29 results on '"Chabrol, Olivier"'
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2. Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits
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Bertrand, Stephanie, Camasses, Alain, Somorjai, Ildiko, Belgacem, Mohamed R., Chabrol, Olivier, Escande, Marie-Line, Pontarotti, Pierre, and Escriva, Hector
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- 2011
3. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga
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Flot, Jean-François, Hespeels, Boris, Li, Xiang, Noel, Benjamin, Arkhipova, Irina, Danchin, Etienne G. J., Hejnol, Andreas, Henrissat, Bernard, Koszul, Romain, Aury, Jean-Marc, Barbe, Valérie, Barthélémy, Roxane-Marie, Bast, Jens, Bazykin, Georgii A., Chabrol, Olivier, Couloux, Arnaud, Da Rocha, Martine, Da Silva, Corinne, Gladyshev, Eugene, Gouret, Philippe, Hallatschek, Oskar, Hecox-Lea, Bette, Labadie, Karine, Lejeune, Benjamin, Piskurek, Oliver, Poulain, Julie, Rodriguez, Fernando, Ryan, Joseph F., Vakhrusheva, Olga A., Wajnberg, Eric, Wirth, Bénédicte, Yushenova, Irina, Kellis, Manolis, Kondrashov, Alexey S., Mark Welch, David B., Pontarotti, Pierre, Weissenbach, Jean, Wincker, Patrick, Jaillon, Olivier, and Van Doninck, Karine
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- 2013
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4. The functional convergence of antibiotic resistance in β‐lactamases is not conferred by a simple convergent substitution of amino acid
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Keshri, Vivek, Arbuckle, Kevin, Chabrol, Olivier, Rolain, Jean‐Marc, Raoult, Didier, Pontarotti, Pierre, 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 de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), University of Liverpool, and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
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[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,antibiotic resistance ,[SDV]Life Sciences [q-bio] ,lcsh:Evolution ,Original Articles ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,β-lactam antibiotics ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,lcsh:QH359-425 ,Original Article ,β‐lactamase ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,β‐lactam antibiotics ,convergent evolution ,ComputingMilieux_MISCELLANEOUS ,β-lactamase | 1813 - Abstract
Bacterial resistance to antibiotics is a serious medical and public health concern worldwide. Such resistance is conferred by a variety of mechanisms, but the extensive variability in levels of resistance across bacteria is a common finding. Understanding the underlying evolutionary processes governing this functional variation in antibiotic resistance is important as it may allow the development of appropriate strategies to improve treatment options for bacterial infections. The main objective of this study was to examine the functional evolution of β‐lactamases, a common mechanism of enzymatic resistance that inactivates a widely used class of antibiotics. We first obtained β‐lactamase protein sequences and minimal inhibitory concentration (MIC), a measure of antibiotic function, from previously published literature. We then used a molecular phylogenetic framework to examine the evolution of β‐lactamase functional activity. We found that the functional activity of antibiotic resistance mediated by β‐lactamase has evolved in a convergent manner within molecular classes, but is not associated with any single amino acid substitution. This suggests that the dynamics of convergent evolution in this system can vary between the functional and molecular (sequence) levels. Such disassociation may hamper bioinformatic approaches to antibiotic resistance determination and underscore the need for (less efficient but more effective) activity assays as an essential step in evaluating resistance in a given case.
