species-specific LAMP, Schistosoma bovis, 030304 developmental biology, Hybrid, Schistosoma, 0303 health sciences, biology, business.industry, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:R, General Medicine, medicine.disease, biology.organism_classification, DNA extraction, Virology, 3. Good health, Genus-specific LAMP, Molecular diagnosis, business
Abstract

13 páginas, 3 figuras, 2 tablas, Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions caused by different species of parasitic flatworms of the genus Schistosoma. The emergence of natural hybrids of schistosomes indicate the risk of possible infection to humans and their zoonotic potential, specifically for Schistosoma haematobium and S. bovis. Hybrid schistosomes have the potential to replace existing species, generate new resistances, pathologies and extending host ranges. Hybrids may also confuse the serological, molecular and parasitological diagnosis. Currently, LAMP technology based on detection of nucleic acids is used for detection of many agents, including schistosomes. Here, we evaluate our previously developed species-specific LAMP assays for S. haematobium, S. mansoni, S. bovis and also the genus-specific LAMP for the simultaneous detection of several Schistosoma species against both DNA from pure and, for the first time, S. haematobium x S. bovis hybrids. Proper operation was evaluated with DNA from hybrid schistosomes and with human urine samples artificially contaminated with parasites’ DNA. LAMP was performed with and without prior DNA extraction. The genus-specific LAMP properly amplified pure Schistosoma species and different S. haematobium-S. bovis hybrids with different sensitivity. The Schistosoma spp.-LAMP method is potentially adaptable for field diagnosis and disease surveillance in schistosomiasis endemic areas where human infections by schistosome hybrids are increasingly common, This research was funded by the Institute of Health Carlos III, ISCIII, Spain (www.isciii.es), grants: RICET RD16/0027/0018 (A.M.), PI19/01727 (P.F.-S.), European Union cofinancing by FEDER (Fondo Europeo de Desarrollo Regional) ‘Una manera de hacer Europa’. We also acknowledge support by the Predoctoral Fellowship Program of University of Salamanca and cofinancing by Santander Bank, and Predoctoral Fellowship Program of Junta de Castilla y León cofinancing by Fondo Social Europeo

Published
2021

38. Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)

Author

Delphine Gourcilleau, Christoph Grunau, Sara Marin, Mathieu Latutrie, Benoit Pujol, Pierick Mouginot, Nelia Luviano Aparicio, Jean-Louis Hemptinne, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), 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), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-13-JSV7-0002,CAPA,Prédire la capacité des populations à s'adapter en fonction de leur histoire évolutive et de leur contexte environnemental(2013), European Project: 681484,H2020,ERC-2015-CoG,ANGI(2016), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), 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), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0106 biological sciences, 0301 basic medicine, lcsh:QH426-470, Population, epiGBS, Biology, 01 natural sciences, Genome, phenotypic plasticity, Article, Epigenesis, Genetic, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Shade avoidance, Antirrhinum majus, Genetics, Antirrhinum, Epigenetics, education, shade avoidance, Genetics (clinical), education.field_of_study, Phenotypic plasticity, epigenetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, stem elongation, Genetic Variation, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DNA Methylation, biology.organism_classification, Adaptation, Physiological, Plant Leaves, lcsh:Genetics, 030104 developmental biology, Phenotype, Evolutionary biology, Reduced representation bisulfite sequencing, DNA methylation, Sunlight, 010606 plant biology & botany
Abstract

International audience; The phenotypic plasticity of plants in response to change in their light environment, and in particularly, to shade is a schoolbook example of ecologically relevant phenotypic plasticity with evolutionary adaptive implications. Epigenetic variation is known to potentially underlie plant phenotypic plasticity. Yet, little is known about its role in ecologically and evolutionary relevant mechanisms shaping the diversity of plant populations in nature. Here we used a reference-free reduced representation bisulfite sequencing method for non-model organisms (epiGBS) to investigate changes in DNA methylation patterns across the genome in snapdragon plants (Antirrhinum majus L.). We exposed plants to sunlight versus artificially induced shade in four highly inbred lines to exclude genetic confounding effects. Our results showed that phenotypic plasticity in response to light versus shade shaped vegetative traits. They also showed that DNA methylation patterns were modified under light versus shade, with a trend towards global effects over the genome but with large effects found on a restricted portion. We also detected the existence of a correlation between phenotypic and epigenetic variation that neither supported nor rejected its potential role in plasticity. While our findings imply epigenetic changes in response to light versus shade environments in snapdragon plants, whether these changes are directly involved in the phenotypic plastic response of plants remains to be investigated. Our approach contributed to this new finding but illustrates the limits in terms of sample size and statistical power of population epigenetic approaches in non-model organisms. Pushing this boundary will be necessary before the relationship between environmentally induced epigenetic changes and phenotypic plasticity is clarified for ecologically relevant mechanisms with evolutionary implications

