Author: "Marine Pratlong" - Searchworks@Jio Institute Digital Library Search Results

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30 results on '"Marine Pratlong"'

1. Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

Author: Carla de la Fuente, Alexandre Grondin, Bassirou Sine, Marilyne Debieu, Christophe Belin, Amir Hajjarpoor, Jonathan A Atkinson, Sixtine Passot, Marine Salson, Julie Orjuela, Christine Tranchant-Dubreuil, Jean-Rémy Brossier, Maxime Steffen, Charlotte Morgado, Hang Ngan Dinh, Bipin K Pandey, Julie Darmau, Antony Champion, Anne-Sophie Petitot, Celia Barrachina, Marine Pratlong, Thibault Mounier, Princia Nakombo-Gbassault, Pascal Gantet, Prakash Gangashetty, Yann Guedon, Vincent Vadez, Jean-Philippe Reichheld, Malcolm J Bennett, Ndjido Ardo Kane, Soazig Guyomarc'h, Darren M Wells, Yves Vigouroux, and Laurent Laplaze
Subjects: pearl millet, redox, cell elongation, GWAS, stress pattern, root meristem, Medicine, Science, Biology (General), QH301-705.5
Abstract: Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.
Published: 2024
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2. NRG1/ErbB signalling controls the dialogue between macrophages and neural crest-derived cells during zebrafish fin regeneration

Author: Béryl Laplace-Builhé, Audrey Barthelaix, Said Assou, Candice Bohaud, Marine Pratlong, Dany Severac, Gautier Tejedor, Patricia Luz-Crawford, Mai Nguyen-Chi, Marc Mathieu, Christian Jorgensen, and Farida Djouad
Subjects: Science
Abstract: Some fish can regenerate appendages by formation of a structure called the blastema. Here, the authors use single-cell RNA sequencing to characterize the cells required for blastema formation and fin regeneration and identified neural crest cells that orchestrate regeneration via the NRG1/ErbB axis
Published: 2021
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3. Single cell RNA sequencing reveals hemocyte heterogeneity in Biomphalaria glabrata: Plasticity over diversity

Author: Rémi Pichon, Silvain Pinaud, Emmanuel Vignal, Cristian Chaparro, Marine Pratlong, Anaïs Portet, David Duval, Richard Galinier, and Benjamin Gourbal
Subjects: single cell RNA seq, B. glabrata, hemocytes, innate immune system, S. mansoni, Immunologic diseases. Allergy, RC581-607
Abstract: The freshwater snail Biomphalaria glabrata is an intermediate host of Schistosoma mansoni, the agent of human intestinal schistosomiasis. However, much is to be discovered about its innate immune system that appears as a complex black box, in which the immune cells (called hemocytes) play a major role in both cellular and humoral response towards pathogens. Until now, hemocyte classification has been based exclusively on cell morphology and ultrastructural description and depending on the authors considered from 2 to 5 hemocyte populations have been described. In this study, we proposed to evaluate the hemocyte heterogeneity at the transcriptomic level. To accomplish this objective, we used single cell RNA sequencing (scRNAseq) technology coupled to a droplet-based system to separate hemocytes and analyze their transcriptome at a unique cell level in naive Biomphalaria glabrata snails. We were able to demonstrate the presence of 7 hemocyte transcriptomic populations defined by the expression of specific marker genes. As a result, scRNAseq approach showed a high heterogeneity within hemocytes, but provides a detailed description of the different hemocyte transcriptomic populations in B. glabrata supported by distinct cellular functions and lineage trajectory. As a main result, scRNAseq revealed the 3 main population as a super-group of hemocyte diversity but, on the contrary, a great hemocytes plasticity with a probable capacity of hemocytes to engage to different activation pathways. This work opens a new field of research to understand the role of hemocytes particularly in response to pathogens, and towards S. mansoni parasites.
Published: 2022
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4. Genetic pathways underpinning hormonal stress responses in fish exposed to short- and long-term warm ocean temperatures

Author: Alexander Goikoetxea, Bastien Sadoul, Eva Blondeau-Bidet, Johan Aerts, Marie-Odile Blanc, Hugues Parrinello, Célia Barrachina, Marine Pratlong, and Benjamin Geffroy
Subjects: Cortisol, Glucocorticoid receptors, Transcriptomics, Scales, Commercial fish, Ecology, QH540-549.5
Abstract: Changes in ocean water temperature associated with global climate change are bound to enormously affect fish populations, with potential major economic consequences in the aquaculture and fisheries industries. A link between temperature fluctuations and changes in fish stress response is well established. In this study, we aimed to assess the effects of a short- (4 days) or a long-term (4 months) exposure to warm temperature in the stress physiology of European sea bass (Dicentrarchus labrax) larvae and juveniles. First, cortisol (i.e. the main stress hormone in fishes) analysis was used to confirm that a steady and short-term elevation of temperature acts as a physiological stressful event in these fish, and cortisol release is indeed above a metabolic increase linked to temperature. Moreover, our results verified that measurement of cortisol released into the water can be reliably employed as a non-invasive indicator of acute thermal stress in experimental conditions. Secondly, the different effects on the genetic cascade underlying the stress response between long-term low or high thermal treatments were evaluated at two larval development stages via candidate-gene and whole-transcriptome approaches. Interestingly, opposite expression for some key stress genes (nr3c1, nr3c2 and hsd11b2) were observed between developmental stages, highlighting the distinct adaptive mechanisms controlling the primary and secondary responses to a stressor. Surprising expression patterns for some understudied genes involved in the stress axis were also revealed, including crhr1, mc2r, mc5r, trh or trhr, which should be further explored. Finally, evaluation of cortisol content in scales was successfully used as a biomarker of chronic thermal stress, with 10x more cortisol in fish kept at 21 °C vs 16 °C after 4 months, supporting the gene expression results observed. The use of such a method as a proxy of long-term stress, unprecedented in the literature, holds a vast array of applications in further research, in particular, in the investigation of the impact of global warming on wild fish populations.
Published: 2021
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5. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

Author: Kelly Brener-Raffalli, Camille Clerissi, Jeremie Vidal-Dupiol, Mehdi Adjeroud, François Bonhomme, Marine Pratlong, Didier Aurelle, Guillaume Mitta, and Eve Toulza
Subjects: Coral holobiont, Microbiota, Bacterial communities, Symbiodinium assemblages, Thermal adaptation, Scleractinian corals, Microbial ecology, QR100-130
Abstract: Abstract Background Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues. Results We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions
Published: 2018
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6. Ribosomal Protein S6 Phosphorylation Is Involved in Novelty-Induced Locomotion, Synaptic Plasticity and mRNA Translation

