URGV - Plant Genomics Research
Unité de Recherche en Génomique Végétale

Bioinformatics for Predictive Genomics

Group leader: Sébastien Aubourg aubourg@evry.inra.fr +33 1 60 87 45 16

Table of Contents Running Projects Genome wide characterization of gene expression regulation in plants Topological organization of regulatory sequences in promoters - Véronique Brunaud Orphan and orthologous genes in plants - Sébastien Aubourg Statistical methods for microarray data - Marie-Laure Martin Magniette Structural and functional plant genome annotation Prediction of protein-protein interactions in Arabidopsis - Sébastien Aubourg Annotation of grape genome - Sébastien Aubourg Improvement of the Arabidopsis genome annotation – Sébastien Aubourg Other Projects A model for T-DNA integration in Arabidopsis thaliana - Véronique Brunaud The terpenoid synthase gene family in Arabidopsis - Sébastien Aubourg Publications Publications of the Bioinformatics Group Miscellaneous Previous Members

Publications

 

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the regulation of transcription.

Virginie Bernard, Vironique Brunaud and Alain Lecharny
BMC Genomics (2010) 11:166
Abstract

Sélection de motifs candidates pour la régulation des gènes chez Arabidopsis thaliana sur des critères topologiques.

Bernard V., Brunaud V., Serizet C., Martin-Magniette M.-L., Caboche M., Aubourg S. & Lecharny A.
JOBIM 2006 Journées Ouvertes Biologie Informatique et Mathématiques. Bordeaux, France. 5-7 juillet 2006, Actes Session 1, 17-28

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes.

Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M, Lecharny A
Plant Biotechnol J. 2004 Sep;2(5):401-15. PMID : 17168887

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Features and evolution of single-copy genes in plant.

Unique genes in plants: specificities and conserved features throughout evolution.

Armisén D, Lecharny A, Aubourg S.
BMC Evol Biol. 2008 Oct 10;8:280. PMID: 18847470

Background: Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and species-specific unique genes

Results: We identified the unique genes within both A. thaliana and O. sativa genomes and classified them according to the number of homologs in the alternative species: none (U{1:0}), one (U{1:1}) or several (U{1:m}). Regardless of the species, all the genes in these groups present some conserved characteristics, such as small average protein size and abnormal intron number. In order to understand the origin and function of unique genes, we further characterized the U{1:1} gene pairs. The possible involvement of sequence convergence in the creation of U{1:1} pairs was discarded due to the frequent conservation of intron positions. Furthermore, an orthology relationship between the two members of each U{1:1} pair was strongly supported by a high conservation in the protein sizes and transcription levels. Within the promoter of the unique conserved genes, we found a number of TATA and TELO boxes that specifically differed from their mean number in the whole genome. Many unique genes have been conserved as unique through evolution from the green alga Ostreococcus lucimarinus to higher plants. Plant unique genes may also have homologs in bacteria and we showed a link between the targeting towards plastids of proteins encoded by plant nuclear unique genes and their homology with a bacterial protein

Conclusion: Many of the A. thaliana and O. sativa unique genes are conserved in plants for which the ancestor diverged at least 725 million years ago (MYA). Half of these genes are also present in other eukaryotic and/or prokaryotic species. Thus, our results indicate that (i) a strong negative selection pressure has conserved a number of genes as unique in genomes throughout evolution, (ii) most unique genes are subjected to a low divergence rate, (iii) they have some features observed in housekeeping genes but for most of them there is no functional annotation and (iv) they may have an ancient origin involving a possible gene transfer from ancestral chloroplasts or bacteria to the plant nucleus

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Statistical methods for microarray data

PI: Marie-Laure Martin-Magniette
The need of statistical methods to analyze the data of DNA microarray appeared very quickly. The abundance of the data requires automatic methods which take their technical and biological variabilities into account. The objective of this project is to develop statistical methods to analyse microarray data.