Published
2021
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39. The Pacific Oyster Mortality Syndrome, a Polymicrobial and Multifactorial Disease: State of Knowledge and Future Directions

Author

Julien de Lorgeril, Guillaume Mitta, Lionel Degremont, Eve Toulza, Fabrice Pernet, Bruno Petton, Delphine Destoumieux-Garzón, 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 national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), ANR-19-CE20-0004,DECICOMP,Déchiffrer toute la complexité du syndrome de mortalité des huîtres du Pacifique pour modéliser le risque épidémiologique.(2019), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), 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), 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 de Génétique et Pathologie des Mollusques Marins (LGPMM), and Santé, Génétique et Microbiologie des Mollusques (SGMM)

Subjects
0301 basic medicine, lcsh:Immunologic diseases. Allergy, Oyster, animal structures, 030106 microbiology, Immunology, Review, Disease, multifactorial disease, 03 medical and health sciences, Aquaculture, biology.animal, medicine, Pacific oyster mortality syndrome, Animals, Immunology and Allergy, Colonization, 14. Life underwater, Crassostrea, Panzootic, Vibrio, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, OsHV-1, Ecology, business.industry, Microbiota, fungi, Age Factors, DNA Viruses, Temperature, Outbreak, food and beverages, Herpesviridae Infections, Pacific oyster, medicine.disease, biology.organism_classification, opportunistic bacterial pathogens, 030104 developmental biology, polymicrobial disease, Crassostrea gigas, [SDV.IMM]Life Sciences [q-bio]/Immunology, business, lcsh:RC581-607, Dysbiosis
Abstract

The Pacific oyster (Crassostreae gigas) has been introduced from Asia to numerous countries around the world during the 20th century. C. gigas is the main oyster species farmed worldwide and represents more than 98% of oyster production. The severity of disease outbreaks that affect C. gigas, which primarily impact juvenile oysters, has increased dramatically since 2008. The most prevalent disease, Pacific oyster mortality syndrome (POMS), has become panzootic and represents a threat to the oyster industry. Recently, major steps towards understanding POMS have been achieved through integrative molecular approaches. These studies demonstrated that infection by Ostreid herpesvirus type 1 µVar (OsHV-1 µvar) is the first critical step in the infectious process and leads to an immunocompromised state by altering hemocyte physiology. This is followed by dysbiosis of the microbiota, which leads to a secondary colonization by opportunistic bacterial pathogens, which in turn results in oyster death. Host and environmental factors (e.g. oyster genetics and age, temperature, food availability, and microbiota) have been shown to influence POMS permissiveness. However, we still do not understand the mechanisms by which these different factors control disease expression. The present review discusses current knowledge of this polymicrobial and multifactorial disease process and explores the research avenues that must be investigated to fully elucidate the complexity of POMS. These discoveries will help in decision-making and will facilitate the development of tools and applied innovations for the sustainable and integrated management of oyster aquaculture.

Published
2021

40. Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages

Author

Eglantine Mathieu-Bégné, Eve Toulza, Olivier Rey, Bonnie L. Webster, Jean-François Allienne, Julien Kincaid-Smith, Jérôme Boissier, David Rollinson, Cristian Chaparro, Fiona Allan, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), CEEED Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, The Natural History Museum [London] (NHM), Parasites and Vectors Division, London Centre for Neglected Tropical Disease Research, and Natural History Museum

Subjects
0106 biological sciences, Range (biology), Introgression, Single Nucleotide Polymorphisms, 01 natural sciences, Mathematical and Statistical Techniques, Invertebrate Genomics, Schistosomiasis, Biology (General), Genetics, Schistosoma haematobium, 0303 health sciences, Principal Component Analysis, Genome, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Statistics, Eukaryota, Genomics, 3. Good health, Physical Sciences, Schistosoma, Research Article, Evolutionary Processes, QH301-705.5, Immunology, Single-nucleotide polymorphism, Biology, Research and Analysis Methods, 010603 evolutionary biology, Microbiology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Species Specificity, Virology, Helminths, parasitic diseases, Animals, Statistical Methods, Caenorhabditis elegans, Molecular Biology, Gene, 030304 developmental biology, Hybrid, Evolutionary Biology, Whole Genome Sequencing, Organisms, Biology and Life Sciences, Computational Biology, Paleontology, RC581-607, biology.organism_classification, Genome Analysis, Invertebrates, Schistosoma Haematobium, Animal Genomics, Schistosoma bovis, Multivariate Analysis, Africa, Earth Sciences, Hybridization, Genetic, Parasitology, Immunologic diseases. Allergy, Paleogenetics, Zoology, Mathematics
Abstract

Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples initially classified as S. haematobium (n = 11), S. bovis (n = 6) and S. haematobium x S. bovis hybrids (n = 2). Based on a whole genomic sequencing approach, we developed 56,181 SNPs that allowed a clear differentiation of S. bovis isolates from a genomic cluster including all S. haematobium isolates and a natural S. haematobium-bovis hybrid. All the isolates from the S. haematobium cluster except the isolate from Madagascar harbored signatures of genomic introgression from S. bovis. Isolates from Corsica, Mali and Egypt harbored the S. bovis-like Invadolysin gene, an introgressed tract that has been previously detected in some introgressed S. haematobium populations from Niger. Together our results highlight the fact that introgression from S. bovis is widespread across S. haematobium and that the observed introgression is unidirectional., Author summary Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here we conducted a comparative genomic study to assess the genomic diversity within S. haematobium and S. bovis species and genetic differentation at the genome scale between these two sister species over the African continent. We also investigated traces of possible ancient introgression from one species to another. We found that S. haematobium display low genetic diversity compared to S. bovis. We also found that most S. haematobium samples harbor signature of past introgression with S. bovis at some genomic positions. Our results strongly suggest that introgression occurred long time ago and that such introgression is unidirectional from S. bovis within S. haematobium. Such introgresssion event(s) result in diverging patterns of genomic introgression across S. haematobium lineages.

Published
2021

41. A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Author

Laura Núñez Pons, Alexey Vorobev, Ezequiel M. Marzinelli, Derek J. Skillings, Ehsan Kayal, François H. Lallier, Enora Briand, Eve Toulza, Tilmann Harder, Paco Cárdenas, Willem Stock, Fabrice Not, José Pintado, Johan Decelle, Marc André Selosse, Claire M. M. Gachon, Jean-Christophe Auguet, Mónica Medina, Sarah M. Griffiths, Damien Eveillard, Ulisse Cardini, Arite Bigalke, Mahasweta Saha, Catherine Leblanc, Soizic Prado, Elena Kazamia, Simon M. Dittami, Shinichi Sunagawa, Aschwin H. Engelen, Enrique Arboleda, Teresa Maria Morganti, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Laboratoire Phycotoxines, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Uppsala University, Stazione Zoologica Anton Dohrn (SZN), Photosymbiose, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Scottish Marine Institute, School of Science and the Environment (Manchester Metropolitan University), University of Bremen, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), Pennsylvania State University (Penn State), Penn State System, Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, NSW 2052 Australia, Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigaciones Marinas de Vigo, Instituto de Investigaciones Marinas, Helmholtz Center for Ocean Research, Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, 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), University of Gdańsk (UG), University of Pennsylvania, University of Ghent, Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Microbiology and Swiss Institute of Bioinformatics, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), CEA / Institut de Biologie François Jacob / Génoscope, 2, Rue Gaston Crémieux, CP5706, 91057 Evry cedex, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Phycotoxines (PHYC), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), 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), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Biodiversity, DIVERSITY, lcsh:Medicine, 01 natural sciences, Ecosystem services, CORAL-REEF FISH, Evolutionsbiologi, Evolution, Symbiosis, Host-microbiota interactions, Marine holobionts, Dysbiosis, SponGES, MICROORGANISMS, Sociology, 0303 health sciences, Ecology, General Neuroscience, Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation, Environmental resource management, General Medicine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Holobiont, Engineering ethics, Current (fluid), General Agricultural and Biological Sciences, Ecology (disciplines), Complex system, Genetics and Molecular Biology, Marine Biology, BACTERIAL INTERACTIONS, Community perspective, ECOLOGY, 010603 evolutionary biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Marine ecosystem, 14. Life underwater, PLANT, 030304 developmental biology, 0105 earth and related environmental sciences, Evolutionary Biology, Horizon 2020, business.industry, Experimental model, 010604 marine biology & hydrobiology, lcsh:R, ANIMALS, Biology and Life Sciences, Grant Agreement No 679849, MICROBIOME, 13. Climate action, General Biochemistry, European Union (EU), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

34 pages, 4 figures.-- Distributed under Creative Commons CC-BY 4.0, Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever, This paper is based on the results of a foresight workshop funded by the EuroMarine network, Sorbonne University, and the UMRs 8227 and 7144 of the Roscoff Biological Station. Ezequiel M. Marzinelli was funded by an Australian Research Council Discovery Project (DP180104041), and José Pintado Valverde was funded by the Galician Innovation Agency (IN607A 2017/4). The work of Simon M. Dittami ad Catherine Leblanc was funded by the ANR project IDEALG (ANR-10-TBR-04). Claire M.M. Gachon, Catherine Leblanc, and SimonMDittami received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement number 624575 (ALFF). The work of Fabrice Not was funded by the ANR project IMPEKAB (ANR-15-CE02-001). Ulisse Cardini was funded by the Research Council of Lithuania project INBALANCE (09.3.3-LMT-K-712-01-0069). Johan Decelle was supported by the CNRS and the ATIP-Avenir program, the LabEx GRAL (ANR-10-LABX-49-01) and Pôle Dittami et CBS from the University of Grenoble Alpes. Paco Cardenas received support from the European Union's Horizon 2020 research and innovation program through the SponGES project (grant agreement No. 679849). Elena Kazamia was funded by a Marie Curie Individual Fellowship (Horizon 2020, IRONCOMM). Aschwin H Engelen was supported by Portuguese national funds from FCT - Foundation for Science and Technology through projects UID/Multi/04326/2019 and UIDB/04326/2020

