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1. Multi-locus sequence analysis reveals great genetic diversity among Mycoplasma capricolum subsp. capripneumoniae strains in Asia

Author: Arooba Akhtar, Anne Boissière, Huafang Hao, Muhammad Saeed, Virginie Dupuy, Antoni Exbrayat, Farhan Anwar Khan, Yuefeng Chu, and Lucía Manso-Silván
Subjects: Mycoplasma capricolum subsp. capripneumoniae, contagious caprine pleuropneumonia, multi-locus sequence analysis, molecular epidemiology, Asia, Africa, Veterinary medicine, SF600-1100
Abstract: Abstract Multi-Locus Sequence Analysis (MLSA) of Mycoplasma capricolum subsp. capripneumoniae (Mccp) strains from Asia revealed unforeseen diversity and a central position for genotyping groups representing strains from Central/East Asia, suggesting a possible origin of contagious caprine pleuropneumonia in this continent. A better assessment of the emergence, diversity and distribution of Mccp in Asia and Africa calls for renewed efforts to dramatically enlarge the sample of strains. Availability and affordability in the field, added to superior typeability (directly from poor samples) and high stability, discriminatory power and concordance with epidemiological and phylogenetic analyses, make MLSA an excellent tool for such investigations.
Published: 2022
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2. Fatal Outbreak of Mycoplasma capricolum Pneumonia in Endangered Markhors

Author: Stéphane Ostrowski, Francois Thiaucourt, Mulojon Amirbekov, Abdurahmon Mahmadshoev, Lucía Manso-Silván, Virginie Dupuy, Dustmurod Vahobov, Orom Ziyoev, and Stefan Michel
Subjects: outbreak, Mycoplasma, goats, animals, wild, conservation of natural resources, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: A pneumonia outbreak reduced the numbers of a wild population of endangered markhors (Capra falconeri) in Tajikistan in 2010. The infection was diagnosed by histologic examination and bacteriologic testing. Mycoplasma capricolum subsp. capricolum was the sole infectious agent detected. Cross-species transmission from domestic goats may have occurred.
Published: 2011
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3. Genetic architecture of sexual selection: QTL mapping of male song and female receiver traits in an acoustic moth.

Author: Denis Limousin, Réjane Streiff, Brigitte Courtois, Virginie Dupuy, Sylvain Alem, and Michael D Greenfield
Subjects: Medicine, Science
Abstract: Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings on species recognition suggest that such linkage disequilibria may result from physical linkage or pleiotropy, but very little work has addressed this possibility within the context of sexual selection. We studied the genetic architecture of sexually selected traits by analyzing signals and preferences in an acoustic moth, Achroia grisella, in which males attract females with a train of ultrasound pulses and females prefer loud songs and a fast pulse rhythm. Both male signal characters and female preferences are repeatable and heritable traits. Moreover, female choice is based largely on male song, while males do not appear to provide direct benefits at mating. Thus, some genetic correlation between song and preference traits is expected. We employed a standard crossing design between inbred lines and used AFLP markers to build a linkage map for this species and locate quantitative trait loci (QTL) that influence male song and female preference. Our analyses mostly revealed QTLs of moderate strength that influence various male signal and female receiver traits, but one QTL was found that exerts a major influence on the pulse-pair rate of male song, a critical trait in female attraction. However, we found no evidence of specific co-localization of QTLs influencing male signal and female receiver traits on the same linkage groups. This finding suggests that the sexual selection process would proceed at a modest rate in A. grisella and that evolution toward exaggerated character states may be tempered. We suggest that this equilibrium state may be more the norm than the exception among animal species.
Published: 2012
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4. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides 'Small Colony'.

Author: Virginie Dupuy, Lucía Manso-Silván, Valérie Barbe, Patricia Thebault, Emilie Dordet-Frisoni, Christine Citti, François Poumarat, Alain Blanchard, Marc Breton, Pascal Sirand-Pugnet, and François Thiaucourt
Subjects: Medicine, Science
Abstract: Mycoplasma mycoides subsp. mycoides "Small Colony" (MmmSC) is responsible for contagious bovine pleuropneumonia (CBPP) in bovidae, a notifiable disease to the World Organization for Animal Health (OIE). Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th) century through the cattle trade and was eradicated from most continents by stamping-out policies. During the 20(th) century it persisted in Africa, and it reappeared sporadically in Southern Europe. Yet, classical epidemiology studies failed to explain the re-occurrence of the disease in Europe in the 1990s. The objectives of this study were to obtain a precise phylogeny of this pathogen, reconstruct its evolutionary history, estimate the date of its emergence, and determine the origin of the most recent European outbreaks. A large-scale genomic approach based on next-generation sequencing technologies was applied to construct a robust phylogeny of this extremely monomorphic pathogen by using 20 representative strains of various geographical origins. Sixty two polymorphic genes of the MmmSC core genome were selected, representing 83601 bp in total and resulting in 139 SNPs within the 20 strains. A robust phylogeny was obtained that identified a lineage specific to European strains; African strains were scattered in various branches. Bayesian analysis allowed dating the most recent common ancestor for MmmSC around 1700. The strains circulating in Sub-Saharan Africa today, however, were shown to descend from a strain that existed around 1810. MmmSC emerged recently, about 300 years ago, and was most probably exported from Europe to other continents, including Africa, during the 19(th) century. Its diversity is now greater in Africa, where CBPP is enzootic, than in Europe, where outbreaks occurred sporadically until 1999 and where CBPP may now be considered eradicated unless MmmSC remains undetected.
Published: 2012
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5. III. Collectionner l’Antique sur les rivages de l’Atlantique. Fortuné Parenteau (1814-1882), une figure fondatrice pour le musée Dobrée

Author: Virginie Dupuy and Muriel Rouaud
Published: 2022
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6. A library preparation optimized for metagenomics of RNA viruses