Author: Emma Puighermanal, Anne Biever, Vincent Pascoli, Su Melser, Marine Pratlong, Laura Cutando, Stephanie Rialle, Dany Severac, Jihane Boubaker-Vitre, Oded Meyuhas, Giovanni Marsicano, Christian Lüscher, and Emmanuel Valjent
Subjects: mRNA translation, striatum, LTP (long-term potentiation), ribosomal proteins, rpS6 phosphorylation, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: The phosphorylation of the ribosomal protein S6 (rpS6) is widely used to track neuronal activity. Although it is generally assumed that rpS6 phosphorylation has a stimulatory effect on global protein synthesis in neurons, its exact biological function remains unknown. By using a phospho-deficient rpS6 knockin mouse model, we directly tested the role of phospho-rpS6 in mRNA translation, plasticity and behavior. The analysis of multiple brain areas shows for the first time that, in neurons, phospho-rpS6 is dispensable for overall protein synthesis. Instead, we found that phospho-rpS6 controls the translation of a subset of mRNAs in a specific brain region, the nucleus accumbens (Acb), but not in the dorsal striatum. We further show that rpS6 phospho-mutant mice display altered long-term potentiation (LTP) in the Acb and enhanced novelty-induced locomotion. Collectively, our findings suggest a previously unappreciated role of phospho-rpS6 in the physiology of the Acb, through the translation of a selective subclass of mRNAs, rather than the regulation of general protein synthesis.
Published: 2017
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7. Glutaredoxin regulation of primary root growth confers early drought stress tolerance in pearl millet

Author: Carla de la Fuente, Alexandre Grondin, Bassirou Sine, Marilyne Debieu, Christophe Belin, Amir Hajjarpoor, Jonathan A. Atkinson, Sixtine Passot, Marine Salson, Julie Orjuela, Christine Tranchant-Dubreuil, Jean-Rémy Brossier, Maxime Steffen, Charlotte Morgado, Hang Ngan Dinh, Bipin K. Pandey, Julie Darmau, Antony Champion, Anne- Sophie Petitot, Celia Barrachina, Marine Pratlong, Thibault Mounier, Pascal Gantet, Prakash Gangashetty, Yann Guédon, Vincent Vadez, Jean-Philippe Reichheld, Malcolm J. Bennett, Ndjido Kane, Soazig Guyomarc’h, Darren M. Wells, Yves Vigouroux, Laurent Laplaze, Diversité, adaptation, développement des plantes (UMR DIADE), 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 [France-Sud])-Université de Montpellier (UM), LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Centre d'Etude Regional Pour l'Amelioration de l'Adaptation A la Secheresse (CERAAS), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), University of Nottingham, UK (UON), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-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 de Montpellier (UM)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-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), International Crops Research Institute for the Semi-Arid Tropics [Inde] (ICRISAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), 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, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Agropolis Fondation (NewPearl grant n° AF 1301-015 in the frame of the CERES initiative, ValoRoot grant n°2202-002, and Flagship Project CalClim grant no. 1802-002)Fondazione Cariplo (n° FC 2013-0891)- CGIAR Research Programme on Grain Legumes and Dryland Cereals (GLDC), ANR-17-CE20-0022,RootAdapt,Traits racinaires pour l'adaptation du mil au climat futur en Afrique de l'Ouest(2017), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-16-IDEX-0006,MUSE,MUSE(2016), and European Project
Subjects: [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modelling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including GWAS and QTL approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re- annotation of one of these genomic regions identified a glutaredoxin-encoding genePgGRXC9as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homologAtROXY19revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.
Published: 2023
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8. Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

Author: Didier Aurelle, Marine Pratlong, Nicolas Oury, Anne Haguenauer, Pauline Gélin, Hélène Magalon, Mehdi Adjeroud, Pascal Romans, Jeremie Vidal-Dupiol, Michel Claereboudt, Camille Noûs, Lauric Reynes, Eve Toulza, François Bonhomme, Guillaume Mitta, Pierre Pontarotti, 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), Ecologie Marine et BIOdiversité (EMBIO), 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 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 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), 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 Pythéas (OSU PYTHEAS), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aix Marseille Université (AMU), Université de La Réunion (UR), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Universités (COMUE), 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), Sultan Qaboos University (SQU), Laboratoire Cogitamus, 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)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: Genetic Structures, species delineation, Sequence Analysis, DNA, Plant Science, General Medicine, RAD sequencing, Anthozoa, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Species Specificity, Insect Science, Genetics, genetic structure, Animals, Animal Science and Zoology, Metagenomics, Pocillopora, clonal reproduction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, coral
Abstract: International audience; Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test for species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RADsequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e. PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.
Published: 2022
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9. Major transcriptomic, epigenetic and metabolic changes underlie the pluripotency continuum in rabbit preimplantation embryos

Author: Wilhelm Bouchereau, Luc Jouneau, Catherine Archilla, Irène Aksoy, Anais Moulin, Nathalie Daniel, Nathalie Peynot, Sophie Calderari, Thierry Joly, Murielle Godet, Yan Jaszczyszyn, Marine Pratlong, Dany Severac, Pierre Savatier, Véronique Duranthon, Marielle Afanassieff, Nathalie Beaujean, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (SBRI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED), École nationale vétérinaire - Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Cellules Environnement - UR (ICE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Isara, Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-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 de Montpellier (UM)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unité sous contrat plate-forme biotechnologique de cellules souches plate-forme PrimaStem, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (U1208 Inserm - UCBL1 / SBRI - USC 1361 INRAE), Institut méditerranéen d'océanologie (MIO), and 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)
Subjects: Pluripotent Stem Cells, Embryo transcriptome, Pluripotency continuum, Epigenesis, Genetic, Single-cell RNAseq, Mice, Blastocyst, Rabbit preimplantation embryo, Animals, Rabbits, Naive pluripotency, Transcriptome, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Germ Layers, Developmental Biology
Abstract: Despite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of embryos at the molecular level is still poorly documented. We conducted a transcriptome analysis of rabbit preimplantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using bulk and single-cell RNA-sequencing. In parallel, we studied oxidative phosphorylation and glycolysis, and analysed active and repressive epigenetic modifications during blastocyst formation and expansion. We generated a transcriptomic, epigenetic and metabolic map of the pluripotency continuum in rabbit preimplantation embryos, and identified novel markers of naive pluripotency that might be instrumental for deriving naive pluripotent stem cell lines. Although the rabbit is evolutionarily closer to mice than to primates, we found that the transcriptome of rabbit epiblast cells shares common features with those of humans and non-human primates.
Published: 2022
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10. The mouse HP1 proteins are essential for preventing liver tumorigenesis