1. Analysis of CATMA arrays produced by the team 'Analyse Of Transcriptome' led by Jean Pierre Renou . Software in R was written to normalise raw data and to determine genes differentially expressed using statistical tests. This work is a collaboration with the Statistics and Genome team of UMR AgroParisTech/INRA MIA 518 .
   All functions were generalized for other arrays and are in a R package named anapuce.
   All these C A T M A data are stored in a database C A T d b and are used to investigate gene functional analysis.

2. In collaboration with the Select team of INRIA Futurs . We study model-based clustering to determine co-expressed genes (PhD of Cathy Maugis).

3. Analysis of the tiling array of chromosome 4 produced by the team 'Functional Genomics and Epigenetics' led by Vincent Colot. For expression data, Software in R was written to normalise raw data and to determine genes differentially expressed using statistical tests. The tiling array is also used to perform ChIP-chip experiments and we devise statistical methods to interpret them.

Other external collaboration: MIA-Jouy team.

Publications:

Normalization for triple-target microarray experiments

BMC Bioinformatics. 2008 Apr 28;9(1):216 PMID: 18442385
Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou and Jean-Jacques Daudin

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance.

BMC Genomics. 2007 Dec 5;8(1):450 PMID: 18053238Ramel F, Sulmon C, Cabello-Hurtado F, Taconnat L, Martin-Magniette ML, Jean-Pierre Renou, Elamrani A, Couee I, Gouesbet G.

Evaluation of the gene-specific dye bias in cDNA microarray experiments.

1569 1855 Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.
Bioinformatics. br /> 2005 May 1;21(9):1995-2000. Epub 2005 Feb 2. PMID: 15691855

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Prediction of protein-protein interactions in Arabidopsis

PI: Sébastien Aubourg
Collaborations: Claire Lurin
Funding: This project APPI (2003-2005) is financed by the ACI IMP Bio (Informatique, Mathématiques, Physique en Biologie moléculaire)
Keywords : interactions, Rosetta Stone, positional regulation, PFAM motifs, evolution, relationship structure-function

As for prokaryotes, the topological organization of genes along the chromosomes of eukaryotes is under a positive selection depending on the nature of gene function. A particular case is when two sequences coding two different protein domains are observed both separately in two genes, the component genes, and together in one gene, the composite gene. These situations may be efficiently used for the functional annotation of genomes. In plants, rare occurrences of evolutionary or functional relationships between genes either duplicated in tandem or merged have been described. For instance, we have characterized the multigene family of terpene synthases in Arabidopsis thaliana and showed some occurrences of genes in tandem and coding for two enzymes, TPS and GGPS, involved in the same metabolic pathway. In this project, we use an exhaustive approach of the topological associations of protein domains to contribute to the study of the interactome of the model plant Arabidopsis thaliana. The bioinformatics part of the project is an exhaustive search of the conserved organizations of topologically associated genes and of composite genes.

The bioinformatics prediction step is ended and the experimental validation of the protein-protein interactions is in progress in the team of Claire Lurin. The confirmed results will be available through the database FLAGdb++ .

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Annotation of grape genome

PI: Sébastien Aubourg (CR1-INRA)
Participants: Cécile Guichard, Franck Samson

Collaboration:

• Coordination of the grapevine project: Anne-Françoise Adam-Blondon
• Sequencing : Francis Quétier quetier@genoscope.cnrs.fr
• Annotation in Genoscope : Olivier Jaillon ojaillon@genoscope.cns.fr
• EuGène support: Thomas Schiex tschiex@toulouse.inra.fr
  and Jérome Gouzy gouzy@toulouse.inra.fr
• cDNA project : Christian Clépet
• MIGALE platform, INRA-MIG team: Christophe Caron christophe.caron@jouy.inra.fr

Links:

• Grapevine and Forest Trees Genomics team at URGV
• Vitis vinifera at Genoscope
• EuGène at BIA
• The Vitis genome in FLAGdb++
• The MIGALE platform

The genomic sequences generated and clustered by GENOSCOPE will be annotated using different approaches. The annotation will be carried out at GENOSCOPE by a pipeline including the EXOFISH tool and at URGV by the integrated predictions of the EuGène software (collaboration B I A, INRA Toulouse) The final annotation and the results of the different predictive approaches will be available at Genoscope (Genome Browser) and at URGV through the FLAGdb++ application allowing data navigation and analysis at the genomic scale. The annotation release will be synchronised with the availability of the full-length cDNA clones and sequences obtained in this project.