Author: Biram Biteye, Marc Eloit, Ignace Rakotoarivony, Thomas Balenghien, Claire Garros, Rachid Koual, Patricia Gil, Virginie Dupuy, Serafin Gutierrez, Antoni Exbrayat, Assane Gueye Fall, Grégory L'Ambert, Emmanuel Albina, Etienne Loire, Geoffrey Gimonneau, Albane Marie, Benoit Francés, Julie Reveillaud, Momar Talla Seck, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), École nationale vétérinaire - Alfort (ENVA), Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris] (IP), Centre Collaborateur de l'OIE de Détection et identification chez l’homme des pathogènes animaux émergents et développement d’outils pour leur diagnostic / Collaborating Center for the Detection and identification in humans of emerging animal pathogens and development of tools for their diagnoses (CCOIE-OIECC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé Animale / World Organisation Animal Health [Paris] (OIE), This work was funded by the Direction Générale de l’Alimentation from the French Ministry in charge of agriculture. This work was also funded by the European Union’s Seventh Framework Programme through grants Vmerge (FP7‐613996) and CuliOme (FP7‐291815)., European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012), European Project: 613996,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,VMERGE(2013), European Project: 7247564(1972), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), École nationale vétérinaire d'Alfort (ENVA), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Organisation Mondiale de la Santé Animale / World Animal Health Information System (OIE-WAHIS)
Subjects: 0106 biological sciences, 0301 basic medicine, Viral metagenomics, [SDV]Life Sciences [q-bio], Banque de gènes, Caulimovirus mosaïque du chou fleur, L73 - Maladies des animaux, 01 natural sciences, Genome, shotgun sequencing, Aedes vexans, Culex pipiens, insects, viromevirus, education.field_of_study, Shotgun sequencing, Virome, [SDV.BA]Life Sciences [q-bio]/Animal biology, Culicoides, PCR, Vecteur de maladie, S50 - Santé humaine, L72 - Organismes nuisibles des animaux, Biotechnology, Population, Computational biology, Genome, Viral, Biology, 010603 evolutionary biology, génomique, 03 medical and health sciences, Virus bluetongue, Genetics, Animals, RNA Viruses, Human virome, education, Ecology, Evolution, Behavior and Systematics, Virus classification, Gene Library, metagenomics, Virus maladie de newcastle, Bacteriome, 030104 developmental biology, Metagenomics, Metagenome, library preparation
Abstract: International audience; Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR-based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field-caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus-like sequences compared to other studies, and nearly-full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field-caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.
Published: 2021
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7. The Protohistoric sword from Le Gué-de-Velluire (Vendée, France): a pasticcio's history unveiled by archaeometrical research

Author: Virginie Dupuy, Guy De Mulder, Charlène Pelé-Meziani, Théophane Nicolas, Léonard Dumont, Universiteit Gent = Ghent University [Belgium] (UGENT), Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Ministère de la Culture et de la Communication (MCC)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Grand Patrimoine de Loire-Atlantique, Musée Dobrée, Institut national de recherches archéologiques préventives (Inrap), Trajectoires - UMR 8215, Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Arc'Antique, and Arc'antique
Subjects: Archeology, History, Sword, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, 0211 other engineering and technologies, Art history, Computed tomography, 02 engineering and technology, engineering.material, X-Ray Fluorescence spectroscopy, 01 natural sciences, TOMOGRAPHY, medicine, BRONZE-AGE, Bronze, SWORD, 021101 geological & geomatics engineering, medicine.diagnostic_test, History and Archaeology, 010401 analytical chemistry, Pasticcio, X-Ray Fluorescence Spectroscopy, 0104 chemical sciences, engineering, Blade (archaeology), Protohistory
Abstract: International audience; The Gué-de-Velluire sword (Vendée, France) is part of the Rochebrune collection collected during the 19 th and the 20 th centuries and now preserved in the Dobrée Museum in Nantes (Loire-Atlantique, France). The unusual shape of its hilt, its uncorroded rivets and the rather uncommon combination of a bronze grip with an iron blade made this sword an exceptional object. It has been depicted in a large number of papers since the 20 th century, but the question of its authenticity has hardly ever been tackled. New analyses performed with the support of the Dobrée Museum, the Arc'Antique laboratory and Ghent University delivered new data enabling us to discuss this delicate question. First, a CT-scan of the sword was performed by the BCRX company (Mordelles, Ille-et-Vilaine, France), offering the opportunity to visualise the inner structure of the hilt and especially the way it is fixed to the iron blade. Secondly, X-Ray Fluorescence analyses were performed by the Arc'Antique laboratory (Nantes, Loire-Atlantique, France) to determine the composition of the different parts of the sword (hilt, rivets and blade). Comparing the results of both analyses with Rochebrune's archives allowed us to assert this weapon is a fake, most likely consisting of two authentic archaeological artefacts, and to reconstruct its production process, shedding light on early 20 th century collector's practices.
Published: 2020
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8. Phylogeny and molecular typing of Mycoplasma agalactiae and Mycoplasma bovis by multilocus sequencing

Author: François Thiaucourt, Umit Ozdemir, Inna Lysnyansky, Lucia Manso-Silvan, and Virginie Dupuy
Subjects: Mycoplasma bovis, Phylogénie, Identification, Turkey, Mycoplasma agalactiae, ved/biology.organism_classification_rank.species, L73 - Maladies des animaux, Polymerase Chain Reaction, Genotype, Israel, Phylogeny, Genetics, Phylogenetic tree, Strain (biology), Biodiversity, General Medicine, Petits ruminants, Ruminant, Biology, Microbiology, Variation génétique, Species Specificity, Phylogenetics, Biotype, Animals, Bovin, General Veterinary, ved/biology, Biologie moléculaire, Genetic Variation, 16S ribosomal RNA, rpoB, Genes, Bacterial, Multilocus sequence typing, Cattle, Multilocus Sequence Typing
Abstract: Mycoplasma agalactiae and Mycoplasma bovis are important pathogens producing similar pathologies in small ruminants and cattle, respectively. They share many phenotypic and genotypic traits and comparison of their 16S rDNA sequences lacks sufficient resolution for phylogenetic analysis. The aim of this study was to develop a multilocus sequence typing (MLST) scheme to analyse the phylogenetic relationships between M. agalactiae and M. bovis and to assess its use for unequivocal strain characterisation and molecular typing. An MLST based on fusA, gyrB, lepA and rpoB was applied to a sample of strains from both species, some of which could not be classified by serology or PCR. A robust phylogenetic tree was inferred, where the two species were clearly resolved. The use of this tool for the molecular typing of M. agalactiae strains was further evaluated on 19 presumably unrelated isolates, resulting in the discrimination of 14 sequence types (ST). The discriminatory power was increased (17 ST) by including an alternative target located in a more variable region. The diversity of M. agalactiae in Turkey (9 strains) and Israel (15 strains) was also assessed. Five closely related ST were evidenced in Turkey and 6 in Israel, with one ST common to both countries. Each country showed a predominant type that persisted over years. The MLST scheme developed here constitutes a universal tool for unequivocal strain characterisation and global, long-term screening of dissemination of M. agalactiae and M. bovis, whereas addition of more variable, non-housekeeping gene targets allows precise epidemiological investigations.
Published: 2012
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9. Genetic Architecture of Sexual Selection: QTL Mapping of Male Song and Female Receiver Traits in an Acoustic Moth