Author: Marine Pratlong, Eric Fabbrizio, Lakdhar Khellaf, Nelly Pirot, Amélie Sarrazin, Damien Grégoire, Yannick Perez, Shefqet Hajdari, Jean-Yohan Noël, Eric Julien, Nehmé Saksouk, Aliki Zavoriti, Florence Cammas, Céline Graber, Célia Barrachina, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), and CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: 0301 basic medicine, endocrine system, Cancer Research, animal structures, Euchromatin, Liver cytology, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Endogenous retrovirus, Biology, liver, transcriptional silencing, 03 medical and health sciences, 0302 clinical medicine, endogenous retrovirus, Genetics, cancer, Heterochromatin organization, Molecular Biology, Regulation of gene expression, HP1, Cell biology, Chromatin, 030104 developmental biology, 030220 oncology & carcinogenesis, embryonic structures, chromatin, Heterochromatin protein 1, Corepressor
Abstract: International audience; Chromatin organization is essential for appropriate interpretation of the genetic information. Here, we demonstrated that the chromatin associated proteins HP1 are dispensable for hepatocytes survival but are essential within hepatocytes to prevent liver tumor development in mice with HP1β being pivotal in these functions. Yet, we found that the loss of HP1 per se is not sufficient to induce cell transformation but renders cells more resistant to specific stress such as the expression of oncogenes and thus in fine, more prone to cell transformation. Molecular characterization of HP1-Triple KO pre-malignant livers and BMEL cells revealed that HP1 are essential for the maintenance of heterochromatin organization and for the regulation of specific genes with most of them having well characterized functions in liver functions and homeostasis. We further showed that some specific retrotransposons get reactivated upon loss of HP1, correlating with over-expression of genes in their neighborhood. Interestingly, we found that, although HP1-dependent genes are characterized by enrichment H3K9me3, this mark does not require HP1 for its maintenance and is not sufficient to maintain gene repression in absence of HP1. Finally, we demonstrated that the loss of TRIM28 association with HP1 recapitulated several phenotypes induced by the loss of HP1 including the reactivation of some retrotransposons and the increased incidence of liver cancer development. Altogether, our findings indicate that HP1 proteins act as guardians of liver homeostasis to prevent tumor development by modulating multiple chromatin-associated events within both the heterochromatic and euchromatic compartments, partly through regulation of the corepressor TRIM28 activity.
Published: 2020
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11. The landscape of cancer-associated fibroblasts in colorectal cancer liver metastases

Author: Ambre Giguelay, Evgenia Turtoi, Lakhdar Khelaf, Guillaume Tosato, Ikrame Dadi, Tommy Chastel, Marie-Alix Poul, Marine Pratlong, Stefan Nicolescu, Dany Severac, Antoine Adenis, Olivia Sgarbura-Popescu, Sébastien Carrère, Philippe Rouanet, François Quenet, Marc Ychou, Didier Pourqier, Pierre-Emmanuel Colombo, Andrei Turtoi, and Jacques Colinge
Subjects: Cancer-Associated Fibroblasts, Latent TGF-beta Binding Proteins, Liver Neoplasms, Tumor Microenvironment, Medicine (miscellaneous), Humans, Fibroblasts, Colorectal Neoplasms, Pharmacology, Toxicology and Pharmaceutics (miscellaneous)
Published: 2022

12. The regenerative response of cardiac interstitial cells

Author: Laura Rolland, Alenca Harrington, Adèle Faucherre, Jourdano Mancilla Abaroa, Girisaran Gangatharan, Laurent Gamba, Dany Severac, Marine Pratlong, Thomas Moore-Morris, Chris Jopling, Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), BioCampus (BCM), ANR-20-CE14-0003,MetabOx-Heart,Role de l'interaction hypoxie-metabolisme dans la regeneration cardiaque(2020), ANR-18-ECVD-0006,FIBER(2018), and European Project: 680969,H2020,H2020-HCO-2015,ERA-CVD(2015)
Subjects: heart regeneration, endothelium, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Cell Biology, General Medicine, interstitial cells, macrophage, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], fibroblast, inflammation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, single-cell RNA-sequencing, Molecular Biology
Abstract: Understanding how certain animals are capable of regenerating their hearts will provide much needed insights into how this process can be induced in humans in order to reverse the damage caused by myocardial infarction. Currently, it is becoming increasingly evident that cardiac interstitial cells play crucial roles during cardiac regeneration. To understand how interstitial cells behave during this process, we performed single-cell RNA sequencing of regenerating zebrafish hearts. Using a combination of immunohistochemistry, chemical inhibition, and novel transgenic animals, we were able to investigate the role of cell type-specific mechanisms during cardiac regeneration. This approach allowed us to identify a number of important regenerative processes within the interstitial cell populations. Here, we provide detailed insight into how interstitial cells behave during cardiac regeneration, which will serve to increase our understanding of how this process could eventually be induced in humans.
Published: 2022
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13. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system

Author: Benjamin Geffroy, Mathieu Besson, Núria Sánchez-Baizán, Frederic Clota, Alexander Goikoetxea, Bastien Sadoul, François Ruelle, Marie-Odile Blanc, Hugues Parrinello, Sophie Hermet, Eva Blondeau-Bidet, Marine Pratlong, Francesc Piferrer, Marc Vandeputte, François Allal, 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), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-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), European Maritime and Fisheries Fund, Ministerio de Ciencia, Innovación y Universidades (España), and Agencia Estatal de Investigación (España)
Subjects: Male, 0106 biological sciences, Multifactorial Inheritance, Genotype, sex determination, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, 010603 evolutionary biology, 01 natural sciences, Histones, 03 medical and health sciences, genomics, Animals, Body Size, 14. Life underwater, Gonads, SOX Transcription Factors, 030304 developmental biology, fish, 0303 health sciences, Temperatures, Multidisciplinary, Temperature, Reproducibility of Results, temperature, Epigenetic, Genomics, DNA Methylation, Sex Determination Processes, Biological Sciences, Sex determination, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Fish, Gene Expression Regulation, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, Bass, Female, Energy Metabolism, epigenetic, Body Temperature Regulation
Abstract: 12 pages, 6 figures, supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2112660118/-/DCSupplemental.-- Data Availability: RNA-Seq and .xls tables data have been deposited in a publicly accessible database: SEXTAN (https://sextant.ifremer.fr/record/5cb1485f-385e-46e9-9cc1-4b4d77802183/). All other study data are included in the article and/or supporting information, In most animals, sex determination occurs at conception, when sex chromosomes are segregated following Mendelian laws. However, in multiple reptiles and fishes, this genetic sex can be overridden by external factors after fertilization or birth. In some species, the genetic sex may also be governed by multiple genes, further limiting our understanding of sex determination in such species. We used the European sea bass (Dicentrarchus labrax) as a model and combined genomic (using a single nucleotide polymorphism chip) and transcriptomic (RNA-Sequencing) approaches to thoroughly depict this polygenic sex determination system and its interaction with temperature. We estimated genetic sex tendency (eGST), defined as the estimated genetic liability to become a given sex under a liability threshold model for sex determination, which accurately predicts the future phenotypic sex. We found evidence that energetic pathways, concerning the regulation of lipids and glucose, are involved in sex determination and could explain why females tend to exhibit higher energy levels and improved growth compared to males. Besides, early exposure to high-temperature up-regulated sox3, followed by sox9a in individuals with intermediate eGST, but not in individuals showing highly female-biased eGST, providing the most parsimonious explanation for temperature-induced masculinization. This gonadal state was maintained likely by DNA methylation and the up-regulation of several genes involved in histone modifications, including jmjd1c. Overall, we describe a sex determination system resulting from continuous genetic and environmental influences in an animal. Our results provide significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish, The study was supported by the European Maritime and Fisheries Fund (3S, Seabass Sex and Stress, Grant No. 4320175237) allocated to B.G. Production of the fish benefited from AQUAEXCEL2020 Transnational access grant “Transsexbass” to F.P. and M.V. Research at the F.P. laboratory was supported by Spanish Ministry of Science Grant No. PID2019-108888RB-I00., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021
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14. The regenerative response of cardiac interstitial cells