Published
2021

42. La méthylation de l'ADN chez Biomphalaria glabrata, rôle et impact sur la génération de la plasticité phénotypique

Author

Luviano Aparicio, Nelia, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Université de Perpignan, Christoph Grunau, and Céline Cosseau

Subjects
DNA methylation, Mollusk, Heredity, Épimutations, Mollusque, Plasticité phénotypique, Hérédité, Epigenetics, ADN methylation, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Phenotypic plasticity, Epigénétique, Epimutations
Abstract

The understanding of the molecular mechanisms that allows the rapid adaptation of mollusks that are vector of parasites, to new environments is important for disease control. Rapid adaptation is difficult to explain by traditional Mendelian genetics and there is strong evidence supporting that epigenetic mechanisms, are behind rapid adaptations in other species. I studied one epigenetic mark called DNA methylation that has demonstrated to be environmentally modulated and to play a role in phenotypic plasticity in many species, principally plants and vertebrates. Nevertheless, the role of DNA methylation in generating phenotypic variation in invertebrates has been poorly studied. I addressed the question of the role of DNA methylation in the generation of phenotypic plasticity and its heritability in the snail Biomphalaria glabrata, the intermediate host of the parasite Schistosoma mansoni, the causal agent of schistosomiasis, a neglected tropical disease. DNA methylation in B. glabrata has been found to be modulated by the infection of the parasite S. mansoni and by environmental stress, furthermore, it was demonstrated that DNA methylation affects its gene expression, suggesting that DNA methylation can affect phenotypic variation and therefore the adaptation of the snail to new environments. To study the role of DNA methylation in the generation of phenotypic variation, experimental manipulation of the DNA methylation in the snail was necessary. Therefore, two approaches were proposed in this thesis to introduce epimutations in the snail B. glabrata: 1) Random epi-mutagenesis using chemical DNA methyltransferase (DNMT) inhibitors and by consequent segregation of epimutations in self-fertilization lines and 2) Methylate the cytosines of a targeted locus with a targeted epigenome editing tool consisting in the use of the DNA methyltransferase (DNMT3) construct fused to the nuclease-inactivated dCas9. For the random epi-mutagenesis approach, a novel DNMT inhibitor has shown methylation inhibiting effects in two subsequent generations, showing a2multigenerational epigenetic effect and without showing toxic effects in either survival nor fecundity of the snail B. glabrata. In addition, the inhibitor Flv1 has been shown to be effective in other two mollusk species, the freshwater snail Physa acuta and the pacific oyster Crassostrea gigas, which suggests that this inhibitor represents a molecular tool to modulate the methylation of DNA in other mollusks. In the case of the targeted epimutagenesis approach, I used a transfection method that allows introducing two plasmid vectors with an SV40 viral promoter in vivo in embryos of the snail B. glabrata. The transfection was performed at the gastrula stage, which resulted in mosaic incorporation of the vector into the transfected cells. However, the method was able to methylate some CpG sites of the targeted gene.; La compréhension des mécanismes moléculaires qui permettent l'adaptation rapide des mollusques vecteurs de parasites à de nouveaux environnements est importante pour le contrôle des maladies. L'adaptation rapide est difficile à expliquer par la génétique mendélienne traditionnelle et il existe des preuves solides qui soutiennent que les mécanismes épigénétiques sont à l'origine des adaptations rapides chez plusieurs espèces. Je me suis focalisée sur une marque épigénétique appelée la méthylation de l’ADN, qui est modulée par l'environnement et joue un rôle dans la plasticité phénotypique chez de nombreuses espèces, principalement les plantes et les vertébrés. Néanmoins, le rôle de la méthylation de l'ADN dans la génération de variations phénotypiques chez les invertébrés a été très peu étudié. J'ai abordé la question du rôle de la méthylation de l'ADN dans la génération de la plasticité phénotypique et de son héritabilité chez l'escargot B. glabrata, l'hôte intermédiaire du parasite Schistosoma mansoni, l'agent pathogène de la schistosomiase, une maladie tropicale négligée. La méthylation de l'ADN chez B. glabrata est régulée par l'infection3du parasite S. mansoni et par le stress environnemental, de plus, il a été démontré que la méthylation de l'ADN affecte son expression génique, suggérant que la méthylation de l'ADN peut affecter la variation phénotypique et donc l'adaptation de l'escargot à de nouveaux environnements. Pour étudier le rôle de la méthylation de l'ADN dans la génération de la variation phénotypique, une manipulation expérimentale de la méthylation de l'ADN chez l'escargot était nécessaire. Par conséquent, deux approches ont été proposées dans cette thèse pour introduire des épimutations chez l'escargot B. glabrata: 1) Épi-mutagenèse aléatoire en utilisant des inhibiteurs chimiques des enzymes ADN methyltransferases (DNMT) et par ségrégation conséquente des épimutations dans des lignées d'autofécondation et 2) Par la méthylation des cytosines d'un locus ciblé avec un outil d'édition épigénétique qui consiste à l'utilisation d'une vecteur plasmidique codant pour l’ADN méthyltranférase (DNMT3) fusionnée avec l’enzyme dCas9 (Cas9 avec l’activité nucléase désactivé). Pour l’approche d’épimutagenèse aleatoire, un nouvel inhibiteur des enzymes DNMT a montré des effets d’inhibition de la méthylation dans deux générations consécutives, en montrant un effet épigénétique multigénérationnelle et sans montrer d’effet toxique ni dans la survie ni dans la fécondité de l’escargot B. glabrata. De plus l’inhibiteur Flv1 a montré être efficace dans deux autres espèces de mollusques, l’escargot d’eau douce Physa acuta et l’huître creuse Crassostrea gigas, ce qui suggère que cet inhibiteur représente un potentiel outil moléculaire pour moduler la méthylation de l’ADN chez d’autres mollusques. Dans le cas de l’approche ciblée, j’ai utilisé une méthode de transfection qui permet d’introduire deux vecteurs plasmidiques avec un promoteur viral SV40 de façon in vivo dans des embryons de l’escargot B. glabrata. La transfection a été effectuée au stade gastrula, ce qui a entrainé une incorporation mosaïque du vecteur dans les cellules transfectées. Toutefois, la méthode a permis de méthyler certains sites CpG du gène ciblé.