The storage of the grape genomic sequences and annotations in FLAGdb++ should also help in the functional interpretation of transcriptome data obtained from the URGV-Affymetrix platform and for which a grape DNA chip is available.

We have also characterized the Vitis Terpene Synthase and the Stilbene Synthase families in collaboration with Philippe Hugueney, hugueney@colmar.inra.fr and compared them with Arabidopsis: The terpenoid synthase gene family in Arabidopsis - Sébastien Aubourg.

Publications:

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny , Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier & Patrick Wincker
Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007 PMID: 17721507

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Improvement of the Arabidopsis genome annotation

PI : Sébastien Aubourg (CR1-INRA)
Participants:
Véronique Brunaud, Marie-Laure Martin-Magniette, Alain Lecharny, Jean-Pierre Renou and his group, Vincent Thareau and all the GeneFarm Network


GeneFarm db
Swiss-Prot plant section

Publications:

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.

Sébastien Aubourg, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Alain Lecharny, Jean-Pierre Renou
BMC Genomics. 2007 Nov 2;8(1):401 PMID: 17980019

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.

Aubourg S, Brunaud V, Bruyere C, Cock M, Cooke R, Cottet A, Couloux A, Dehais P, Deleage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlne G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Riviere S, Rombauts S, Rouze P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M and Lecharny A
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6. PMID: 15608279

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A model for T-DNA integration in Arabidopsis thaliana

PI: Véronique Brunaud
Participants:
Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lecharny A. Lepiniec L.
Funding: The FLAGdb/FST project is supported by Génoplante .
FLAGdb/FST has been registered at APP under the key IDDN.FR.001.380012.00.R.P.2001.000.10300.
Keywords : Arabidopsis, database, FST (Flanking Sequence Tag), genome, T-DNA, insertion mutant.

ADT 29 FST Poster (.ppt 301KB)

A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented database, FLAGdb/FST. The main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested. FSTs are anchored to the genome sequences of A.thaliana and positions of both predicted genes and FSTs are shown graphically on sequences. Requests to locate the genomic position of a query sequence are made using BLAST programs. The response delivered by FLAGdb/FST is a graphical representation of the putative FSTs and of predicted genes in a 20 kb region.

FST data are now acessible in F L A G d b + +

The thousands of FST produced have been used to characterize and understand the different molecular steps of the T-DNA integration in the genome. The unsolved question of preferential insertion sites is approached, in collaboration with the L. Lepiniec team (INRA-Versailles). The high number of FST and the available whole Arabidopsis genome allow one of the first statistical study on the nature of the T-DNA insertion sites. The localization of the sites is correlated to other features such the base composition, the gene density and the sequence nature (coding/uncoding, intron/exon, repeat sequences, promoter, UTR...). Results show that T-DNA insertion involves sequence microhomologies and clarify the molecular model described by Tinland (1995).

Publications

T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.

Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A.
EMBO Rep. 2002 Dec;3(12):1152-7. Epub 2002 Nov 21. PMID: 12446565

FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.

Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A.
Nucleic Acids Res. 2002 Jan 1;30(1):94-7. PMID: 11752264

Improved PCR-walking for large-scale isolation of plant T-DNA borders.

Biotechniques. 2001 Mar;30(3):496-8, 502, 504. PMID: 11252785
141 Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L.
INRA, Evry, France.

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The terpenoid synthase gene family in Arabidopsis

PI: Sébastien Aubourg
Collaboration: Jörg Bohlmann
Keywords : gene evolution, secondary metabolism, isoprenoid, terpene cyclase, prenyl transferase.

The Arabidopsis thaliana genome contains 40 terpenoid synthases (AtTPS). Surprisingly, thirty AtTPS closely resemble in all aspects of gene architecture, sequence relatedness and phylogenetic placement the plant monoterpene synthases, sesquiterpene synthases or diterpene synthases, characteristic of secondary metabolism. Several AtTPS genes are organized in tandem repeats and some AtTPS are localized with prenyltransferase genes in contiguous genomic clusters of consecutive steps of terpenoid biosynthesis. Phylogenetic analyses highlight events in the divergence of the TPS paralogs and suggest orthologous genes and a model for the evolution of the TPS gene family.