Author: Chris Jopling, Laura Rolland, Laurent Gamba, Dany Severac, Alenca Harrington, Thomas Moore-Morris, Marine Pratlong, Adèle Faucherre, Girisaran Gangatharan, Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BioCampus (BCM), and Faucherre, Adèle
Subjects: biology, [SDV]Life Sciences [q-bio], Transgene, Cell type specific, cardiac regeneration, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, scRNAseq, biology.organism_classification, Interstitial cell, [SDV.BDD.MOR] Life Sciences [q-bio]/Development Biology/Morphogenesis, Cell biology, [SDV] Life Sciences [q-bio], Cardiac regeneration, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Chemical inhibition, Zebrafish
Abstract: Understanding how certain animals are capable of regenerating their hearts will provide much needed insights into how this process can be induced in humans in order to reverse the damage caused by myocardial infarction. Currently, it is becoming increasingly evident that cardiac interstitial cells play crucial roles during cardiac regeneration. To understand how interstitial cells behave during cardiac regeneration, we performed single-cell RNA sequencing (scRNA-seq) of regenerating zebrafish hearts. Using a combination of immunohistochemistry, chemical inhibition and novel transgenic animals, we were able to investigate the role of cell type specific responses during cardiac regeneration. This approach allowed us to identify a number of important regenerative mechanisms within the interstitial cell populations. Here, we provide here a detailed insight into how interstitial cells behave during cardiac regeneration and identify a number of novel features of these cells which will serve to increase our understanding of how this process could eventually be induced in humans.
Published: 2021
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15. 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

16. Major transcriptomic, epigenetic and metabolic changes underly the pluripotency continuum in rabbit preimplantation embryos

Author: Anaïs Moulin, Sophie Calderari, Murielle Godet, Yan Jaszczyszyn, Irène Aksoy, Catherine Archilla, Marielle Afanassieff, Nathalie Daniel, Marine Pratlong, Dany Severac, Luc Jouneau, Wilhelm Bouchereau, Véronique Duranthon, Thierry Joly, Nathalie Peynot, Pierre Savatier, and Nathalie Beaujean
Subjects: Transcriptome, medicine.anatomical_structure, Epiblast, Primitive streak, embryonic structures, medicine, Glycolysis, Embryo, Epigenetics, Blastocyst, Biology, Induced pluripotent stem cell, Cell biology
Abstract: Despite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of embryos at the molecular level is still poorly documented. We conducted a transcriptome analysis of rabbit pre-implantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using bulk and single-cell RNA-sequencing. In parallel, we studied oxidative phosphorylation and glycolysis and analysed active and repressive epigenetic modifications during blastocyst formation and expansion. We generated a transcriptomic, epigenetic, and metabolic map of the pluripotency continuum in rabbit preimplantation embryos and identified novel markers of naive pluripotency that might be instrumental for deriving naive pluripotent stem cell lines. Although the rabbit is evolutionarily closer to mice than to primates, we found that the transcriptome of rabbit epiblast cells shares common features with that of humans and non-human primates.Summary StatementRabbit preimplantation embryos share characteristics with human and monkey embryos with respect to timing of early lineage segregation and expression of marker genes for naive and primed pluripotency.
Published: 2021
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17. 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

18. Lamin C Counteracts Glucose Intolerance in Aging, Obesity, and Diabetes Through β-Cell Adaptation

Author: Patricia Cavelier, Jean-Sébastien Annicotte, Isabel C. Lopez-Mejia, Marion de Toledo, Célia Barrachina, Marine Pratlong, Jamal Tazi, Carine Chavey, Xavier Gromada, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), This work was supported by grants from the Swiss National Science Foundation (Ambizione PZ00P3-168077 to I.C.L.-M.), Conseil Régional Hauts de France et Métropole Européenne de Lille (to X.G. and J.-S.A.), European Genomic Institute for Diabetes (ANR-10-LABX-46 to J.-S.A.), Agence Nationale de la Recherche (BETAPLASTICITY, ANR-17-CE14-0034 to J.-S.A.), European Foundation for the Study of Diabetes (to J.-S.A.), I-SITE Université Lille Nord-Europe (EpiRNA-Diab to J.-S.A.), Société Francophone du Diabète (to J.-S.A.), INSERM, CNRS, Lille University, Association pour la Recherche sur le Diabète (to J.-S.A.), and OSEO Innovation Stratégique Industrielle CaReNA (I 13 03 008W to J.T.)., ANR-17-CE14-0034,BETAPLASTICITY,Identification du rôle du facteur de transcription E2F1 dans l'identité et la plasticité de la cellule bétâ pancréatique(2017), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), de Toledo, Marion, and Identification du rôle du facteur de transcription E2F1 dans l'identité et la plasticité de la cellule bétâ pancréatique - - BETAPLASTICITY2017 - ANR-17-CE14-0034 - AAPG2017 - VALID
Subjects: 0301 basic medicine, Gene isoform, Blood Glucose, medicine.medical_specialty, Aging, [SDV.IMM] Life Sciences [q-bio]/Immunology, Endocrinology, Diabetes and Metabolism, [SDV]Life Sciences [q-bio], 030209 endocrinology & metabolism, Mice, Transgenic, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, LMNA, 03 medical and health sciences, Mice, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Internal medicine, Diabetes mellitus, Insulin-Secreting Cells, Glucose Intolerance, Internal Medicine, medicine, Diabetes Mellitus, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Animals, Insulin, Secretion, Obesity, Pancreas, ComputingMilieux_MISCELLANEOUS, geography, geography.geographical_feature_category, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, integumentary system, Islet, medicine.disease, Progerin, Glucagon, Lamin Type A, [SDV] Life Sciences [q-bio], 030104 developmental biology, Endocrinology, Mitochondrial biogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, Energy Metabolism, Lamin, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Aging-dependent changes in tissue function are associated with the development of metabolic diseases. However, the molecular connections linking aging, obesity, and diabetes remain unclear. Lamin A, lamin C, and progerin, products of the Lmna gene, have antagonistic functions on energy metabolism and life span. Lamin C, albeit promoting obesity, increases life span, suggesting that this isoform is crucial for maintaining healthy conditions under metabolic stresses. Because β-cell loss during obesity or aging leads to diabetes, we investigated the contribution of lamin C to β-cell function in physiopathological conditions. We demonstrate that aged lamin C only–expressing mice (LmnaLCS/LCS) become obese but remain glucose tolerant due to adaptive mechanisms including increased β-cell mass and insulin secretion. Triggering diabetes in young mice revealed that LmnaLCS/LCS animals normalize their fasting glycemia by both increasing insulin secretion and regenerating β-cells. Genome-wide analyses combined to functional analyses revealed an increase of mitochondrial biogenesis and global translational rate in LmnaLCS/LCS islets, two major processes involved in insulin secretion. Altogether, our results demonstrate for the first time that the sole expression of lamin C protects from glucose intolerance through a β-cell–adaptive transcriptional program during metabolic stresses, highlighting Lmna gene processing as a new therapeutic target for diabetes treatment.
Published: 2020
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19. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity

