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Dive into the research topics where Philippe Bardou is active.

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Featured researches published by Philippe Bardou.


Nature Communications | 2014

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Camille Berthelot; Frédéric Brunet; Domitille Chalopin; Amélie Juanchich; Maria Bernard; Benjamin Noel; Pascal Bento; Corinne Da Silva; Karine Labadie; Adriana Alberti; Jean-Marc Aury; Alexandra Louis; Patrice Dehais; Philippe Bardou; Jérôme Montfort; Christophe Klopp; Cédric Cabau; Christine Gaspin; Gary H. Thorgaard; Mekki Boussaha; Edwige Quillet; René Guyomard; Delphine Galiana; Julien Bobe; Jean-Nicolas Volff; Carine Genet; Patrick Wincker; Olivier Jaillon; Hugues Roest Crollius

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.


BMC Bioinformatics | 2014

jvenn: an interactive Venn diagram viewer

Philippe Bardou; Jérôme Mariette; Frédéric Escudié; Christophe Djemiel; Christophe Klopp

BackgroundVenn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.Resultsjvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams.Conclusionsjvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.


PLOS ONE | 2014

Design and Characterization of a 52K SNP Chip for Goats

Gwenola Tosser-Klopp; Philippe Bardou; Olivier Bouchez; Cédric Cabau; R.P.M.A. Crooijmans; Yang Dong; Cécile Donnadieu-Tonon; A. Eggen; H.C.M. Heuven; Saadiah Jamli; Abdullah Johari Jiken; Christophe Klopp; Cynthia T. Lawley; J. C. McEwan; Patrice Martin; Carole Moreno; Philippe Mulsant; Ibouniyamine Nabihoudine; Eric Pailhoux; Isabelle Palhiere; Rachel Rupp; Julien Sarry; Brian L Sayre; Aurélie Tircazes; Jun Wang; Wen Wang; Wenguang Zhang

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.


PLOS Genetics | 2013

The Highly Prolific Phenotype of Lacaune Sheep Is Associated with an Ectopic Expression of the B4GALNT2 Gene within the Ovary

Laurence Drouilhet; Camille Mansanet; Julien Sarry; Kamila Tabet; Philippe Bardou; Florent Woloszyn; Jérôme Lluch; Grégoire Harichaux; Catherine Viguié; Danielle Monniaux; Loys Bodin; Philippe Mulsant; Stéphane Fabre

Prolific sheep have proven to be a valuable model to identify genes and mutations implicated in female fertility. In the Lacaune sheep breed, large variation in litter size is genetically determined by the segregation of a fecundity major gene influencing ovulation rate, named FecL and its prolific allele FecLL. Our previous work localized FecL on sheep chromosome 11 within a locus of 1.1 Mb encompassing 20 genes. With the aim to identify the FecL gene, we developed a high throughput sequencing strategy of long-range PCR fragments spanning the locus of FecLL carrier and non-carrier ewes. Resulting informative markers defined a new 194.6 kb minimal interval. The reduced FecL locus contained only two genes, insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) and beta-1,4-N-acetyl-galactosaminyl transferase 2 (B4GALNT2), and we identified two SNP in complete linkage disequilibrium with FecLL. B4GALNT2 appeared as the best positional and expressional candidate for FecL, since it showed an ectopic expression in the ovarian follicles of FecLL/FecLL ewes at mRNA and protein levels. In FecLL carrier ewes only, B4GALNT2 transferase activity was localized in granulosa cells and specifically glycosylated proteins were detected in granulosa cell extracts and follicular fluids. The identification of these glycoproteins by mass spectrometry revealed at least 10 proteins, including inhibin alpha and betaA subunits, as potential targets of B4GALNT2 activity. Specific ovarian protein glycosylation by B4GALNT2 is proposed as a new mechanism of ovulation rate regulation in sheep, and could contribute to open new fields of investigation to understand female infertility pathogenesis.


RNA | 2011

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

Marie-Josée Cros; Antoine de Monte; Jérôme Mariette; Philippe Bardou; Benjamin Grenier-Boley; Daniel Gautheret; Hélène Touzet; Christine Gaspin

The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene finders and a set of tools for the comparison, visualization, editing, and export of ncRNA candidates. Predictions can be filtered according to a large set of characteristics. Based on this environment, we created a public website located at http://RNAspace.org. It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project (http://rnaspace.sourceforge.net/).