Intron-exon structure of the AtTPS genes

Topological organization of the AtTPS gene family

Predicted Sequences of the AtTPS Family

Publications

Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana.

Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29. PMID: 12207221
Aubourg S, Lecharny A, Bohlmann J.

Biochemical, molecular genetic and evolutionary aspects of defense-related terpenoid metabolism in conifers.

EVOLUTION OF METABOLIC PATHWAYS Elsevier Science, Amsterdam, pp. 109-149 JUN-2000 ISBN-13: 978-0-08-043860-3 ISBN-10: 0-08-043860-1
Bohlmann J, Gershenzon J, Aubourg S

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Publications of the Bioinformatics Group (Since 2001)

2012     2011     2010     2009     2008     2007     2006     2005     2004     2003     2002     2001

2011

Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids.

Moghaddam AM, Roudier F, Seifert M, Bérard C, Martin-Magniette ML, Ashtiyani RK, Houben A, Colot V, Mette MF (2011)
Plant J. 67(4):691-700.

Speeding Cis-Trans Regulation Discovery by Phylogenomic Analyses Coupled with Screenings of an Arrayed Library of Arabidopsis Transcription Factors.

Castrillo G, Turck F, Leveugle M, Lecharny A, Carbonero P, Coupland G, Paz-Ares J, Oñate-Sánchez L (2011)
PLoS ONE 6(6):e21524.

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.

Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V (2011)
EMBO J., 30:1928-1938.

Exploration of plant genomes in the FLAGdb++ environment.

Dèrozier S, Samson F, Tamby JP, Guichard C, Brunaud V, Grevet P, Gagnot S, Label P, Leplé JC, Lecharny A, Aubourg S (2011)
Plant Methods, 7: 8.

Variable selection in model-based discriminant analysis.

Maugis, C, Celeux, G, Martin-Magniette ML (2011)
Journal of Multivariate Analysis. 102(10):1374-1387.

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.

Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Martin-Magniette ML, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C (2011).
BMC Genomics. 12(1):292.

2010

Annotation structurale et fonctionnelle des génomes.

Aubourg S (2010)
Bio-informatique, Principes d’utilisation des outils. Série Savoir-faire, Editions Quæ (D. Tagu, J.L Risler coord.) pp. 166-178.

A python module to normalize microarray data by the quantile adjustment method.

Baber I, Tamby JP, Manoukis NC, Sangaré D, Doumbia S, Traoré SF, Maiga MS, Dembélé D (2010)
Infect. Genet. Evol., 11(4):765-8.

Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.

Cohen C, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I (2010)
BMC Genomics, 11:630.

Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays.

Martin S*, Aubourg S*, Schouwey M, Daviet L, Schalk M, Toub O, Lund S, Bohlmann J (2010)
BMC Plant Biol., 10: 226. (* co-premier auteur)

Improved detection of motifs with preferential location in promoters.

Bernard V, Lecharny A, Brunaud V (2010)
Genome, 9:739-752

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the regulation of transcription.

Bernard V, Brunaud V, Lecharny A (2010)
BMC Genomics. 11:166.

Brain transcriptional stability upon prion protein-encoding gene invalidation in zygotic or adult mouse.

Chadi, S, Young R, Le Guillou S, Tilly G, Bitton F, Martin-Magniette ML, Soubigou-Taconnat L, Balzergue S, Vilotte M, Peyre C, Passet B, Beringue V, Renou JP, Le Provost F, Laude H, Vilotte JL. (2010)
BMC Genomics, 11(1): 448.

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.

BMC Genomics. 2010 Mar 12;11:166. PMID: 20222994
Bernard V, Brunaud V, Lecharny A.

2009

Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients.

PLoS One. 2009 Aug 27;4(8):e6803. PMID: 19710928
Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E.

Identification of germinal disk region derived genes potentially involved in hen fertility.