Author: Sébastien Sagnol, Pascal de Santa Barbara, Tom Lesluyes, Amandine Guérin, Marine Pratlong, Sandrine Faure, Delphine Martire, Eva Trenquier, Fréderic Chibon, Elise Lefebvre, MORNET, Dominique, Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Cancer Research Center of Toulouse, University of Toulouse, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), BioCampus (BCM), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), and Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, sarcoma, [SDV]Life Sciences [q-bio], Cell Plasticity, Autophagy-Related Proteins, Cell Cycle Proteins, Chick Embryo, smooth muscle, 0302 clinical medicine, Tumor Cells, Cultured, ComputingMilieux_MISCELLANEOUS, Gastrointestinal Neoplasms, YAP1, GiST, Effector, Prognosis, 3. Good health, Gene Expression Regulation, Neoplastic, Survival Rate, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, 030220 oncology & carcinogenesis, symbols, Molecular Medicine, Original Article, Sarcoma, signaling pathway, Gastrointestinal Stromal Tumors, Mesenchyme, Biology, 03 medical and health sciences, symbols.namesake, Biomarkers, Tumor, medicine, Animals, Humans, cancer, Progenitor cell, Cell Proliferation, Mesenchymal stem cell, Original Articles, LIX1, Cell Biology, medicine.disease, gastrointestinal, digestive system diseases, Interstitial cell of Cajal, 030104 developmental biology, Cancer research, Neoplasm Recurrence, Local, Transcription Factors
Abstract: Gastrointestinal stromal tumours (GISTs), the most common mesenchymal neoplasm of the gastrointestinal tract, result from deregulated proliferation of transformed KIT‐positive interstitial cells of Cajal that share mesenchymal progenitors with smooth muscle cells. Despite the identification of selective KIT inhibitors, primary resistance and relapse remain a major concern. Moreover, most patients develop resistance partly through reactivation of KIT and its downstream signalling pathways. We previously identified the Limb Expression 1 (LIX1) gene as a unique marker of digestive mesenchyme immaturity. We also demonstrated that LIX1 regulates mesenchymal progenitor proliferation and differentiation by controlling the Hippo effector YAP1, which is constitutively activated in many sarcomas. Therefore, we wanted to determine LIX1 role in GIST development. We found that LIX1 is strongly up‐regulated in GIST samples and this is associated with unfavourable prognosis. Moreover, LIX1 controls GIST cell proliferation in vitro and in vivo. Upon LIX1 inactivation in GIST cells, YAP1/TAZ activity is reduced, KIT (the GIST signature) is down‐regulated, and cells acquire smooth muscle lineage features. Our data highlight LIX1 role in digestive mesenchyme‐derived cell‐fate decisions and identify this novel regulator as a target for drug design for GIST treatment by influencing its differentiation status.
Published: 2020
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20. The mouse HP1 proteins are essential for preventing liver tumorigenesis

Author: Nehmé, Saksouk, Shefqet, Hajdari, Yannick, Perez, Marine, Pratlong, Célia, Barrachina, Céline, Graber, Damien, Grégoire, Aliki, Zavoriti, Amélie, Sarrazin, Nelly, Pirot, Jean-Yohan, Noël, Lakhdar, Khellaf, Eric, Fabbrizio, Eric, Julien, and Florence M, Cammas
Subjects: Male, Mice, Knockout, Retroelements, Chromosomal Proteins, Non-Histone, Liver Neoplasms, Tripartite Motif-Containing Protein 28, Cell Line, Gene Expression Regulation, Neoplastic, Disease Models, Animal, Mice, Cell Transformation, Neoplastic, Liver, Chromobox Protein Homolog 5, Heterochromatin, Hepatocytes, Animals, Humans, Female, RNA-Seq, Protein Binding
Abstract: Chromatin organization is essential for appropriate interpretation of the genetic information. Here, we demonstrated that the chromatin-associated proteins HP1 are dispensable for hepatocytes survival but are essential within hepatocytes to prevent liver tumor development in mice with HP1β being pivotal in these functions. Yet, we found that the loss of HP1 per se is not sufficient to induce cell transformation but renders cells more resistant to specific stress such as the expression of oncogenes and thus in fine, more prone to cell transformation. Molecular characterization of HP1-Triple KO premalignant livers and BMEL cells revealed that HP1 are essential for the maintenance of heterochromatin organization and for the regulation of specific genes with most of them having well characterized functions in liver functions and homeostasis. We further showed that some specific retrotransposons get reactivated upon loss of HP1, correlating with overexpression of genes in their neighborhood. Interestingly, we found that, although HP1-dependent genes are characterized by enrichment H3K9me3, this mark does not require HP1 for its maintenance and is not sufficient to maintain gene repression in absence of HP1. Finally, we demonstrated that the loss of TRIM28 association with HP1 recapitulated several phenotypes induced by the loss of HP1 including the reactivation of some retrotransposons and the increased incidence of liver cancer development. Altogether, our findings indicate that HP1 proteins act as guardians of liver homeostasis to prevent tumor development by modulating multiple chromatin-associated events within both the heterochromatic and euchromatic compartments, partly through regulation of the corepressor TRIM28 activity.
Published: 2019

21. Genetic pathways underpinning hormonal stress responses in fish exposed to short- and long-term warm ocean temperatures