Author: Michael D. Greenfield, Réjane Streiff, Denis Limousin, Virginie Dupuy, Brigitte Courtois, Sylvain Alem, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Laboratoire de l'intégration, du matériau au système (IMS), Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Greenfield, Michaël, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université Sciences et Technologies - Bordeaux 1, INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Evolutionary Genetics, Male, Linkage disequilibrium, Sexual Selection, Anatomy and Physiology, Heredity, Sensory Physiology, Evolutionary Selection, lcsh:Medicine, Moths, 01 natural sciences, Linkage Disequilibrium, Behavioral Ecology, Sexual Behavior, Animal, Génétique des populations, Pleiotropy, Sex Preselection, lcsh:Science, Genetics, 0303 health sciences, Multidisciplinary, Animal Behavior, Ecology, Linkage (Genetics), [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Phenotype, Mate choice, Sexual selection, Female, L72 - Organismes nuisibles des animaux, Research Article, Locus des caractères quantitatifs, Evolutionary Processes, Genotype, Son (acoustique), Quantitative Trait Loci, Singing, Context (language use), Quantitative trait locus, Biology, 010603 evolutionary biology, Genetic correlation, Neurological System, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, Sex Factors, Animals, Pyralidae, Crosses, Genetic, 030304 developmental biology, DNA Primers, Evolutionary Biology, Comportement sexuel, Models, Genetic, lcsh:R, Acoustics, Genetic architecture, Animal Communication, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Evolutionary Ecology, Karyotyping, lcsh:Q, Vocalization, Animal, Zoology, Entomology
Abstract: International audience; Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings on species recognition suggest that such linkage disequilibria may result from physical linkage or pleiotropy, but very little work has addressed this possibility within the context of sexual selection. We studied the genetic architecture of sexually selected traits by analyzing signals and preferences in an acoustic moth, Achroia grisella, in which males attract females with a train of ultrasound pulses and females prefer loud songs and a fast pulse rhythm. Both male signal characters and female preferences are repeatable and heritable traits. Moreover, female choice is based largely on male song, while males do not appear to provide direct benefits at mating. Thus, some genetic correlation between song and preference traits is expected. We employed a standard crossing design between inbred lines and used AFLP markers to build a linkage map for this species and locate quantitative trait loci (QTL) that influence male song and female preference. Our analyses mostly revealed QTLs of moderate strength that influence various male signal and female receiver traits, but one QTL was found that exerts a major influence on the pulse-pair rate of male song, a critical trait in female attraction. However, we found no evidence of specific colocalization of QTLs influencing male signal and female receiver traits on the same linkage groups. This finding suggests that the sexual selection process would proceed at a modest rate in A. grisella and that evolution toward exaggerated character states may be tempered. We suggest that this equilibrium state may be more the norm than the exception among animal species.
Published: 2016
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10. High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species

Author: Marie-Line Iskra-Caruana, Laboureau Nathalie, Frédérique Bauffe, Jean-Heinrich Daugrois, Laurence Blondin, Virginie Dupuy, and Emmanuelle Muller
Subjects: Cancer Research, Genotype, Sequence analysis, Molecular Sequence Data, Polymerase Chain Reaction, Genome, Phylogenetics, Virology, Polyphyly, Plant virus, Banana streak virus, Cluster Analysis, Badnavirus, Guadeloupe, Phylogeny, H20 - Maladies des plantes, Immunoassay, Saccharum officinarum, biology, Phylogenetic tree, Genetic Variation, Sequence Analysis, DNA, Virus des végétaux, biology.organism_classification, Saccharum, Infectious Diseases
Abstract: Thirty-five unique partial sugarcane bacilliform virus (SCBV) sequences extending over 529 bp were identified in sugarcane samples from Guadeloupe diagnosed by Immunocapture-PCR (IC-PCR) using specific badnavirus primers. Phylogenetic analysis of these sequences along with the two known genome sequences of Sugarcane bacilliform Mor virus (SCBMV) and Sugarcane bacilliform IM virus (SCBIMV) revealed high molecular variability in the SCBV genome. Seven phylogenetic groups, named A to G, were characterized: virus isolates from groups A-B, C and D are proposed to be members of three additional SCBV species. The two (7446 and 7444 bp) and one (7317 bp) complete sequences of SCBV isolates from groups A and D, respectively, likely represented the genome of two new species. Phylogenetic analysis of the complete genome and RT/RNase H sequences confirmed the polyphyletic structure of SCBV isolates and the absence of a clear separation between SCBV and Banana streak virus (BSV) isolates within badnavirus group 1. These results showed that reconsideration of taxonomy and classification of SCBV and BSV are necessary.
Published: 2011
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11. SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods to Reveal Genetic Variability Within a Virus Species

Author: Agnès, Delaunay, Sylvie, Dallot, Denis, Filloux, Virginie, Dupuy, Philippe, Roumagnac, and Emmanuel, Jacquot
Subjects: Cost-Benefit Analysis, DNA, Viral, Potyvirus, DNA, Single-Stranded, Electrophoresis, Capillary, Sequence Analysis, DNA, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Polymorphism, Single-Stranded Conformational, DNA Primers
Abstract: The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (500 bases in length) genomic regions of viral genomes. The different steps of SNaPshot and CE-SSCP setup procedures are presented using Potato virus Y (PVY, Potyvirus) and Plum pox virus (PPV, Potyvirus) RNA viruses as molecular targets, respectively.
Published: 2015

12. A large-scale genomic approach affords unprecedented resolution for the molecular epidemiology and evolutionary history of contagious caprine pleuropneumonia

Author: Lucia Manso-Silvan, François Thiaucourt, Axel Verdier, and Virginie Dupuy
Subjects: Mutation rate, Asia, Genotyping Techniques, Turkey, 040301 veterinary sciences, chèvre, [SDV]Life Sciences [q-bio], L73 - Maladies des animaux, Mycoplasma capricolum, 0403 veterinary science, Evolution, Molecular, 03 medical and health sciences, Contagious caprine pleuropneumonia, Phylogenetics, medicine, Animals, caprin, Pleuropneumonia, Contagious, Genotyping, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Genetic diversity, Disease surveillance, Goat Diseases, General Veterinary, biology, Molecular epidemiology, pleuropneumonie contagieuse caprine, Goats, Genetic Variation, Bayes Theorem, 04 agricultural and veterinary sciences, biology.organism_classification, medicine.disease, veterinary(all), maladie respiratoire, Evolutionary biology, maladie animale, Africa, épidémiologie, Genome, Bacterial, Research Article
Abstract: Contagious caprine pleuropneumonia (CCPP), caused by Mycoplasma capricolum subsp. capripneumoniae (Mccp), is a devastating disease of domestic goats and of some wild ungulate species. The disease is currently spreading in Africa and Asia and poses a serious threat to disease-free areas. A comprehensive view of the evolutionary history and dynamics of Mccp is essential to understand the epidemiology of CCPP. Yet, analysing the diversity of genetically monomorphic pathogens, such as Mccp, is complicated due to their low variability. In this study, the molecular epidemiology and evolution of CCPP was investigated using a large-scale genomic approach based on next-generation sequencing technologies, applied to a sample of strains representing the global distribution of this disease. A highly discriminatory multigene typing system was developed, allowing the differentiation of 24 haplotypes among 25 Mccp strains distributed in six genotyping groups, which showed some correlation with geographic origin. A Bayesian approach was used to infer the first robust phylogeny of the species and to date the principal events of its evolutionary history. The emergence of Mccp was estimated only at about 270 years ago, which explains the low genetic diversity of this species despite its high mutation rate, evaluated at 1.3 × 10−6 substitutions per site per year. Finally, plausible scenarios were proposed to elucidate the evolution and dynamics of CCPP in Asia and Africa, though limited by the paucity of Mccp strains, particularly in Asia. This study shows how combining large-scale genomic data with spatial and temporal data makes it possible to obtain a comprehensive view of the epidemiology of CCPP, a precondition for the development of improved disease surveillance and control measures. Electronic supplementary material The online version of this article (doi:10.1186/s13567-015-0208-x) contains supplementary material, which is available to authorized users.
Published: 2015
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13. SNaPshot and CE-SSCP : two simple and cost-effective methods to reveal genetic variability within a virus species