Mol Reprod Dev. 2009 Nov;76(11):1043-55. PMID: 19484757
Elis S, Blesbois E, Couty I, Balzergue S, Martin-Magniette ML, Batellier F, Govoroun MS.

Variable selection for clustering with Gaussian mixture models.

Biometrics. 2009 Sep;65(3):701-9. Epub 2009 Feb 4. PMID: 19210744
Maugis C, Celeux G, Martin-Magniette ML.

Variable selection in model-based clustering: A general variable role modeling.

Computational Statistics and Data Analysis, 53: 3872-3882. (2009)
Maugis C, Celeux G, Martin-Magniette, ML

Semi-parametric estimation of the hazard function in a model with covariate measurement error.

ESAIM Probability and Statistics, 13: 87-114. (2009)
Martin-Magniette ML, Taupin ML

Mélanges gaussiens bidimensionnels pour la comparaison de deux échantillons de chromatine immuno-précipitée.

Revue Modulad, 40: 53-68. (2009)
Bérard C, Martin-Magniette ML, To A, Roudier F, Colot V, Robin S

Sélection de variables pour la classification par mélanges gaussiens pour prédire la fonction des gènes orphelins

Revue Modulad, 40: 69-80. (2009)
Maugis C, Martin-Magniette ML, Tamby JP, Renou JP, Lecharny A, Aubourg S, Celeux G

2008

Unique genes in plants: specificities and conserved features throughout evolution.

BMC Evol Biol. 2008 Oct 10;8:280. PMID: 18847470
Armisén D, Lecharny A, Aubourg S.

Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5.

Plant J. 2008 Jul 4. PMID: 18644002
Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C, De Clercq R, De Meyer B, Buysschaert C, Rombauts S, Villarroel R, Aubourg S, Beynon J, Bhalerao RP, Coupland G, Gruissem W, Menke FL, Weisshaar B, Renou JP, Zhou DX, Hilson P.

UTILLdb, a Pisum sativum in silico forward and reverse genetics tool

Genome Biology 2008, 9:R43 doi:10.1186/gb-2008-9-2-r43 PMID: 18302733
Marion Dalmais, Julien Schmidt, Christine Le Signor, Francoise Moussy, Judith Burstin, Vincent Savois, Gregoire Aubert, Veronique Brunaud, Yannick de Oliveira, Cecile Guichard, Richard Thompson and Abdelhafid Bendahmane

A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance.

BMC Plant Biol. 2008 Jun 13;8:66. PMID: 18554400
Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF.

Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection.

BMC Genomics. 2008 Jun 25;9:301. PMID: 18578863
Navajas M, Migeon A, Alaux C, Martin-Magniette M, Robinson G, Evans J, Cros-Arteil S, Crauser D, Le Conte Y.

Normalization for triple-target microarray experiments

BMC Bioinformatics. 2008 Apr 28;9(1):216 PMID: 18442385
Marie-Laure Martin-Magniette*¹², Julie Aubert¹, Avner Bar-Hen ⁴, Samira Elftieh² , Frederic Magniette³, Jean-Pierre Renou² and Jean-Jacques Daudin¹

Search for the genes involved in oocyte maturation and early embryo development in the hen.

BMC Genomics. 2008 Feb 29;9(1):110 PMID: 18312645
Elis S, Batellier F, Couty I, Balzergue S, Martin-Magniette ML, Monget P, Blesbois E, Govoroun MS.

Transcriptional and metabolic adjustments in AGPase deficient bt2 maize kernels.

Plant Physiol. 2008 Feb 20 PMID: 18287491
Cossegal M, Chambrier P, Mbelo S, Balzergue S, Martin-Magniette ML, Moing A, Deborde C, Guyon V, Perez P, Rogowsky P.

Systemic signaling of the plant N status triggers specific transcriptome responses depending on the N source in Medicago truncatula.

Plant Physiol. 2008 Feb 20 PMID: 18287487
Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR, Udvardi M, Salon C, Gojon A, Lepetit M.

Contrasted Microcolinearity and Gene Evolution Within a Homoeologous Region of Wheat and Barley Species.