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- 2019
5. Origine de l'oeuf amniotique étudiée à l'aide de deux nouvelles méthodes
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Didier, Gilles, Chabrol, Olivier, Laurin, Michel, Institut Montpelliérain Alexander Grothendieck (IMAG), 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), Centre de Recherche en Paléontologie - Paris (CR2P), and Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
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[SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology - Abstract
International audience; L'oeuf amniotique est un caractère-clé des amniotes. Son apparition fut un événement majeur qui contribua probablement au succès spectaculaire des amniotes dans les environnements terrestres, dont ils dominent largement la plupart des habitats. Leur groupe-frère, les lissamphibiens, s'est nettement moins diversifié et représente une biomasse bien plus faible. Nous testons une des hypothèses les plus populaires concernant l'origine de l'oeuf amniotique, hypothèse émise par Carroll (1970). Elle stipule que des amniotes-souches auraient initialement pondu un œuf anamniotique sur la terre ferme (comme le font aujourd'hui certains Plethodontidae). L'absence initiale des annexes extra-embryonnaires qui caractérisent l'oeuf amniotique contemporain aurait limité les échanges gazeux, limitant la taille de l'oeuf à moins de 1 cm de diamètre, et celle des adultes, à moins de 10 cm de longueur museau-cloaque. Ceci implique une diminution de taille chez certains amniotes-souches, car la plupart des stégocéphales permo-carbonifères mesuraient plus de 10 cm. Après l'apparition de l'oeuf amniotique (pourvu des annexes), la taille de l'oeuf et des adultes aurait augmenté.Bien que le registre fossile n'ait pas livré les œufs pertinents, il est possible de tester les prédictions de l'hypothèse de Carroll sur l'évolution de la taille corporelle. L'un d'entre nous avait effectué une première série de tests en 2004 (Laurin, 2004), à l'aide de la parcimonie des moindres carrés et des contrastes phylogénétiques indépendants. Une des prévisions de Carroll s'était vérifiée (il semble bien y avoir eu une légère tendance à l'augmentation de taille chez les premiers amniotes), mais pas les autres.Nous testons à nouveau l'hypothèse de Carroll à l'aide du même jeu de données (taille corporelle, âge géologique et phylogénie de 107 taxons permo-carbonifères) mais en utilisant des méthodes plus appropriées : la parcimonie linéaire asymétrique (Didier, 2017), permettant de mieux estimer la taille des ancêtres hypothétiques en présence de tendance évolutive, et une nouvelles méthode utilisant cette parcimonie pour identifier les régions de l'arbre où les tendances évolutives changent. En effet, l'hypothèse de Carroll suggère deux changements de tendances au sein des amniotes-souches ; une diminution de taille suivant le début de la ponte en milieu terrestre, puis une augmentation de taille suite à l'apparition de l'oeuf amniotique. Nos résultats (Didier et al., 2019) ne soutiennent pas l'hypothèse de Carroll. La plupart des estimations de taille des ancêtres sur la souche des amniotes suggèrent une longueur museau-cloaque supérieure à 10 cm ; seules des estimations pour certains nœuds sont inférieures à ce seuil, et uniquement si on postule la présence d'une tendance évolutive très forte vers une augmentation de taille corporelle. De plus, la souche des amniotes ne semble pas être une partie de l'arbre montrant un taux plus élevé que la moyenne de changements de tendances ; au contraire, un seul changement de tendance, sur 517 changements possibles, se situe dans cette partie de l'arbre. Nous ne pouvons cependant pas rejeter catégoriquement l'hypothèse de Carroll car cette partie de l'arbre est peu représentée dans le registre fossile, selon notre phylogénie préférée (mais elle l'est nettement mieux selon l'alternative plus ancienne, plus populaire, mais à notre avis moins bien soutenue). Une meilleure compréhension de l'origine des amniote attendra donc la découverte de fossiles supplémentaires.RéférencesCarroll R.L. (1970). Quantitative aspects of the amphibian-reptilian transition. Forma et Functio, 3 : 165-178.Didier G. (2017). Time-dependent-asymmetric-linear-parsimonious ancestral state reconstruction. Bulletin of mathematical biology, 79(10) : 2334-2355.Didier G., Chabrol O. & Laurin M. (2019). Parsimony-based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg. Cladistics, doi:10.1111/cla.12371.Laurin M. (2004). The evolution of body size, Cope's rule and the origin of amniotes. Syst. Biol., 53(4) : 594-622.
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- 2019
6. An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales
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Le Phuong, Ramulu Hemalatha, Guijarro Laurent, Paganini Julien, Gouret Philippe, Chabrol Olivier, Raoult Dider, and Pontarotti Pierre
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Horizontal gene transfer ,Rickettsiales ,Candidatus Pelagibacter ubique ,Sympatry ,Evolution ,QH359-425 - Abstract
Abstract Background Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species. Results We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as “rhizome-like”. Conclusions Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.