PLOS ONE | 2014

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

Jérôme Mariette; Céline Noirot; Ibounyamine Nabihoudine; Philippe Bardou; Claire Hoede; Anis Djari; Cédric Cabau; Christophe Klopp

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.


Scientific Reports | 2017

A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content

Pauline Martin; Isabelle Palhiere; Cyrielle Maroteau; Philippe Bardou; Kamila Canale-Tabet; Julien Sarry; Florent Woloszyn; Justine Bertrand-Michel; Ines Racke; Hüseyin Besir; Rachel Rupp; Gwenola Tosser-Klopp

The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.


Molecular Biology and Evolution | 2017

Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep

Julie Demars; Margarita Cano; L. Drouilhet; Florence Plisson-Petit; Philippe Bardou; Stéphane Fabre; Bertrand Servin; Julien Sarry; Florent Woloszyn; Philippe Mulsant; Didier Foulquier; Fabien Carrière; Mathias Aletru; Nathalie Rodde; Stéphane Cauet; Olivier Bouchez; Maarten Pirson; Gwenola Tosser-Klopp; Daniel Allain

Abstract The composition and structure of fleece variation observed in mammals is a consequence of a strong selective pressure for fiber production after domestication. In sheep, fleece variation discriminates ancestral species carrying a long and hairy fleece from modern domestic sheep (Ovis aries) owning a short and woolly fleece. Here, we report that the “woolly” allele results from the insertion of an antisense EIF2S2 retrogene (called asEIF2S2) into the 3′ UTR of the IRF2BP2 gene leading to an abnormal IRF2BP2 transcript. We provide evidence that this chimeric IRF2BP2/asEIF2S2 messenger 1) targets the genuine sense EIF2S2 RNA and 2) creates a long endogenous double-stranded RNA which alters the expression of both EIF2S2 and IRF2BP2 mRNA. This represents a unique example of a phenotype arising via a RNA-RNA hybrid, itself generated through a retroposition mechanism. Our results bring new insights on the sheep population history thanks to the identification of the molecular origin of an evolutionary phenotypic variation.


PLOS ONE | 2016

Correction: Design and Characterization of a 52K SNP Chip for Goats.

Gwenola Tosser-Klopp; Philippe Bardou; Olivier Bouchez; Cédric Cabau; R.P.M.A. Crooijmans; Yang Dong; Cécile Donnadieu-Tonon; A. Eggen; H.C.M. Heuven; Saadiah Jamli; Abdullah Johari Jiken; Christophe Klopp; Cynthia T. Lawley; J. C. McEwan; Patrice Martin; Carole Moreno; Philippe Mulsant; Ibouniyamine Nabihoudine; Eric Pailhoux; Isabelle Palhiere; Rachel Rupp; Julien Sarry; Brian L Sayre; Aurélie Tircazes; Jun Wang; Wen Wang; Wenguang Zhang

We have forgotten to thank our collaborators who provided the Creole samples. The Acknowledgements section should read:


bioRxiv | 2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

Sylvain Foissac; Sarah Djebali; Kylie Munyard; Andrea Rau; Kévin Muret; Diane Esquerre; Matthias Zytnicki; Thomas Derrien; Philippe Bardou; Fany Blanc; Cédric Cabau; Elisa Crisci; Sophie Dhorne-Pollet; Françoise Drouet; Ignacio Gonzales; Adeline Goubil; Sonia Lacroix-Lamandé; Fabrice Laurent; Sylvain Marthey; Maria Marti-Marimon; Raphaelle Momal-Leisenring; Florence Mompart; Pascale Quéré; David Robelin; Magali San Cristobal; Gwenola Tosser-Klopp; Silvia Vincent-Naulleau; Stéphane Fabre; Marie-Hélène Pinard-van der Laan; Christophe Klopp

Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays considerably extended the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species confirms previous findings in model animals. Overall, these results emphasize the value of FAANG for research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.Abstract Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

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Dive into the Philippe Bardou's collaboration.

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Christophe Klopp

Institut national de la recherche agronomique

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Christine Gaspin

Institut national de la recherche agronomique

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Cédric Cabau

Institut national de la recherche agronomique

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Julien Sarry

Institut national de la recherche agronomique

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Isabelle Palhiere

Institut national de la recherche agronomique

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Jérôme Mariette

Institut national de la recherche agronomique

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Philippe Mulsant

Institut national de la recherche agronomique

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Rachel Rupp

Institut national de la recherche agronomique

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