Author: Denis Filloux, Sylvie Dallot, Virginie Dupuy, Philippe Roumagnac, Emmanuel Jacquot, Agnès Delaunay, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, viruses, Single-nucleotide polymorphism, 01 natural sciences, polymorphism, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Multiplex, Genetic variability, Virus classification, H20 - Maladies des plantes, 030304 developmental biology, Genetics, 0303 health sciences, biology, Potyvirus, Single-strand conformation polymorphism, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, genomic RNA, fluorescent-labeled ss-DNA, Potato virus Y, electrophoresis, Snapshot (computer storage), U30 - Méthodes de recherche, 010606 plant biology & botany
Abstract: BGPI : équipe 6 et 7; International audience; The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (
Published: 2015
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14. Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa

Author: Virginie Dupuy and François Thiaucourt
Subjects: Genetics, Whole genome sequencing, biology, Strain (biology), L73 - Maladies des animaux, medicine.disease, biology.organism_classification, Virology, Mycoplasma capricolum, Contagious caprine pleuropneumonia, medicine, bacteria, Prokaryotes, Molecular Biology
Abstract: Mycoplasma capricolum subsp. capripneumoniae is the etiological agent of contagious caprine pleuropneumonia. We report here the complete and annotated genome sequence of M. capricolum subsp. capripneumoniae strain 9231-Abomsa.
Published: 2014
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15. Fatal transmission of contagious caprine pleuropneumonia to an Arabian oryx (Oryx leucoryx)

Author: Lucia Manso-Silvan, Virginie Dupuy, François Thiaucourt, Louis Lignereux, Claude Saegerman, M Al Qassimi, Anne-Lise Chaber, RENECO Wildlife Consultants LLC, Université de Liège, Environment Agency – Abu Dhabi, Partenaires INRAE, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)
Subjects: Veterinary medicine, Genotype, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], United Arab Emirates, Arabian oryx, Subspecies, Wildlife, L73 - Maladies des animaux, Microbiology, Mycoplasma capricolum, Contagious caprine pleuropneumonia, 0403 veterinary science, 03 medical and health sciences, biology.animal, medicine, Animals, Pleuropneumonia, Contagious, Genotyping, 030304 developmental biology, 0303 health sciences, Goat Diseases, General Veterinary, biology, Transmission (medicine), Goats, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, medicine.disease, Oryx leucoryx, Oryx, 3. Good health, Nasal discharge, Antelopes
Abstract: International audience; Contagious caprine pleuropneumonia (CCPP) is an infectious respiratory disease mainly affecting domestic goats. As CCPP has never been documented in grazing antelopes (subfamily hippotraginae), they were not considered susceptible. Mycoplasma capricolum subspecies capripneumoniae (Mccp) was isolated from pleural liquid collected during the necropsy of a severely emaciated Arabian oryx with mild nasal discharge. The Mccp isolate was then genotyped using a multilocus sequence scheme; the sequence type was identical to the Mccp strain previously identified in a sand gazelle from a nearby enclosure. This case shows for the first time that members of the hippotraginae subfamily, here the Arabian oryx, can be affected by CCPP. In addition, genotyping shows that the oryx was most probably infected, at a distance, by sand gazelles.
Published: 2014
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16. Evolutionary history of contagious bovine pleuropneumonia using Next generation sequencing of Mycoplasma mycoides subsp. mycoides 'small colony'

Author: Virginie Dupuy, Lucía Manso-Silván, Valérie Barbe, Patricia Thébault, Emilie Dordet Frisoni, Christine Citti, François Poumarat, Alain Blanchard, Marc Breton, Pascal SIRAND-PUGNET, François Thiaucourt, ProdInra, Migration, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Bayer Cropscience, Centre de Génomique Fonctionnelle de Bordeaux (CGFB), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UPE, European Union Reference Laboratory for equine diseases (EURL), Biologie du fruit et pathologie (BFP), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2014

17. Development of eight microsatellite markers in the parsley frog (Pelodytes punctatus)

Author: Patrice David, Antoine Nicot, Virginie Dupuy, Pierre-André Crochet, and Helene Jourdan‐Pineau
Subjects: Amphibian, Genetics, biology, Population structure, Zoology, Locus (genetics), Parsley frog, biology.organism_classification, biology.animal, Microsatellite, Allele, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: We characterized eight microsatellite loci to study spatial and temporal population structure of Pelodytes punctatus, a European anuran that has a peculiar breeding pattern among amphibians. The eight loci proved to be highly polymorphic with the number of alleles per locus ranging from two to 15 within two populations. Cross-amplification indicates that those markers may be also useful for closely related species from the same family.
Published: 2009
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18. Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae