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- 2012
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7. Oocyte-somatic cells interactions, lessons from evolution
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Charlier Cathy, Montfort Jérôme, Chabrol Olivier, Brisard Daphné, Nguyen Thaovi, Le Cam Aurélie, Richard-Parpaillon Laurent, Moreews François, Pontarotti Pierre, Uzbekova Svetlana, Chesnel Franck, and Bobe Julien
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, especially in non-mammalian species. The present work aimed at identifying key molecular signals from somatic origin that would be shared by vertebrates. Results Using a parallel transcriptomic analysis in 4 vertebrate species - a teleost fish, an amphibian, and two mammals - at similar key steps of developmental competence acquisition, we identified a large number of species-specific differentially expressed genes and a surprisingly high number of orthologous genes exhibiting similar expression profiles in the 3 tetrapods and in the 4 vertebrates. Among the evolutionary conserved players participating in developmental competence acquisition are genes involved in key processes such as cellular energy metabolism, cell-to-cell communications, and meiosis control. In addition, we report many novel molecular actors from somatic origin that have never been studied in the vertebrate ovary. Interestingly, a significant number of these new players actively participate in Drosophila oogenesis. Conclusions Our study provides a comprehensive overview of evolutionary-conserved mechanisms from somatic origin participating in oocyte developmental competence acquisition in 4 vertebrates. Together our results indicate that despite major differences in ovarian follicular structure, some of the key players from somatic origin involved in oocyte developmental competence acquisition would be shared, not only by vertebrates, but also by metazoans. The conservation of these mechanisms during vertebrate evolution further emphasizes the important contribution of the somatic compartment to oocyte quality and paves the way for future investigations aiming at better understanding what makes a good egg.
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- 2012
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8. Genome-wide approaches to elucidate evolution of sex determination systems and sex determining genes in fish
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Pan, Qiaowei, Feron, Romain, Jouanno, Elodie, Wen, Ming, Imarazene, Boudjema, Anderson, Jennifer, Kottler, Verena A., Santacruz Roco, Alvaro, Du, Kang, Kneitz, Suzanne, Wang, Zhongwei, Adolfi, Mateus C., Wilson, Catherine, McCluskey, Braedan M., Amores, Angel, Desvignes, Thomas, Klopp, Christophe, Lopez-Roques, Celine, Chabrol, Olivier, Donnadieu, Cecile, Parrinello, Hugues, Journot, Laurent, Herpin, Amaury, Postlethwait, John H, Schartl, Manfred, Guiguen, Yann, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Physiological Chemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institute of Neuroscience, University of Oregon [Eugene], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)
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détermination du sexe ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,GeneralLiterature_INTRODUCTORYANDSURVEY ,[SDV]Life Sciences [q-bio] ,gène déterminant majeur du sexe ,approche génomique ,GeneralLiterature_MISCELLANEOUS ,reproduction ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,séquençage du génome ,poisson ,ComputerApplications_MISCELLANEOUS ,phylogénie ,ComputingMilieux_COMPUTERSANDEDUCATION ,chromosome sexuel ,[INFO]Computer Science [cs] ,[MATH]Mathematics [math] ,ComputingMilieux_MISCELLANEOUS - Abstract
[YG: Invited Keynote Lecture]; International audience
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- 2018
9. Additional file 1: of Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect
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Fritz, Shirley, Andriamiharimamy Rajaonison, Chabrol, Olivier, Raoult, Didier, Jean-Marc Rolain, and Merhej, Vicky
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polycyclic compounds - Abstract
Figure S1. A Venn diagram of PKS, NRPS, and hybrid gene-cluster numbers in NRPUR database. The gene-cluster numbers of the total, bacteria, eukarya and archaea are shown in black, red, green, and grey, respectively. Table S1. The 164 NRPS-PKS BGC sequences identified from the literature search resulting from experimental data with validated antibacterial activity. Table S2. Summary of NRPS and PKS gene clusters found in the genomes of bacteria from the gut. Figure S2. Distribution of NRPS, PKS, and hybrid gene clusters in bacteria from the gut a) in all studied bacteria, b) in the studied phyla (PDF 313 kb)