Author: Johan Aerts, Hugues Parrinello, Célia Barrachina, Marine Pratlong, Alexander Goikoetxea, Bastien Sadoul, Benjamin Geffroy, Eva Blondeau-Bidet, Marie-Odile Blanc, 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), Universiteit Gent = Ghent University [Belgium] (UGENT), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), and Sadoul, Bastien
Subjects: 0106 biological sciences, Scales, General Decision Sciences, Zoology, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Acclimatization, Cortisol, Transcriptome, Glucocorticoid receptor, Aquaculture, Commercial fish, 14. Life underwater, Sea bass, Glucocorticoid receptors, Transcriptomics, QH540-549.5, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Ecology, biology, business.industry, Stressor, biology.organism_classification, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Sea surface temperature, 13. Climate action, Dicentrarchus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: International audience; Changes in ocean water temperature associated with global climate change are bound to enormously affect fish populations, with potential major economic consequences in the aquaculture and fisheries industries. A link between temperature fluctuations and changes in fish stress response is well established. In this study, we aimed to assess the effects of a short- (4 days) or a long-term (4 months) exposure to warm temperature in the stress physiology of European sea bass (Dicentrarchus labrax) larvae and juveniles. First, cortisol (i.e. the main stress hormone in fishes) analysis was used to confirm that a steady and short-term elevation of temperature acts as a physiological stressful event in these fish, and cortisol release is indeed above a metabolic increase linked to temperature. Moreover, our results verified that measurement of cortisol released into the water can be reliably employed as a non-invasive indicator of acute thermal stress in experimental conditions. Secondly, the different effects on the genetic cascade underlying the stress response between long-term low or high thermal treatments were evaluated at two larval development stages via candidate-gene and whole-transcriptome approaches. Interestingly, opposite expression for some key stress genes (nr3c1, nr3c2 and hsd11b2) were observed between developmental stages, highlighting the distinct adaptive mechanisms controlling the primary and secondary responses to a stressor. Surprising expression patterns for some understudied genes involved in the stress axis were also revealed, including crhr1, mc2r, mc5r, trh or trhr, which should be further explored. Finally, evaluation of cortisol content in scales was successfully used as a biomarker of chronic thermal stress, with 10x more cortisol in fish kept at 21 ◦C vs 16 ◦C after 4 months, supporting the gene expression results observed. The use of such a method as a proxy of long-term stress, unprecedented in the literature, holds a vast array of applications in further research, in particular, in the investigation of the impact of global warming on wild fish populations.
Published: 2021
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22. Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum

Author: Didier Aurelle, Pierre Pontarotti, Guillaume Mitta, Nathaniel Bensoussan, Marine Pratlong, Kelly Brener, Joaquim Garrabou, Anne Haguenauer, Eve Toulza, 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), 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), 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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 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), Aix Marseille Université (AMU), 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), IPSO FACTO [Marseille], Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Ecologie Marine et BIOdiversité (EMBIO), 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 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), 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), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, Cnidaria, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, biology, Coral, [SDV]Life Sciences [q-bio], biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Chaff, Evolutionary biology, Genetic structure, Identification (biology), 14. Life underwater, Corallium rubrum, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Selection (genetic algorithm), 030304 developmental biology, Local adaptation, Environmental gradient
Abstract: Genomic data allow an in-depth and renewed study of local adaptation. The red coral (Corallium rubrum, Cnidaria) is a highly genetically structured species and a promising model for the study of adaptive processes along an environmental gradient. Here, we used RAD-Sequencing in order to study the vertical genetic structure of this species and to search for signals of local adaptation to depth and thermal regime in the red coral. Previous studies have shown different thermotolerance levels according to depth in this species which could correspond to genetic or environmental differences. We designed a sampling scheme with six pairs of ‘shallow vs deep’ populations distributed in three geographical regions as replicates. Our results showed significant differentiation among locations and among sites separated by around 20 m depth. The tests of association between genetics and environment allowed the identification of candidate loci under selection but with a potentially high rate of false positive. We discuss the methodological obstacles and biases encountered for the detection of selected loci in such a strongly genetically structured species. On this basis, we also discuss the significance of the candidate loci for local adaptation detected in each geographical region and the evolution of red coral populations along environmental gradients.A colony of red coral,Corallium rubrum, near Marseille. Photo: F. Zuberer / OSU Pythéas / CNRS
Published: 2018
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23. The mouse HP1 proteins are essential for preventing liver tumorigenesis

Author: Jean-Yohan Noël, Aliki Zavoriti, Amélie Sarrazin, Shefqet Hajdari, Céline Graber, Eric Julien, Eric Fabbrizio, Célia Barrachina, Nelly Pirot, Nehmé Saksouk, Lakhdar Khellaf, Marine Pratlong, and Florence Cammas
Subjects: endocrine system, animal structures, TRIM28, Euchromatin, Heterochromatin, Endoplasmic reticulum, embryonic structures, Heterochromatin protein 1, Steroid biosynthesis, Biology, Corepressor, Chromatin, Cell biology
Abstract: Chromatin organization is essential for appropriate interpretation of the genetic information. Here, we demonstrated that the chromatin associated proteins HP1 are dispensable for cell survival but are essential within hepatocytes to prevent liver tumor development. Molecular characterization of pre-malignant HP1-Triple KO livers revealed that HP1 are essential for the maintenance of the structural organization of heterochromatin but surprisingly, not for several well known heterochromatin functions such as the maintenance of the genome stability nor the regulation of major satellite repeat expression within liver. We further show that some specific retrotransposons, mainly of the ERV family, get reactivated in HP1-TKO livers correlating, in some cases, with the activation of the adjacent genes. We present evidence that this reactivation of ERV relies on the HP1-dependent ability of the corepressor TRIM28 to regulate KRAB-ZFP repressive activity. Intriguingly, we found that in contrast to the observation in young animals, the HP1-dependent maintenance of ERV silencing becomes independent of TRIM28 in old animals. Finally, we showed that HP1 are also essential directly or indirectly for the regulation of single genes with most of them having well characterized functions in liver homeostasis such as regulation of the redox and endoplasmic reticulum equilibrium, lipid metabolism and steroid biosynthesis.Altogether, our findings indicate that HP1 proteins, through the modulation of multiple chromatin-associated events both within the heterochromatic and euchromatic compartments, act as guardians of liver homeostasis to prevent tumor development.
Published: 2018
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24. Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals

Author: Oliver Rey, François Bonhomme, Guillaume Mitta, Anne Haguenauer, K. Brener-Raffalli, Marine Pratlong, Pauline Gélin, Pierre Pontarotti, Didier Aurelle, Mehdi Adjeroud, L. Feuillassier, Eve Toulza, Michel R. Claereboudt, Hélène Magalon, Jeremie Vidal-Dupiol, Pascal Romans, Rémi Pillot, 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 de Recherche pour le Développement (IRD), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Perpignan]), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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, 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), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Sultan Qaboos University (SQU), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), 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), 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)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), 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), 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 de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), 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), and 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)
Subjects: 0106 biological sciences, Genetics, Regulation of gene expression, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, 13. Climate action, Heat shock protein, DNA methylation, Gene expression, 14. Life underwater, Epigenetics, Pocillopora, Gene, 030304 developmental biology
Abstract: Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response in Pocillopora coral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.
Published: 2018
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25. Molecular Forensics into the Sea: How Molecular Markers Can Help to Struggle Against Poaching and Illegal Trade in Precious Corals?