Author: Claire Lemaitre, Pascal Sirand-Pugnet, Laurent-Xavier Nouvel, Lucia Manso-Silvan, Emilie Dordet-Frisoni, François Poumarat, François Thiaucourt, Patricia Thebault, Eric Baranowski, Marc Breton, Patrice Gaurivaud, Alain Blanchard, Florence Tardy, Virginie Dupuy, Carole Couture, Daniel J. Jacob, Macha Nikolski, Christine Citti, Sébastien Theil, Aurélien Barré, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Bordeaux Segalen - Bordeaux 2, Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Génomique, développement et pouvoir pathogène (GD2P), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité de Microbiologie (MIC), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Lyon [ANSES], Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Financial support was provided by the EVOLMYCO project (ANR-07-GMGE-001) from ANR to A.B. (principal investigator [PI]), F. Thiaucourt (Co-PI), F.P. (Co-PI), and C.C. (Co-PI)., ANR-07-GMGE-0001,EVOLMYCO,Etude à grande échelle des génomes des mycoplasmes de ruminants : évolution et adaptation de bactéries minimales à des hôtes complexes(2007), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Interactions hôtes-agents pathogènes [Toulouse] ( IHAP ), Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), VetAgro Sup ( VAS ), Centre de Bioinformatique de Bordeaux ( CBIB ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA-D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ), Contrôle des maladies animales exotiques et émergentes [Montpellier] ( CMAEE ), Institut National de la Recherche Agronomique ( INRA ) -Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR15, Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Génomique, développement et pouvoir pathogène ( GD2P ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ), Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Vétérinaire de Toulouse, and ANSES
Subjects: education, Biology, medicine.disease_cause, Genome, Microbiology, Caprinae, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], otorhinolaryngologic diseases, Genetics, medicine, Prokaryotes, Ear canal, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Biology, health care economics and organizations, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Mycoplasma, Mycoplasma arginini, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Mycoplasma auris, 3. Good health, medicine.anatomical_structure, sense organs, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Mycoplasma yeatsii
Abstract: We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii , two species commonly isolated from the external ear canal of Caprinae .
Published: 2013
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19. Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle

Author: Alain Blanchard, Lucia Manso-Silvan, Emilie Dordet-Frisoni, Daniel J. Jacob, François Poumarat, Christine Citti, Laurent-Xavier Nouvel, Pascal Sirand-Pugnet, Claire Lemaitre, Patricia Thebault, Aurélien Barré, Macha Nikolski, Patrice Gaurivaud, Marc Breton, François Thiaucourt, Sébastien Theil, Florence Tardy, Virginie Dupuy, Carole Couture, Eric Baranowski, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Université Bordeaux Segalen - Bordeaux 2, Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Ecole Nationale Vétérinaire de Toulouse (ENVT), Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Financial support was provided by the EVOLMYCO project (ANR-07-GMGE-0001) from ANR to Alain Blanchard (Principal Investigator [PI]), François Thiaucourt (Co-PI), François Poumarat (Co-PI), and Christine Citti (Co-PI)., ANR-07-GMGE-0001,EVOLMYCO,Etude à grande échelle des génomes des mycoplasmes de ruminants : évolution et adaptation de bactéries minimales à des hôtes complexes(2007), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Lyon, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Contrôle des maladies animales exotiques et émergentes [Montpellier] ( CMAEE ), Institut National de la Recherche Agronomique ( INRA ) -Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR15, ANSES, Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Interactions hôtes-agents pathogènes [Toulouse] ( IHAP ), Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Ecole Nationale Vétérinaire de Toulouse, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), VetAgro Sup ( VAS ), Centre de Bioinformatique de Bordeaux ( CBIB ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA-D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique, développement et pouvoir pathogène ( GD2P ), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA )
Subjects: 0303 health sciences, 030306 microbiology, Biology, Mycoplasma arginini, L73 - Maladies des animaux, Genome, Virology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Microbiology, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, Prokaryotes, Mycoplasma bovigenitalium, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Biology, health care economics and organizations, 030304 developmental biology, Mycoplasma alkalescens
Abstract: We report here the draft genome sequences of Mycoplasma alkalescens , Mycoplasma arginini , and Mycoplasma bovigenitalium . These three species are regularly isolated from bovine clinical specimens, although their role in disease is unclear.
Published: 2013
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20. Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

Author: Aurélien Barré, Alain Blanchard, Florence Tardy, Pascal Sirand-Pugnet, Daniel J. Jacob, Lucia Manso-Silvan, Christine Citti, Emilie Dordet-Frisoni, Patricia Thebault, Sébastien Theil, Patrice Gaurivaud, François Thiaucourt, Virginie Dupuy, Laurent-Xavier Nouvel, Carole Couture, François Poumarat, Macha Nikolski, Eric Baranowski, Claire Lemaitre, Marc Breton, INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Génomique, développement et pouvoir pathogène (GD2P), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Bordeaux Segalen - Bordeaux 2, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Microbiologie (MIC), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Lyon [ANSES], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS), INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Génomique, développement et pouvoir pathogène ( GD2P ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ), Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Interactions hôtes-agents pathogènes [Toulouse] ( IHAP ), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), VetAgro Sup ( VAS ), Centre de Bioinformatique de Bordeaux ( CBIB ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA-D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ), Contrôle des maladies animales exotiques et émergentes [Montpellier] ( CMAEE ), Institut National de la Recherche Agronomique ( INRA ) -Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR15, Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, ANSES, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Vétérinaire de Toulouse, Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), The annotation of the genome was performed within the EVOLMYCO project, financed by the French national agency for research (ANR-07-GMGE-001)., and ANR-07-GMGE-0001,EVOLMYCO,Etude à grande échelle des génomes des mycoplasmes de ruminants : évolution et adaptation de bactéries minimales à des hôtes complexes(2007)
Subjects: Whole genome sequencing, Genetics, 0303 health sciences, 030306 microbiology, Strain (biology), education, Biology, L73 - Maladies des animaux, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Microbiology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Mycoplasma putrefaciens, Prokaryotes, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Biology, 030304 developmental biology
Abstract: Mycoplasma putrefaciens is one of the etiologic agents of contagious agalactia in goats. We report herein the complete genome sequence of Mycoplasma putrefaciens strain 9231.
Published: 2013
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21. Finishing bacterial genome assemblies with Mix

Author: Virginie Dupuy, Alexis Groppi, Florence Tardy, Christine Citti, Pascal Sirand-Pugnet, Hayssam Soueidan, Florence Maurier, Macha Nikolski, NKI-AVL, The National Cancer Institute, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Lyon, Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Netherlands Cancer Institute, Centre de Bioinformatique de Bordeaux, Université Sciences et Technologies - Bordeaux 1, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., and Nikolski, Macha
Subjects: [SDV]Life Sciences [q-bio], Sequence assembly, Bacterial genome size, Biology, computer.software_genre, Genome, Biochemistry, Market fragmentation, 03 medical and health sciences, Mycoplasma, Structural Biology, Software Design, génome bactérien, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, computer.programming_language, H20 - Maladies des plantes, 0303 health sciences, Contig, 030306 microbiology, business.industry, qualité, U10 - Informatique, mathématiques et statistiques, Applied Mathematics, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Python (programming language), [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biotechnology, Computer Science Applications, séquence du génome, Proceedings, Graph (abstract data type), Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Algorithms, Genome, Bacterial, Reference genome
Abstract: Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions produce draft assemblies that often require a resource intensive finishing phase. In this paper we address these two aspects by developing Mix , a tool that mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length. We evaluate the performance of Mix on bacterial NGS data from the GAGE-B study and apply it to newly sequenced Mycoplasma genomes. Resulting final assemblies demonstrate a significant improvement in the overall assembly quality. In particular, Mix is consistent by providing better overall quality results even when the choice is guided solely by standard assembly statistics, as is the case for de novo projects. Mix is implemented in Python and is available at https://github.com/cbib/MIX , novel data for our Mycoplasma study is available at http://services.cbib.u-bordeaux2.fr/mix/ .
Published: 2013
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22. Type 2 diabetes mellitus in mice aggravates the renal impact of hemorrhagic shock