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- 2018
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10. An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees
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Keshri, Vivek, primary, Diene, Seydina M., additional, Estienne, Adrien, additional, Dardaillon, Justine, additional, Chabrol, Olivier, additional, Tichit, Laurent, additional, Rolain, Jean-Marc, additional, Raoult, Didier, additional, and Pontarotti, Pierre, additional
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- 2019
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11. Parsimony‐based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg
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Didier, Gilles, primary, Chabrol, Olivier, additional, and Laurin, Michel, additional
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- 2019
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12. Se saisir des plans de vigilance
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Chabrol, Olivier, primary and Delépine, Justin, additional
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- 2018
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13. CASSIOPE: An expert system for conserved regions searches
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Grusea Simona, Chabrol Olivier, Levasseur Anthony, Rascol Virginie, Gouret Philippe, Danchin Etienne GJ, and Pontarotti Pierre
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in genome evolution and their implications for the study of biological systems. Detection of conserved regions (descending from a common ancestor) not only helps clarify genome evolution but also makes it possible to identify quantitative trait loci (QTLs) and investigate gene function. The identification and comparison of conserved regions on a genome scale is computationally intensive, making process automation essential. Three key requirements are necessary: consideration of phylogeny to identify orthologs between multiple species, frequent updating of the annotation and panel of compared genomes and computation of statistical tests to assess the significance of identified conserved gene clusters. Results We developed a modular system superimposed on a multi-agent framework, called CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution). CASSIOPE automatically identifies statistically significant conserved regions between multiple genomes based on automated phylogenies and statistical testing. Conserved regions were searched for in 19 species and 1,561 hits were found. To our knowledge, CASSIOPE is the first system to date that integrates evolutionary biology-based concepts and fulfills all three key requirements stated above. All results are available at http://194.57.197.245/cassiopeWeb/displayCluster?clusterId=1 Conclusion CASSIOPE makes it possible to study conserved regions from a chosen query genetic region and to infer conserved gene clusters based on phylogenies and statistical tests assessing the significance of these conserved regions. Source code is freely available, please contact: Pierre.pontarotti@univ-provence.fr
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- 2009
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14. Detecting the molecular basis of phenotypic convergence
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Chabrol, Olivier, primary, Royer‐Carenzi, Manuela, additional, Pontarotti, Pierre, additional, and Didier, Gilles, additional
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- 2018
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15. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes
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Cahill, Abigail E., primary, De Jode, Aurélien, additional, Dubois, Sophie, additional, Bouzaza, Zoheir, additional, Aurelle, Didier, additional, Boissin, Emilie, additional, Chabrol, Olivier, additional, David, Romain, additional, Egea, Emilie, additional, Ledoux, Jean-Baptiste, additional, Mérigot, Bastien, additional, Weber, Alexandra Anh-Thu, additional, and Chenuil, Anne, additional
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- 2017
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16. Parsimonious identification of evolutionary shifts for quantitative characters
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Chabrol, Olivier, primary and Didier, Gilles, additional
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- 2017