Published
2021

43. A simple ATAC-seq protocol for population epigenetics

Author

Vicki A. Thomson, Olivier Rey, Sina Tönges, Patrice David, Christoph Grunau, David Duval, Cristian Chaparro, Jeremie Vidal-Dupiol, Aki Minoda, Mariana Gomes Lima, Emilien Luquet, Déborah Federico, Etienne Danchin, Dominique Joly, Silvain Pinaud, Fabien Aubret, Céline Cosseau, Ronaldo de Carvalho Augusto, Mamadou Dia Sow, Jean-François Allienne, Ranja Andriantsoa, 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), Cancer Research UK Cambridge Institute [Cambridge, Royaume-Uni] (CRUK), University of Cambridge [UK] (CAM), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Équipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes (BAH), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Station d'écologie théorique et expérimentale (SETE), Observatoire Midi-Pyrénées (OMP), 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 -Institut national des sciences de l'Univers (INSU - CNRS)-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 -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), University of Adelaide, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), 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, Laboratory for Cardiovascular Genomics and Informatics [Yokohama] (RIKEN IMS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), 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), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), 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), Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Évolution, génomes, comportement et écologie (EGCE), and Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11)

Subjects
0106 biological sciences, 0301 basic medicine, Euchromatin, [SDV]Life Sciences [q-bio], Population, Medicine (miscellaneous), ATAC-seq, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Epigenetics, education, Protocol (object-oriented programming), Transposase, Epigenomics, Protocol (science), education.field_of_study, epigenetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Articles, Schistosoma mansoni, Method Article, Chromatin, 030104 developmental biology, epigenomics, Daphnia pulex
Abstract

version 2; peer review: 2 approved; International audience; We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.

Published
2021

44. The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching

Author

Céline Cosseau, Pascal Romans, Guillaume Mitta, Kelly Brener Raffalli, Patrick Masanet, David Roquis, Jeremie Vidal-Dupiol, Christoph Grunau, Agroscope, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Aquarium de Canet-en-Roussillon

Subjects
Coral bleaching, viruses, Pocillopora acuta, Medicine (miscellaneous), Hermatypic coral, Pocillopora damicornis, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Histone H3, 0302 clinical medicine, Histone H3 clipping, Nucleosome, 14. Life underwater, 030304 developmental biology, chromatin structure, 0303 health sciences, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, virus diseases, Epigenome, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, digestive system diseases, Chromatin, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Histone, Evolutionary biology, biology.protein, invertebrate epigenetics, 030217 neurology & neurosurgery
Abstract

Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average ~90% of sequence similarities with mice and ~96% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta. The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.