Author: Vincent Minville, Acil Jaafar, Virginie Dupuy, Talal al Saati, Françoise Praddaude, Ivan Tack, Stéphane Schaak, Marie Buléon, and Nicolas Mayeur
Subjects: Male, medicine.medical_specialty, Mice, Obese, Shock, Hemorrhagic, Critical Care and Intensive Care Medicine, Kidney, Diabetic nephropathy, chemistry.chemical_compound, Mice, Diabetes mellitus, Internal medicine, Medicine, Animals, biology, business.industry, Acute kidney injury, Kidney metabolism, Hypoxia (medical), Acute Kidney Injury, medicine.disease, Nitric oxide synthase, Vascular endothelial growth factor, medicine.anatomical_structure, Endocrinology, chemistry, Diabetes Mellitus, Type 2, Gene Expression Regulation, Emergency Medicine, biology.protein, medicine.symptom, business, Glomerular Filtration Rate
Abstract: The objectives of this study were to determine whether type 2 diabetic mice would exhibit a more severe renal impact of hemorrhagic shock (HS) based on a recently described model of acute kidney injury and to determine the impact of HS on renal responses to hypoxia. We induced HS or sham procedure in type 2 diabetic and obese db/db mice. Creatininemia, glomerular filtration rate, urine output, histologic injury score, and kidney inductible molecule 1 mRNA were used to investigate the renal impact of HS. Tissular hypoxia and its impact were quantified using pimonidazole immunostaining and mRNA of hypoxic inducible factor, vascular endothelial growth factor receptors 1 and 2, Tie-2, endothelial nitric oxide synthase, and inducible nitric oxide synthase. Diabetic mice exhibiting mild diabetic nephropathy express hypoxic signals at baseline. The renal impact of HS was more severe in diabetic mice, with a worsening of tissular hypoxia and an altered response to hypoxia. Furthermore, endothelial nitric oxide synthase was highly overexpressed in diabetic shocked mice when compared with nondiabetic shocked mice. Renal impact of HS in type 2 diabetic mice is more intense than in nondiabetic ones. Preexisting hypoxia during diabetes could result in a renal preconditioning that modifies endothelial and tissular responses to acute kidney injury.
Published: 2012

23. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides 'Small Colony'

Author: Pascal Sirand-Pugnet, Valérie Barbe, Christine Citti, François Thiaucourt, Alain Blanchard, Marc Breton, Lucia Manso-Silvan, Emilie Dordet-Frisoni, François Poumarat, Patricia Thebault, Virginie Dupuy, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), EVOLMYCO project (ANR-07-GMGE-001), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Thiaucourt, François
Subjects: Most recent common ancestor, Phylogénie, Time Factors, Epidemiology, Veterinary Microbiology, lcsh:Medicine, L73 - Maladies des animaux, Disease Outbreaks, Péripneumonie contagieuse bovine, Contagious bovine pleuropneumonia, Genome Sequencing, lcsh:Science, Genome Evolution, Phylogeny, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, biology, Geography, Microbial Mutation, Mycoplasma mycoides, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Épidémiologie, Europe, Enzootic, Medicine, Veterinary medicine and animal Health, Research Article, DNA, Bacterial, Distribution géographique, Notifiable disease, Molecular Sequence Data, Zoology, Cattle Diseases, Polymorphism, Single Nucleotide, Microbiology, Infectious Disease Epidemiology, Histoire, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Phylogenetics, medicine, Animals, Pleuropneumonia, Contagious, Biology, 030304 developmental biology, Génie génétique, Bacterial Evolution, Bactériologie, Base Sequence, 030306 microbiology, lcsh:R, Outbreak, Genetic Variation, Bayes Theorem, Bacteriology, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Médecine vétérinaire et santé animal, Emerging Infectious Diseases, Africa, Microbial Evolution, Bovidae, lcsh:Q, Cattle, Veterinary Science, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract: International audience; Mycoplasma mycoides subsp. mycoides "Small Colony" (MmmSC) is responsible for contagious bovine pleuropneumonia (CBPP) in bovidae, a notifiable disease to the World Organization for Animal Health (OIE). Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th) century through the cattle trade and was eradicated from most continents by stamping-out policies. During the 20(th) century it persisted in Africa, and it reappeared sporadically in Southern Europe. Yet, classical epidemiology studies failed to explain the re-occurrence of the disease in Europe in the 1990s. The objectives of this study were to obtain a precise phylogeny of this pathogen, reconstruct its evolutionary history, estimate the date of its emergence, and determine the origin of the most recent European outbreaks. A large-scale genomic approach based on next-generation sequencing technologies was applied to construct a robust phylogeny of this extremely monomorphic pathogen by using 20 representative strains of various geographical origins. Sixty two polymorphic genes of the MmmSC core genome were selected, representing 83601 bp in total and resulting in 139 SNPs within the 20 strains. A robust phylogeny was obtained that identified a lineage specific to European strains; African strains were scattered in various branches. Bayesian analysis allowed dating the most recent common ancestor for MmmSC around 1700. The strains circulating in Sub-Saharan Africa today, however, were shown to descend from a strain that existed around 1810. MmmSC emerged recently, about 300 years ago, and was most probably exported from Europe to other continents, including Africa, during the 19(th) century. Its diversity is now greater in Africa, where CBPP is enzootic, than in Europe, where outbreaks occurred sporadically until 1999 and where CBPP may now be considered eradicated unless MmmSC remains undetected.
Published: 2012
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24. Fatal outbreak of Mycoplasma capricolum pneumonia in endangered markhors