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17. Detecting molecular basis of phenotypic convergence
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Chabrol, Olivier, primary, Royer-Carenzi, Manuela, additional, Pontarotti, Pierre, additional, and Didier, Gilles, additional
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- 2017
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18. Pithovirus sibericum, a new bona fide member of the 'Fourth TRUC' club
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Sharma, Vikas, Colson, Philippe, Chabrol, Olivier, Pontarotti, Pierre, Raoult, Didier, 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, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and I2m, Aigle
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[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,informational genes ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,nucleocytoplasmic large DNA viruses ,Pithovirus sibericum ,Megavirales ,domains of life ,TRUC ,phylogeny ,Microbiology ,giant virus ,Original Research - Abstract
International audience; Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, include giant viruses of Acanthamoeba that were discovered over the last 12 years and are bona fide microbes. Phylogenies based on a few genes conserved amongst these megaviruses and shared by microbes classified as Eukarya, Bacteria, and Archaea, allowed for delineation of a fourth monophylogenetic group or "TRUC" (Things Resisting Uncompleted Classification) composed of the Megavirales representatives. A new Megavirales member named Pithovirus sibericum was isolated from a >30,000-year-old dated Siberian permafrost sample. This virion is as large as recently described pandoraviruses but has a genome that is approximately three to four times shorter. Our objective was to update the classification of P. sibericum as a new member of the "Fourth TRUC" club. Phylogenetic trees were constructed based on four conserved ancient genes and a phyletic analysis was concurrently conducted based on the presence/absence patterns of a set of informational genes from members of Megavirales, Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on the four conserved genes revealed that P. sibericum is part of the fourth TRUC composed of Megavirales members, and is closely related to the families Marseilleviridae and Ascoviridae/Iridoviridae. Additionally, hierarchical clustering delineated four branches, and showed that P. sibericum is part of this fourth TRUC. Overall, phylogenetic and phyletic analyses using informational genes clearly indicate that P. sibericum is a new bona fide member of the "Fourth TRUC" club composed of representatives of Megavirales, alongside Bacteria, Archaea, and Eukarya.
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- 2015
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19. Welcome to pandoraviruses at the ‘Fourth TRUC’ club
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Sharma, Vikas, Colson, Philippe, Chabrol, Olivier, Scheid, Patrick, Pontarotti, Pierre, and Raoult, Didier
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Microbiology (medical) ,informational genes ,nucleocytoplasmic large DNA viruses ,Pandoravirus ,Megavirales ,domains of life ,TRUC ,phylogeny ,Microbiology ,giant virus - Abstract
Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9–2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the ‘Fourth TRUC’ club, encompassing distinct life forms compared with cellular organisms.
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- 2015
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20. Welcome to pandoraviruses at the 'Fourth TRUC' club
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Sharma, Vikas, Colson, Philippe, Chabrol, Olivier, Scheid, Patrick, Pontarotti, Pierre, Raoult, Didier, 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, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Medical Parasitology Laboratory, Central Institute of the Bundeswehr Medical Service, HAL AMU, Administrateur, and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)
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[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,MARSEILLEVIRUS ,ORIGIN ,nucleocytoplasmic large DNA viruses ,Pandoravirus ,DNA VIRUSES ,GENOME SEQUENCE ,Megavirales ,domains of life ,TRUC ,phylogeny ,EVOLUTION ,informational genes ,MIMIVIRUS ,1ST ISOLATION ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,GIANT VIRUSES ,HIGHLIGHTS ,AMEBAS ,giant virus - Abstract
International audience; Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the 'Fourth TRUC' club, encompassing distinct life forms compared with cellular organisms.