Published
2021

45. Mastomys natalensis (Smith, 1834) as a natural host for Schistosoma haematobium (Bilharz, 1852) Weinland, 1858 x Schistosoma bovis Sonsino, 1876 introgressive hybrids

Author

Thalasse T. Avocegan, Hélène Moné, Jonas Etougbétché, François T. Quinsou, Gauthier Dobigny, Philippe Gauthier, Boris A.E.S. Savassi, Gabriel Mouahid, Moudachirou Ibikounlé, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Université d’Abomey-Calavi (UAC), Ecole Polytechnique d'Abomey Calavi (EPAC), University of Abomey Calavi (UAC), 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), This research was funded by the French Ministry of Foreign Affairs, the International Joint Laboratory through the CONS-HELM project, the French Institute for Sustainable Development (IRD), the French National Agency for Research (ANR) [grant ANR-17-CE12-0005- 01] CHRONOGET and CNRS. BS is a student fellow from the SCAC (Service de Coopération et d’Action Culturelle), French Embassy in Benin., ANR-17-CE12-0005,CHRONOGET,Recherche des déterminants génétiques, épigénétiques et transcriptomiques du rythme d'émergence des larves responsables de la transmission des schistosomes à l'Homme(2017), 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), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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)

Subjects
0301 basic medicine, Male, Schistosomiasis haematobia, 0302 clinical medicine, Prevalence, Benin, Schistosomiasis, Cercaria, Schistosome transmission, Schistosoma haematobium, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Cercarial chronobiology, General Medicine, 3. Good health, Infectious Diseases, Schistosoma, Female, Crocidura olivieri, Bulinus, 030231 tropical medicine, Zoology, Immunology and Host-Parasite Interactions - Original Paper, Bulinus globosus, Genetic Introgression, DNA, Mitochondrial, DNA, Ribosomal, Rattus rattus, Host-Parasite Interactions, 03 medical and health sciences, Mastomys natalensis, parasitic diseases, Animals, Internal transcribed spacer, Ecosystem, General Veterinary, Host (biology), Shrews, Cytochrome c oxidase subunit I, biology.organism_classification, Rats, Molecular Typing, 030104 developmental biology, Insect Science, Mastomys, Parasitology, Murinae, Schistosoma haematobium x Schistosoma bovis
Abstract

Cercarial emission of schistosomes is a determinant in the transmission to the definitive host and constitutes a good marker to identify which definitive host is responsible for transmission, mainly in introgressive hybridization situations. Our goal was to test the hypothesis that micro-mammals play a role inSchistosoma haematobium,S.bovis, and/orS.haematobiumxS.bovistransmission. Small mammal sampling was conducted in seven semi-lacustrine villages of southern Benin. Among the 62 animals trapped, 50 individuals were investigated forSchistosomaadults and eggs: 37Rattus rattus, 3Rattus norvegicus, 9Mastomys natalensis, and 1Crocidura olivieri.Schistosomaadults were found in fourR. rattusand twoM. natalensis, with a local prevalence reaching 80% and 50%, respectively.Two cercarial chronotypes were found fromBulinus globosusexperimentally infected with miracidia extracted from naturally infectedM. natalensis: a late diurnal and nocturnal chronotype, and an early diurnal, late diurnal, and nocturnal chronotype. The cytochrome C oxidase subunit I mtDNA gene of the collected schistosomes (adults, miracidia, and cercariae) belonged to theS.bovisclade. Eleven internal transcribed spacer rDNA profiles were found; four belonged toS.bovisand seven toS.haematobiumxS.bovis. These molecular results together with the observed multi-peak chronotypes addM. natalensisas a new host implicated inS.haematobiumxS.bovistransmission. We discuss the origin of the new chronotypes which have become more complex with the appearance of several peaks in a 24-h day. We also discuss how the new populations of offspring may optimize intra-host ecological niche, host spectrum, and transmission time period.

Published
2021

46. The insecticide permethrin induces transgenerational behavioral changes linked to transcriptomic and epigenetic alterations in zebrafish (Danio rerio)

Author

Xavier Cousin, Christoph Grunau, Steffen Keiter, Joëlle Rüegg, Nikolai Scherbak, Philipp Antczak, Mélanie Blanc, Man-Technology-Environment Research Centre, School of Science and Technology, Örebro University, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Molecular Medicine Cologne [Cologne] (CMMC), University Hospital of Cologne [Cologne], Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Department of Organismal Biology, Uppsala University, This study was supported by the Enforce laboratory, funded by the Knowledge Foundation (KK Stiftelsen 20160019, Sweden), and by the Helge Ax:Son Foundation (F19-0339, Sweden). RRBS experiments were performed at the Environmental Epigenetics facility of IHPE with the support of LabEx CeMEB, an Agence Nationale de la Recherche (ANR) 'Investissements d'avenir' program (ANR-10-LABX-04-01, France)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and 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)