Author: Didier Aurelle, Marine Pratlong, Jean-Baptiste Ledoux, Agostinho Antunes, Anne Haguenauer, Federica Costantini, Marco Abbiati, Centre d'Ingénierie Biologique, University of Minho [Braga], Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), Centro Interdipartimentale di Ricerca per le Scienze Ambientali and Dipartimento di Biologia ( CIRSA ), Università di Bologna [Bologna] ( UNIBO ), University of Bologna, 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), Centro Interdipartimentale di Ricerca per le Scienze Ambientali and Dipartimento di Biologia (CIRSA), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Fundação para a Ciência e a Tecnologia (Portugal), Agence Nationale de la Recherche (France), Stefano Goffredo, Zvy Dubinsky, Jean-Baptiste Ledoux, Agostinho Antune, Anne Haguenauer, Marine Pratlong, Federica Costantini, Marco Abbiati, Didier Aurelle, Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and University of Bologna/Università di Bologna
Subjects: 0106 biological sciences, 0301 basic medicine, Marine conservation, Molecular forensics • Precious corals • Corallium • Species identification • DNA barcode • Mitochondrial DNA • Assignment tests • Microsatellites • Next generation sequencing, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, CITES, Ecology, Coral, Precious coral, Poaching, Context (language use), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Fishery, 03 medical and health sciences, 030104 developmental biology, Geography, Alcyonacea, Marine protected area, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: 17 pages, 2 figures, 5 boxes, Precious corals encompass various species belonging to three different orders (Alcyonacea, Zoanthidea and Antipatharia) of the Anthozoan class. These sessile cnidarians are one of the most valuable marine resources due to the use of their skeleton for jewelry and handcrafted artifacts. The exploitation of precious corals beds generally follows a boom and bust cycle resulting in a worldwide overexploitation of this natural resource. The sustainability of coral fisheries is therefore unambiguously questioned. Discussions regarding international regulations on harvesting or trade have regularly risen in the last decades. As an example, the genus Corallium, which includes some of the most harvested and valuables precious coral species, was unsuccessfully proposed for listing in Appendix II of the Convention on the International Trade in Endangered Species (CITES) in 2007 and 2009. To date, there is no international consensus on the management of coral beds (but see 2011 FAO-GFCM recommendations for the Mediterranean Sea). Each country manages independently its stocks of precious corals inducing contrasted conservation policies. Considering the benefit in trading precious corals and the low enforcement of existing regulations, poaching is very attractive and globally expanding, principally within marine protected areas where populations are healthier and colonies are generally bigger. In this context, innovative management tools and strategies should be developed to ensure the protection of these species. Recent advances in wildlife forensics sciences and more particularly in molecular forensics methods and associated statistical analyses open new avenues to struggle against poaching and illegal trade in precious corals. We will introduce this chapter with general considerations regarding the exploitation of biological resources and accordingly the aims of molecular forensics applied in conservation biology. Then, we will present the methods used for species identification with particular emphasize on DNA barcoding methods. We will discuss the application of these methods for precious coral identification. Considering the genetic data available in precious corals, we will illustrate our discussion with an example of DNA barcoding in Corallium/Paracorallium species. We will present the atypical evolutionary features of the mitochondrial genome of these species and the implications for species identification. Once species have been identified, the identification of the geographical origin of individuals or populations may be of interest in order to distinguish between legal and illegal (e.g. within marine protected area) harvesting. In a third part, we will therefore expose different molecular and statistical methods that can be used to assign individuals to their populations of origin. As a case study, we will present the data resulting from the genotyping of nuclear microsatellite loci in the red coral, Corallium rubrum, a precious coral inhabiting the Mediterranean Sea and part of the Eastern Atlantic. The genetic structure and the repartition of the genetic diversity of C. rubrum are thoroughly characterized over the Western Mediterranean Basin. We will discuss the potential of this database of genotypes to characterize the origin of red coral colonies using different assignment methods. An empirical evaluation will be performed to test the statistical power of this dataset. The last part of the chapter will be focused on the perspectives offered by the development of next generation sequencing methods for the molecular forensics in precious corals, JBL was funded by a Postdoctoral grant (SFRH/BPD/74400/2010) from the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia; FCT) (http://www.fct.pt). MP was funded by the Labex OT-Med (n° ANR-11-LABX-0061) funded by the French Government “Investissements d’Avenir” program of the French National Research Agency (ANR) through the A*MIDEX project (n° ANR-11-IDEX-0001-02)
Published: 2016
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26. Animal multicellularity and polarity without Wnt signaling

Author: Quentin Schenkelaars, Marine Pratlong, Laurent Kodjabachian, Laura Fierro-Constain, Jean Vacelet, André Le Bivic, Emmanuelle Renard, Carole Borchiellini, 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), Université de Genève (UNIGE), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and renard, emmanuelle
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:R, lcsh:Medicine, Models, Biological, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Article, Porifera, [SDV] Life Sciences [q-bio], Wnt Proteins, Transforming Growth Factor beta, [SDV.BDD] Life Sciences [q-bio]/Development Biology, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Morphogenesis, Animals, lcsh:Q, lcsh:Science, Wnt Signaling Pathway, [SDV.BDD]Life Sciences [q-bio]/Development Biology
Abstract: International audience; Acquisition of multicellularity is a central event in the evolution of Eukaryota. Strikingly, animal multicellularity coincides with the emergence of three intercellular communication pathways – Notch, TGF-β and Wnt – all considered as hallmarks of metazoan development. By investigating Oopsacas minuta and Aphrocallistes vastus, we show here that the emergence of a syncytium and plugged junctions in glass sponges coincides with the loss of essential components of the Wnt signaling (i.e. Wntless, Wnt ligands and Disheveled), whereas core components of the TGF-β and Notch modules appear unaffected. This suggests that Wnt signaling is not essential for cell differentiation, polarity and morphogenesis in glass sponges. Beyond providing a comparative study of key developmental toolkits, we define here the first case of a metazoan phylum that maintained a level of complexity similar to its relatives despite molecular degeneration of Wnt pathways.
Published: 2017
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27. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

Author: Eve Toulza, S. Chenesseau, Pierre Pontarotti, Kelly Brener, M. Bonabaud, Marine Pratlong, Anne Haguenauer, S. Rialle, Didier Aurelle, Guillaume Mitta, Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-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 ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), BioCampus Montpellier ( BCM ), Université Montpellier 1 ( UM1 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut de Génomique Fonctionnelle-Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Mathématiques de Marseille ( I2M ), Aix Marseille Université ( AMU ) -Ecole Centrale de Marseille ( ECM ) -Centre National de la Recherche Scientifique ( CNRS ), 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), 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), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-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), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-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), BioCampus (BCM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Cnidaria, Range (biology), Single-nucleotide polymorphism, Biology, DNA sequencing, 03 medical and health sciences, cnidaria, Genetics, lcsh:Science, Gene, Allele frequency, ComputingMilieux_MISCELLANEOUS, Corallium rubrum, Multidisciplinary, corallium rubrum, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], RAD-sequencing, biology.organism_classification, Sexual reproduction, genetic sex determination, Multicellular organism, 030104 developmental biology, [ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:Q, rad-sequencing, Research Article
Abstract: Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral ( Corallium rubrum , Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
Published: 2017
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28. Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