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- 2015
21. The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown
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Levasseur, Anthony, Lomascolo, Anne, Chabrol, Olivier, Ruiz-Dueñas, Francisco J, Boukhris-Uzan, Eva, Piumi, François, Kües, Ursula, Ram, Arthur F J, Murat, Claude, Haon, Mireille, Benoit, Isabelle, Arfi, Yonathan, Chevret, Didier, Drula, Elodie, Kwon, Min Jin, Gouret, Philippe, Lesage-Meessen, Laurence, Lombard, Vincent, Mariette, Jérôme, Noirot, Céline, Park, Joohae, Patyshakuliyeva, Aleksandrina, Sigoillot, Jean Claude, Wiebenga, Ad, Wösten, Han A B, Martin, Francis, Coutinho, Pedro M, de Vries, Ronald P, Martínez, Angel T, Klopp, Christophe, Pontarotti, Pierre, Henrissat, Bernard, Record, Eric, Wosten, Han, Molecular Microbiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigaciones Biológicas (CIB), Institut des Sciences Moléculaires de Marseille (ISM2), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Molecular Wood Biotechnology and Technical Mycology, Georg-August-University [Göttingen], Department of Molecular Microbiology and Biotechnology, Universiteit Leiden [Leiden], Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Faculty of Biological Chemistry, Weizmann Institute of Science, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Department of Microbiology, Kluyver Cenre for Genomics of Industrial Fermentation, Utrecht University [Utrecht], Molecular Microbiology, Sub Molecular Microbiology, Sub Molecular Plant Physiology, Molecular Plant Physiology, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Georg-August-University = Georg-August-Universität Göttingen, Universiteit Leiden, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Weizmann Institute of Science [Rehovot, Israël], Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), European Commission, and Ministerio de Economía y Competitividad (España)
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CAZy ,Glycosylation ,Proteome ,Auxiliary activities ,[SDV]Life Sciences [q-bio] ,7. Clean energy ,Lignin ,Fungal Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Manganese peroxidase ,Botany ,Genetics ,Versatile peroxidase ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,Fungal protein ,biology ,030306 microbiology ,Molecular Sequence Annotation ,Lignin peroxidase ,Pycnoporus cinnabarinus ,Sequence Analysis, DNA ,biology.organism_classification ,Wood ,Pycnoporus ,White-rot fungi ,chemistry ,Peroxidases ,Genetic Loci ,Oxidoreductase ,Genome, Fungal ,Protein Processing, Post-Translational ,Lignocellulose ,Biotechnology ,Research Article ,Genome annotation - Abstract
24 p.-8 fig.-4 tab.-- Levasseur, Anthony et al., [Background] Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology., [Results] The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases., [Conclusions] With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass., This work was funded by the Commission of the European Communities through the BIORENEW project (NMP2-CT-2006-026456 “White Biotechnology for added-value products from re newable plant polymers: Design of tailor-made biocatalysts and new industrial bioprocesses”) and the PEROXICATS project (KBBE-2010-4-265397 “Novel and more robust fungal peroxidases as industrial biocatalysts.”), and by the Spanish Ministerio de Economía y Competitividad (MINECO) through the HIPOP project (BIO2011-26694, “Screening and engineering of new high-redox-potential peroxidases”).
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- 2014
22. To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria
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Hernández-López, Antonio, Chabrol, Olivier, Royer-Carenzi, Manuela, Merhej, Vicky, Pontarotti, Pierre, Raoult, Didier, Laboratoire d'Analyse, Topologie, Probabilités (LATP), 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), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
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phylogenomic networks ,[SDV]Life Sciences [q-bio] ,horizontal gene transfer ,bacterial speciation ,Rickettsia ,reticulate evolution - Abstract
International audience; It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of genetic connectivity. HGT and positive selection are therefore two important evolutionary forces in microbial pathogens that drive adaptation to new hosts. In this study, we use genomic distance analyses, phylogenomic networks, tree topology comparisons, and Bayesian inference methods to investigate to what extent HGT has occurred during the evolution of the genus Rickettsia, the effect of the use of different genomic regions in estimating reticulate evolution and HGT events, and the link of these to host range. We show that ecological specialization restricts recombination occurrence in Rickettsia, but other evolutionary processes and genome architecture are also important for the occurrence of HGT. We found that recombi-nation, genomic rearrangements, and genome conservation all show evidence of network-like evolution at whole-genome scale. We show that reticulation occurred mainly, but not only, during the early Rickettsia radiation, and that core proteome genes of every major functional category have experienced reticulated evolution and possibly HGT. Overall, the evolution of Rickettsia bacteria has been tree-like, with evidence of HGT and reticulated evolution for around 10–25% of the core Rickettsia genome. We present evidence of extensive recombination/incomplete lineage sorting (ILS) during the radiation of the genus, probably linked with the emergence of intracellularity in a wide range of hosts.