Subjects
Epigenomics, Male, Insecticides, Environmental Engineering, 010504 meteorology & atmospheric sciences, glutamatergic signaling, Danio, 010501 environmental sciences, 01 natural sciences, Epigenesis, Genetic, Glutamatergic, Environmental Chemistry, Animals, Epigenetics, Transgenerational epigenetic inheritance, Waste Management and Disposal, Zebrafish, Permethrin, pesticide, 0105 earth and related environmental sciences, Genetics, DNA methylation, biology, Behavior, Animal, biology.organism_classification, Pollution, Pesticide, Glutamatergic signaling, Differentially methylated regions, Female, developmental neurotoxicity, Glutamatergic synapse, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Developmental neurotoxicity, Transcriptome
Abstract

International audience; The pyrethroid insecticide permethrin is widely used for agricultural and domestic purposes. Previous data indicated that it acts as a developmental neurotoxicant and can induce transgenerational effects in non-target organisms. However, associated underlying mechanisms remain unclear. The aim of this study was to investigate permethrin-related transgenerational effects in the zebrafish model, and to identify possible molecular mechanisms underlying inheritance. Zebrafish (F0) were exposed to permethrin during early-life (2 hours postfertilization up to 28 days). The F1 and F2 offspring generations were obtained by pairing exposed F0 males and females, and were bred unexposed. Locomotor and anxiety behavior were investigated, together with transcriptomic and epigenomic (DNA methylation) changes in brains. Permethrin exposed F0 fish were hypoactive at adulthood, while males from the F1 and F2 generations showed a specific decrease in anxiety-like behavior. In F0, transcriptomic data showed enrichment in pathways related to glutamatergic synapse activity, which may partly underlie the behavioral effects. In F1 and F2 males, dysregulation of similar pathways was observed, including a subset of differentially methylated regions that were inherited from the F0 to the F2 generation and indicated stable dysregulation of glutamatergic signaling. Altogether, the present results provide novel evidence on the transgenerational neurotoxic effects of permethrin, as well as mechanistic insight: a transient exposure induces persistent transcriptional and DNA methylation changes that may translate into transgenerational alteration of glutamatergic signaling and, thus, into behavioral alterations.

Published
2021

47. Manniindole, an indole derivative from the roots of Anonidium mannii and combined antischistosomal and enzymatic activities

Author

Josette Linda Toussi Matchi, Marc Nothisen, Jean Claude Tchouankeu, Jérôme Boissier, Sylvain Ursuegui, Guilhem Chaubet, Silvère Ngouela, Delphine Garnier, Diderot T. Noungoue, Isabelle Kuhn, Alain Wagner, Conception et application de molécules bioactives (CAMB), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Yaoundé I, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), University of Yaounde I, Dept Chim Inorgan, Lab Physicochim Mat Min, Yaounde, Cameroon, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Stereochemistry, Annonaceae, Plant Science, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, indole alkaloid, 01 natural sciences, Biochemistry, Analytical Chemistry, chemistry.chemical_compound, Anonidium mannii, phytochemical and biological investigation, parasitic diseases, Cytotoxicity, ComputingMilieux_MISCELLANEOUS, Indole test, chemistry.chemical_classification, Indole alkaloid, biology, 010405 organic chemistry, Chemistry, enzymatic activity (SmNACE), Alkaloid, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Organic Chemistry, antischistosomal activity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, anti-schistosomal activity, 3. Good health, 0104 chemical sciences, 010404 medicinal & biomolecular chemistry, Enzyme, cytotoxicity, Derivative (chemistry)
Abstract

International audience; A new alkaloid, manniindole 1, together with four known compounds: aristolactam AII 2, aristolactam BII 3, piperolactam D 4 and polycarpol 5 were isolated from the crude extract EtOHH2O (8:2) of the roots of Anonidium mannii by chromatographic separation. The structure elucidation was performed on the basis of a spectroscopic analysis (IR, HRESI MS, 1D and 2D NMR) as well as a comparison of their spectral data with those reported in the literature. For the first time, the crude extract and those isolated compounds were evaluated for their antischistosomal activity against Schistosoma mansoni and for cytotoxicity activity against Huh7 and A549 cells. Furthermore, they were also tested in vitro on the recent characterized Schistosoma mansoni NADþ catabolizing enzyme (SmNACE) for their impact on this enzyme which is localized on the outer surface of the adult parasite. Compound 2 displayed quite good worm killing capability, while 4 showed significant inhibition of SmNACE

Published
2021

48. Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes

Author

Pierre-Louis Stenger, Chin-Long Ky, Céline M. O. Reisser, Céline Cosseau, Christoph Grunau, Mickaël Mege, Serge Planes, Jeremie Vidal-Dupiol, Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), 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 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 de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), and Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, 0301 basic medicine, environmental pressure, lcsh:QH426-470, depth, engineering.material, 01 natural sciences, Genome, 03 medical and health sciences, Pigment, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, pigmentation, Epigenetics, Gene, Mollusca, Genetics (clinical), DNA methylation, biology, Pinctada margaritifera, methylome characterization, biology.organism_classification, color change, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, lcsh:Genetics, 030104 developmental biology, Evolutionary biology, visual_art, engineering, visual_art.visual_art_medium, Molecular Medicine, pearl oyster, sense organs, Pearl, 010606 plant biology & botany
Abstract