Author: François Thiaucourt, Virginie Dupuy, Mulojon Amirbekov, Dustmurod Vahobov, Orom Ziyoev, Lucia Manso-Silvan, Stéphane Ostrowski, Abdurahmon Mahmadshoev, and Stefan Michel
Subjects: Male, Tajikistan, Epidemiology, lcsh:Medicine, L73 - Maladies des animaux, Communicable Diseases, Emerging, Mycoplasma capricolum, Disease Outbreaks, Caprinae, Mycoplasma, wild, Udder, Phylogeny, Goat Diseases, biology, Transmission (medicine), espèce en danger, Dispatch, Infectious Diseases, medicine.anatomical_structure, markhors, Animals, Domestic, Female, P01 - Conservation de la nature et ressources foncières, Pneumonia (non-human), Microbiology (medical), goats, Animals, Wild, lcsh:Infectious and parasitic diseases, Contagious caprine pleuropneumonia, Species Specificity, medicine, Animals, pneumonia, lcsh:RC109-216, Pleuropneumonia, Contagious, Transmission des maladies, conservation of natural resources, outbreak, lcsh:R, Endangered Species, Impact sur l'environnement, Outbreak, endangered, biology.organism_classification, medicine.disease, Virology, tuberculosis and other mycobacteria, Pneumonie
Abstract: Mycoplasma capricolum subsp. capricolum and M. capricolum subsp. capripneumoniae are closely related subspecies of the M. mycoides cluster (1). Whereas M. capricolum subsp. capripneumoniae is the etiologic agent of contagious caprine pleuropneumonia (CCPP), a severe and typically lethal respiratory disease, M. capricolum subsp. capricolum infection is usually not fatal and instead results in chronic inflammation in a variety of organs, including joints, udder, eyes, and lungs (2). M. capricolum subsp. capricolum infection occurs worldwide and appears widespread but has rarely been found in species of small ruminants other than domestic goats and, more occasionally, sheep (2,3). This lack of evidence may be partially because few studies have applied sensitive molecular techniques for its detection in nondomestic ruminants (2,3). Domestic goats can carry M. capricolum subsp. capricolum asymptomatically, notably in the ear canal (4), and pose an insidious risk for cross-species transmission with sympatric wild caprines (2,3).
Published: 2011

25. Development of 10 microsatellite loci in the pulmonate snail Biomphalaria kuhniana (Mollusca, Gastropoda)

Author: Virginie Dupuy, Antoine Nicot, Philippe Jarne, and Patrice David
Subjects: Biomphalaria straminea, biology, Ecology, Selfing, Zoology, Locus (genetics), Snail, biology.organism_classification, Freshwater snail, biology.animal, parasitic diseases, Gastropoda, Genetics, Microsatellite, Inbreeding, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract: We characterized 10 variable microsatellite loci in the freshwater snail Biomphalaria kuhniana, as well as conditions for multiplexing and co-loading sets of loci. Two to five alleles were detected per locus over the two studied populations in Venezuela. High inbreeding coefficients suggest high selfing rates. Cross-species amplification provided some variability at eight and three loci in the other species belonging to the Biomphalaria straminea complex (B. straminea and B. intermedia), but was unsuccessful in more divergent species.
Published: 2011

26. Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

Author: Valérie Barbe, Marc Breton, Pascal Sirand-Pugnet, Anne Marie Lomenech, Lucia Manso-Silvan, François Thiaucourt, Woubit Salah, Benoit Vacherie, Alain Blanchard, Daniel J. Jacob, Virginie Dupuy, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Sciences et Technologies - Bordeaux 1, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Sciences et Technologies - Bordeaux 1 (UB), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
Subjects: Proteomics, ruminant, Subspecies, L73 - Maladies des animaux, Genome, Plasmid, Contagious bovine pleuropneumonia, Segmental Duplications, Genomic, Pathogen, génomique comparée, Chèvre, bactérie, Genetics, 0303 health sciences, Comparative Genomic Hybridization, biology, santé animale, Strain (biology), Goats, Mycoplasma mycoides, GENOMIQUE, Multigene Family, Horizontal gene transfer, Petits ruminants, Female, bactérie pathogène, CAPRI, Biotechnology, Research Article, Plasmids, DNA, Bacterial, lcsh:QH426-470, lcsh:Biotechnology, Lipoproteins, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, lcsh:TP248.13-248.65, medicine, Animals, pathologie animale, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, GENETIQUE, MYCOIDES SMALL COLONY, 030306 microbiology, génome, Genetic Variation, Molecular Sequence Annotation, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, lcsh:Genetics, DNA Transposable Elements, Genome, Bacterial
Abstract: Background The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagious bovine pleuropneumonia. Its very close relative, Mycoplasma mycoides subsp. capri (Mmc), is a more ubiquitous pathogen in small ruminants causing mastitis, arthritis, keratitis, pneumonia and septicaemia and is also found as saprophyte in the ear canal. To understand the genetics underlying these phenotypic differences, we compared the MmmSC PG1 type strain genome, which was already available, with the genome of an Mmc field strain (95010) that was sequenced in this study. We also compared the 95010 genome with the recently published genome of another Mmc strain (GM12) to evaluate Mmc strain diversity. Results The MmmSC PG1 genome is 1,212 kbp and that of Mmc 95010 is ca. 58 kbp shorter. Most of the sequences present in PG1 but not 95010 are highly repeated Insertion Sequences (three types of IS) and large duplicated DNA fragments. The 95010 genome contains five types of IS, present in fewer copies than in PG1, and two copies of an integrative conjugative element. These mobile genetic elements have played a key role in genome plasticity, leading to inversions of large DNA fragments. Comparison of the two genomes suggested a marked decay of the PG1 genome that seems to be correlated with a greater number of IS. The repertoire of gene families encoding surface proteins is smaller in PG1. Several genes involved in polysaccharide metabolism and protein degradation are also absent from, or degraded in, PG1. Conclusions The genome of MmmSC PG1 is larger than that of Mmc 95010, its very close relative, but has less coding capacity. This is the result of large genetic rearrangements due to mobile elements that have also led to marked gene decay. This is consistent with a non-adaptative genomic complexity theory, allowing duplications or pseudogenes to be maintained in the absence of adaptive selection that would lead to purifying selection and genome streamlining over longer evolutionary times. These findings also suggest that MmmSC only recently adapted to its bovine host.
Published: 2011
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27. Multi-locus sequence analysis of mycoplasma capricolum subsp. capripneumoniae for the molecular epidemiology of contagious caprine pleuropneumonia