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- 2013
23. Mycobacteriophage-drived diversification of Mycobacterium abscessus
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Sassi, Mohamed, primary, Gouret, Philippe, additional, Chabrol, Olivier, additional, Pontarotti, Pierre, additional, and Drancourt, Michel, additional
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- 2014
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24. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown
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Levasseur, Anthony, primary, Lomascolo, Anne, additional, Chabrol, Olivier, additional, Ruiz-Dueñas, Francisco J, additional, Boukhris-Uzan, Eva, additional, Piumi, François, additional, Kües, Ursula, additional, Ram, Arthur F J, additional, Murat, Claude, additional, Haon, Mireille, additional, Benoit, Isabelle, additional, Arfi, Yonathan, additional, Chevret, Didier, additional, Drula, Elodie, additional, Kwon, Min, additional, Gouret, Philippe, additional, Lesage-Meessen, Laurence, additional, Lombard, Vincent, additional, Mariette, Jérôme, additional, Noirot, Céline, additional, Park, Joohae, additional, Patyshakuliyeva, Aleksandrina, additional, Sigoillot, Jean, additional, Wiebenga, Ad, additional, Wösten, Han A B, additional, Martin, Francis, additional, Coutinho, Pedro M, additional, de Vries, Ronald P, additional, Martínez, Angel T, additional, Klopp, Christophe, additional, Pontarotti, Pierre, additional, Henrissat, Bernard, additional, and Record, Eric, additional
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- 2014
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25. To Tree or Not to Tree? Genome-Wide Quantification of Recombination and Reticulate Evolution during the Diversification of Strict Intracellular Bacteria
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Hernández-López, Antonio, primary, Chabrol, Olivier, additional, Royer-Carenzi, Manuela, additional, Merhej, Vicky, additional, Pontarotti, Pierre, additional, and Raoult, Didier, additional
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- 2013
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26. FunGene-DB: A web-based tool for Polyporales strains authentication
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Navarro, David, primary, Favel, Anne, additional, Chabrol, Olivier, additional, Pontarotti, Pierre, additional, Haon, Mireille, additional, and Lesage-Meessen, Laurence, additional
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- 2012
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27. CASSIOPE: An expert system for conserved regions searches
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Rascol, Virginie Lopez, primary, Levasseur, Anthony, additional, Chabrol, Olivier, additional, Grusea, Simona, additional, Gouret, Philippe, additional, Danchin, Etienne GJ, additional, and Pontarotti, Pierre, additional
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- 2009
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28. An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.
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Phuong Thi Le, Ramulu, Hemalatha Golaconda, Guijarro, Laurent, Paganini, Julien, Gouret, Philippe, Chabrol, Olivier, Raoult, Dider, and Pontarotti, Pierre
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GENETIC transformation ,PROKARYOTES ,ANAPLASMA ,NEORICKETTSIA ,OLIGONUCLEOTIDES - Abstract
Background: Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species. Results: We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like". Conclusions: Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest. [ABSTRACT FROM AUTHOR]
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- 2012
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29. The functional convergence of antibiotic resistance in β-lactamases is not conferred by a simple convergent substitution of amino acid.
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Keshri V, Arbuckle K, Chabrol O, Rolain JM, Raoult D, and Pontarotti P
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Bacterial resistance to antibiotics is a serious medical and public health concern worldwide. Such resistance is conferred by a variety of mechanisms, but the extensive variability in levels of resistance across bacteria is a common finding. Understanding the underlying evolutionary processes governing this functional variation in antibiotic resistance is important as it may allow the development of appropriate strategies to improve treatment options for bacterial infections. The main objective of this study was to examine the functional evolution of β-lactamases, a common mechanism of enzymatic resistance that inactivates a widely used class of antibiotics. We first obtained β-lactamase protein sequences and minimal inhibitory concentration (MIC), a measure of antibiotic function, from previously published literature. We then used a molecular phylogenetic framework to examine the evolution of β-lactamase functional activity. We found that the functional activity of antibiotic resistance mediated by β-lactamase has evolved in a convergent manner within molecular classes, but is not associated with any single amino acid substitution. This suggests that the dynamics of convergent evolution in this system can vary between the functional and molecular (sequence) levels. Such disassociation may hamper bioinformatic approaches to antibiotic resistance determination and underscore the need for (less efficient but more effective) activity assays as an essential step in evaluating resistance in a given case., Competing Interests: None declared.
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- 2019
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