Author: Hélène Magalon, Marine Pratlong, Pauline Gélin, J. Henrich Bruggemann, Bautisse Postaire, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), 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), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Population, brooding species, Asexual reproduction, Biology, 010603 evolutionary biology, 01 natural sciences, Analysis of molecular variance, microsatellites, assignment test, Gene flow, 03 medical and health sciences, Sensu, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Isolation by distance, cryptic diversity, education.field_of_study, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Hydrozoa, 030104 developmental biology, Biological dispersal, Marine protected area, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F-IS values (from -0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (11,000km distance), with significant pairwise F-ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
Published: 2017
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29. Genomic resources and their influence on the detection of the signal of positive selection in genome scans

Author: Laurent Abi-Rached, Julien Paganini, Charles Perrier, Didier Aurelle, Pierre Pontarotti, Marine Pratlong, Stéphanie Manel, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Stanford University School of Medicine [Stanford], Stanford University [Stanford], EBM, Laboratoire d'Analyse, Topologie, Probabilités (LATP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS)-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Total Foundation, foundation ECCOREV, 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), European Project: 337365,EC:FP7:ERC,ERC-2013-StG,SHE(2014), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Total Foundation, foundation ECCOREV., ANR-11-IDEX-0001-02/11-LABX-0061,OTMed,Objectif Terre : Bassin Méditerranéen(2011), ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)
Subjects: 0301 basic medicine, conservation biology, population genomics, Genome Scan, Genomics/Proteomics, Genomics, Computational biology, Biology, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, landscape genomics, natural population, Genetics, Animals, Selection, Genetic, Adaptation, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Comparative genomics, Natural selection, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Biological Evolution, 030104 developmental biology, Genetics, Population, Ecological Genetics, Landscape Genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Imputation (genetics), local adaptation, Personal genomics, Reference genome
Abstract: International audience; Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences are also becoming the raw material for selection inferences. Here, we discuss how the increasing availability of such genomic resources, notably genome sequences, influences the detection of signals of selection. Mainly, increasing data density and having the information of physical linkage data expand genome scans by (i) improving the overall quality of the data, (ii) helping the reconstruction of demographic history for the population studied to decrease false-positive rates and (iii) improving the statistical power of methods to detect the signal of selection. Of particular importance, the availability of a high-quality reference genome can improve the detection of the signal of selection by (i) allowing matching the potential candidate loci to linked coding regions under selection, (ii) rapidly moving the investigation to the gene and function and (iii) ensuring that the highly variable regions of the genomes that include functional genes are also investigated. For all those reasons, using reference genomes in genome scan analyses is highly recommended.
Published: 2016
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30. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

Author: Pierre Pontarotti, Marine Pratlong, Anne Haguenauer, Didier Aurelle, Olivier Chabrol, Christophe Klopp, 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), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] ( UBIA ), Institut National de la Recherche Agronomique ( INRA ) -Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Biodiversité et Biotechnologie Fongiques ( BBF ), Ecole Centrale de Marseille ( ECM ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
Subjects: GENES, Coral, Molecular Sequence Data, Adaptation, Biological, DNA-SEQUENCING DATA, Population genetics, Context (language use), Biology, CELL BIOLOGY, Acclimatization, FACTORS TRAFS, cnidarians, CNIDARIAN, Anthozoa, Mediterranean Sea, Genetics, Animals, 14. Life underwater, RNA-SEQ, gene expression, local adaptation, octocoral polymorphism, transcriptome, DIFFERENTIAL EXPRESSION ANALYSIS, CLIMATE-CHANGE, IDENTIFICATION, POLYMORPHISMS, Ecology, Evolution, Behavior and Systematics, Local adaptation, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Phenotypic plasticity, Polymorphism, Genetic, Ecology, Temperature, Sequence Analysis, DNA, biology.organism_classification, Genetics, Population, 13. Climate action, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biotechnology
Abstract: International audience; The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate change. The red coral (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging from 5 to 600m, it meets very contrasted thermal conditions. The shallowest populations of this species suffered from mortality events linked with thermal anomalies that have highlighted thermotolerance differences between individuals. We provide here a new transcriptomic resource, as well as candidate markers for the study of local adaptation. We sequenced the transcriptome of six individuals from 5m and six individuals from 40m depth at the same site of the Marseilles bay, after a period of common garden acclimatization. We found differential expression maintained between the two depths even after common garden acclimatization, and we analysed the polymorphism pattern of these samples. We highlighted contigs potentially implicated in the response to thermal stress, which could be good candidates for the study of thermal adaptation for the red coral. Some of these genes are also involved in the response to thermal stress in other corals. Our method enables the identification of candidate loci of local adaptation useful for other nonmodel organisms.
Published: 2015
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30 results on '"Marine Pratlong"'

1. Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

2. NRG1/ErbB signalling controls the dialogue between macrophages and neural crest-derived cells during zebrafish fin regeneration

3. Single cell RNA sequencing reveals hemocyte heterogeneity in Biomphalaria glabrata: Plasticity over diversity

4. Genetic pathways underpinning hormonal stress responses in fish exposed to short- and long-term warm ocean temperatures

5. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato

6. Ribosomal Protein S6 Phosphorylation Is Involved in Novelty-Induced Locomotion, Synaptic Plasticity and mRNA Translation

7. Glutaredoxin regulation of primary root growth confers early drought stress tolerance in pearl millet

8. Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia)

9. Major transcriptomic, epigenetic and metabolic changes underlie the pluripotency continuum in rabbit preimplantation embryos

10. The mouse HP1 proteins are essential for preventing liver tumorigenesis

11. The landscape of cancer-associated fibroblasts in colorectal cancer liver metastases

12. The regenerative response of cardiac interstitial cells

13. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system

14. The regenerative response of cardiac interstitial cells

15. Population genomics of Pocillopora corals: insights from RAD-sequencing

16. Major transcriptomic, epigenetic and metabolic changes underly the pluripotency continuum in rabbit preimplantation embryos

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

18. Lamin C Counteracts Glucose Intolerance in Aging, Obesity, and Diabetes Through β-Cell Adaptation

19. LIX1 regulates YAP activity and controls gastrointestinal cancer cell plasticity

20. The mouse HP1 proteins are essential for preventing liver tumorigenesis

21. Genetic pathways underpinning hormonal stress responses in fish exposed to short- and long-term warm ocean temperatures

22. Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum

23. The mouse HP1 proteins are essential for preventing liver tumorigenesis

24. Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals

25. Molecular Forensics into the Sea: How Molecular Markers Can Help to Struggle Against Poaching and Illegal Trade in Precious Corals?

26. Animal multicellularity and polarity without Wnt signaling

27. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

28. Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

29. Genomic resources and their influence on the detection of the signal of positive selection in genome scans

30. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies

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