Author: Chu Yuefeng, François Thiaucourt, Lucia Manso-Silvan, and Virginie Dupuy
Subjects: Polymorphisme génétique, L73 - Maladies des animaux, Polymerase Chain Reaction, Mycoplasma capricolum, chemistry.chemical_compound, RNA, Ribosomal, 16S, Molecular marker, Marqueur génétique, Caprin, Genetics, lcsh:Veterinary medicine, biology, Goats, Épidémiologie, Phylogeography, Pleuropneumonia, Ruminant, Sequence analysis, Molecular Sequence Data, Locus (genetics), Analyse microbiologique, Evolution, Molecular, Viral Proteins, Contagious caprine pleuropneumonia, medicine, Animals, Pleuropneumonia, Contagious, Qatar, Goat Diseases, Polymorphism, Genetic, Base Sequence, General Veterinary, Molecular epidemiology, Research, Biologie moléculaire, Sequence Analysis, DNA, Animal sauvage, medicine.disease, biology.organism_classification, veterinary(all), chemistry, Africa, lcsh:SF600-1100, Multilocus sequence typing, U30 - Méthodes de recherche, Mycoplasmose, Multilocus Sequence Typing
Abstract: Mycoplasma capricolum subsp. capripneumoniae (Mccp) is the causative agent of contagious caprine pleuropneumonia (CCPP), a devastating disease of domestic goats. The exact distribution of CCPP is not known but it is present in Africa and the Middle East and represents a significant threat to many disease-free areas including Europe. Furthermore, CCPP has been recently identified in Tajikistan and China. A typing method with an improved resolution based on Multi-Locus Sequence Analysis (MLSA) has been developed to trace new epidemics and to elucidate whether the recently identified cases in continental Asia were due to recent importation of Mccp. The H2 locus, a polymorphic region already in use as a molecular marker for Mccp evolution, was complemented with seven new loci selected according to the analysis of polymorphisms observed among the genome sequences of three Mccp strains. A total of 25 strains, including the two new strains from Asia, were analysed by MLSA resulting in the discrimination of 15 sequence types based on 53 polymorphic positions. A distance tree inferred from the concatenated sequences of the eight selected loci revealed two evolutionary lineages comprising five groups, which showed good correlation with geographic origins. The presence of a distinct Asian cluster strongly indicates that CCPP was not recently imported to continental Asia. It is more likely that the disease has been endemic in the area for a long time, as supported by historical clinical descriptions. In conclusion, this MLSA strategy constitutes a highly discriminative tool for the molecular epidemiology of CCPP.
Published: 2011
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28. Saint-Mont (Saint-Amé, Vosges). Un plate tombe du VIIIe siècle

Author: Kraemer, Charles, Histoire et Cultures de l'Antiquité et du Moyen Âge (HISCANT-MA), Université de Lorraine (UL), Musée de Saint-Dizier, Virginie Dupuy, and KRAEMER, Charles
Subjects: [SHS.ARCHI]Humanities and Social Sciences/Architecture, space management, [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, épigraphie, [SHS.ART]Humanities and Social Sciences/Art and art history, [SHS.MUSEO]Humanities and Social Sciences/Cultural heritage and museology, Saint-Mont, Vosges, sépulture, lapidaire, [SHS.MUSEO] Humanities and Social Sciences/Cultural heritage and museology, [SHS.ENVIR] Humanities and Social Sciences/Environmental studies, [SHS.HIST] Humanities and Social Sciences/History, haut Moyen Âge, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SHS.ART] Humanities and Social Sciences/Art and art history, [SHS.ARCHI] Humanities and Social Sciences/Architecture, space management, [SHS.HIST]Humanities and Social Sciences/History, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2016

29. Les élites d’Austrasie, des aristocrates raffinés ?

Author: Bayard, Adrien, Joye, Sylvie, Bayard, Adrien, and Virginie Dupuy
Subjects: [SHS.HIST] Humanities and Social Sciences/History
Published: 2016

30. L’occupation tardive du Châtelet de Gourzon à Bayard et Fontaines-sur-Marne (milieu du IVe-VIIIe s.)

Author: Kasprzyk, Michel, Archéologie, Terre, Histoire, Sociétés [Dijon] (ARTeHiS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Ministère de la Culture et de la Communication (MCC), Institut national de recherches archéologiques préventives (Inrap), Virginie Dupuy, Archéologie, Terre, Histoire, Sociétés [Dijon] ( ARTeHiS ), Ministère de la Culture et de la Communication ( MCC ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de Recherches Archéologiques Préventives ( INRAP ), Institut national de recherches archéologiques préventives ( Inrap ), and Kasprzyk, Michel
Subjects: [SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [ SHS.ARCHEO ] Humanities and Social Sciences/Archaeology and Prehistory, Haut Moyen Age, ComputingMilieux_MISCELLANEOUS, Agglomération secondaire antique
Abstract: International audience
Published: 2016

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30 results on '"Virginie Dupuy"'

1. Multi-locus sequence analysis reveals great genetic diversity among Mycoplasma capricolum subsp. capripneumoniae strains in Asia

2. Fatal Outbreak of Mycoplasma capricolum Pneumonia in Endangered Markhors

3. Genetic architecture of sexual selection: QTL mapping of male song and female receiver traits in an acoustic moth.

4. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides 'Small Colony'.

5. III. Collectionner l’Antique sur les rivages de l’Atlantique. Fortuné Parenteau (1814-1882), une figure fondatrice pour le musée Dobrée

6. A library preparation optimized for metagenomics of RNA viruses

7. The Protohistoric sword from Le Gué-de-Velluire (Vendée, France): a pasticcio's history unveiled by archaeometrical research

8. Phylogeny and molecular typing of Mycoplasma agalactiae and Mycoplasma bovis by multilocus sequencing

9. Genetic Architecture of Sexual Selection: QTL Mapping of Male Song and Female Receiver Traits in an Acoustic Moth

10. High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species

11. SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods to Reveal Genetic Variability Within a Virus Species

12. A large-scale genomic approach affords unprecedented resolution for the molecular epidemiology and evolutionary history of contagious caprine pleuropneumonia

13. SNaPshot and CE-SSCP : two simple and cost-effective methods to reveal genetic variability within a virus species

14. Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa

15. Fatal transmission of contagious caprine pleuropneumonia to an Arabian oryx (Oryx leucoryx)

16. Evolutionary history of contagious bovine pleuropneumonia using Next generation sequencing of Mycoplasma mycoides subsp. mycoides 'small colony'

17. Development of eight microsatellite markers in the parsley frog (Pelodytes punctatus)

18. Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae

19. Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle

20. Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

21. Finishing bacterial genome assemblies with Mix

22. Type 2 diabetes mellitus in mice aggravates the renal impact of hemorrhagic shock

23. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides 'Small Colony'

24. Fatal outbreak of Mycoplasma capricolum pneumonia in endangered markhors

25. Development of 10 microsatellite loci in the pulmonate snail Biomphalaria kuhniana (Mollusca, Gastropoda)

26. Mycoplasma mycoides, from 'mycoides Small Colony' to 'capri'. A microevolutionary perspective

27. Multi-locus sequence analysis of mycoplasma capricolum subsp. capripneumoniae for the molecular epidemiology of contagious caprine pleuropneumonia

28. Saint-Mont (Saint-Amé, Vosges). Un plate tombe du VIIIe siècle

29. Les élites d’Austrasie, des aristocrates raffinés ?

30. L’occupation tardive du Châtelet de Gourzon à Bayard et Fontaines-sur-Marne (milieu du IVe-VIIIe s.)

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30 results on '"Virginie Dupuy"'

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