Today, it is common knowledge that environmental factors can change the color of many animals. Studies have shown that the molecular mechanisms underlying such modifications could involve epigenetic factors. Since 2013, the pearl oyster Pinctada margaritifera var. cumingii has become a biological model for questions on color expression and variation in Mollusca. A previous study reported color plasticity in response to water depth variation, specifically a general darkening of the nacre color at greater depth. However, the molecular mechanisms behind this plasticity are still unknown. In this paper, we investigate the possible implication of epigenetic factors controlling shell color variation through a depth variation experiment associated with a DNA methylation study performed at the whole genome level with a constant genetic background. Our results revealed six genes presenting differentially methylated CpGs in response to the environmental change, among which four are linked to pigmentation processes or regulations (GART, ABCC1, MAPKAP1, and GRL101), especially those leading to darker phenotypes. Interestingly, the genes perlucin and MGAT1, both involved in the biomineralization process (deposition of aragonite and calcite crystals), also showed differential methylation, suggesting that a possible difference in the physical/spatial organization of the crystals could cause darkening (iridescence or transparency modification of the biomineral). These findings are of great interest for the pearl production industry, since wholly black pearls and their opposite, the palest pearls, command a higher value on several markets. They also open the route of epigenetic improvement as a new means for pearl production improvement.

Published
2021

49. L'épreuve écrite de sciences et technologie

Author

Bächtold, Manuel, Boyer, Antonin, Mouahid, Gabriel, Roca, Pascale, Laboratoire Interdisciplinaire de Recherche en Didactique, Éducation et Formation (LIRDEF), Université Paul-Valéry - Montpellier 3 (UPVM)-Université de Montpellier (UM), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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 Quillien, Philippe-Jean

Subjects
[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE]
Abstract

National audience; Les sciences et la technologie constituent l'une des options de la 3e épreuve écrite d'admissibilité du concours de recrutement des professeurs des écoles (CRPE). L'épreuve se présente sous la forme d'un sujet à traiter en 3 heures. Ce sujet comporte des documents de différentes sources dont le contenu éclaire une problématique générale. Les questions sont d'ordre scientifique, didactique et pédagogique.Cet ouvrage a été conçu pour aider dans leur préparation les candidats aux concours de recrutement des professeurs des écoles, afin qu'ils se préparent de façon autonome ou dans le cadre des INSPE (master Métiers de l'enseignement, de l'éducation et de la formation [MEEF]) pour l'enseignement à l'école primaire. Il s'adresse aussi à tous les professeurs des écoles en poste qui souhaitent parfaire leur formation en sciences et technologie.L'ouvrage vous propose : des repères scientifiques sur l'ensemble des thèmes au programme de l'école primaire, dans les domaines des sciences de la vie et de la terre (SVT), de la physique et de la technologie ; des repères pédagogiques et didactiques sur l'enseignement des sciences et de la technologie et sur les apprentissages des élèves à l'école primaire ; des exemples de sujets - officiels ou inédits - pour la préparation de l'épreuve.

Published
2021

50. Chromatin landscape dynamics in the early development of the plant parasitic nematode Meloidogyne incognita

Author

Hassanaly-Goulamhoussen, Rahim, Augusto, Ronaldo de Carvalho, Marteu-Garello, Nathalie, Péré, Arthur, Favery, Bruno, Da Rocha, Martine, Danchin, Etienne, Abad, Pierre, Grunau, Christoph, Perfus-Barbeoch, Laetitia, De Carvalho Augusto, Ronaldo, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Interactions Hôtes-Pathogènes-Environnements (IHPE), 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), Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), 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), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Modat, Anne

Subjects
0106 biological sciences, root-knot nematode, QH301-705.5, parasitism, ved/biology.organism_classification_rank.species, Development, 01 natural sciences, Cell and Developmental Biology, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BDD] Life Sciences [q-bio]/Development Biology, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Meloidogyne incognita, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Epigenetics, Biology (General), Model organism, development, Gene, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Original Research, 030304 developmental biology, 0303 health sciences, biology, epigenetics, ved/biology, histone modifications, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Cell Biology, Epigenome, biology.organism_classification, Chromatin, Histone, Evolutionary biology, Parasitism, biology.protein, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], H3K4me3, 030217 neurology & neurosurgery, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Developmental Biology, 010606 plant biology & botany
Abstract

In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.Author summaryThe nematode Meloidogyne incognita is one of the most destructive plant parasites worldwide. Its ability to infect a wide range of hosts and its high adaptability contribute to its parasitic success. We investigated the role of epigenetic mechanisms — specifically post-translational histone modifications — in the parasitic life cycle. We showed these modifications are linked to gene expression regulation and likely contribute to nematode development and pathogenicity.

Published
2021

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