J Mol Evol. 2008 Feb 15 PMID: 18274696
Chantret N, Salse J, Sabot F, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Leroy P, Bernard M, Boulos Chalhoub

CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform.

Nucleic Acids Res. 2008 Jan;36(Database issue):D986-90. Epub 2007 Oct 16. PMID: 17940091
Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Sébastien Aubourg, Alain Lecharny, Jean-Pierre Renou, Brunaud V.

2007

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance.

BMC Genomics. 2007 Dec 5;8(1):450 PMID: 18053238
Ramel F, Sulmon C, Cabello-Hurtado F, Taconnat L, Martin-Magniette ML, Jean-Pierre Renou, Elamrani A, Couee I, Gouesbet G.

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome.

BMC Genomics. 2007 Nov 2;8(1):401 PMID: 17980019
Sébastien Aubourg, Martin-Magniette ML, Brunaud V, Taconnat L, Bitton F, Balzergue S, Jullien PE, Ingouff M, Thareau V, Schiex T, Alain Lecharny, Jean-Pierre Renou

Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea.

Plant J. 2007 Sep;51(6):1116-25. Epub 2007 Jul 25. PMID: 17651368
Triques K, Sturbois B, Gallais S, Dalmais M, Chauvin S, Christian Clepet, Sébastien Aubourg, Rameau C, Michel Caboche, Abdel Ihafid Bendahmane

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007 PMID: 17721507
Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier & Patrick Wincker

Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27.

PLoS Genet. 2007 Jun;3(6):e86. Epub 2007 Apr 17. PMID: 17542647
Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G,Colot V.

2006

L'organisation des génomes végétaux révélée par leur annotation.

Biofutur, Vol 25/265 - 2006 - pp.33-37
Aubourg S., Delseny M. and Lecharny A. (2006)
Depuis une dizaine d'années, la communauté internationale des génomistes a considérablement investi dans la caractérisation d'une sélection de génomes végétaux modèles. Les connaissances déduites des séquences génomiques servent maintenant de socle à la compréhension de l'organisation et de l'évolution des génomes, à l'obtention de données fonctionnelles et à leur analyse intégrative.
Biofutur,(Subscribers Only)

2005

Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis.

Plant J. 2005 Nov;44(3):447-58. PMID: 16236154
Jammes F, Lecomte P, de Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B.

Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'.

Bioinformatics. 2005 Jul 15;21(14):3065. Epub 2005 Jun 7. PMID: 15941744
Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

Evaluation of the gene-specific dye bias in cDNA microarray experiments.

Bioinformatics. 2005 May 1;21(9):1995-2000. Epub 2005 Feb 2. PMID: 15691855
Martin-Magniette ML, Aubert J, Cabannes E, Daudin JJ.

Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (triticum and aegilops).

Plant Cell. 2005 Apr;17(4):1033-45. Epub 2005 Mar 4. PMID: 15749759
Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier M-F, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P and Chalhoub B

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6. PMID: 15608279
Aubourg S, Brunaud V, Bruyere C, Cock M, Cooke R, Cottet A, Couloux A, Dehais P, Deleage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlne G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Riviere S, Rombauts S, Rouze P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M and Lecharny A

2004

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes

Plant Biotechnol J. 2004 Sep;2(5):401-15. PMID: 17168887
Mingam A, Toffano-Nioche C, Brunaud V, Boudet N, Kreis M and Lecharny A

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Genome Res. 2004 Oct;14(10B):2176-89. PMID: 15489341
Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, Chardakov V, Cognet-Holliger C, Colot V, Crowe M, Darimont C, Durinck S, Eickhoff H, de Longevialle AF, Farmer EE, Grant M, Kuiper MT, Lehrach H, Leon C, Leyva A, Lundeberg J, Lurin C, Moreau Y, Nietfeld W, Paz-Ares J, Reymond P, Rouze P, Sandberg G, Segura MD, Serizet C, Tabrett A, Taconnat L, Thareau V, Van Hummelen P, Vercruysse S, Vuylsteke M, Weingartner M, Weisbeek PJ, Wirta V, Wittink FR, Zabeau M, Small I.

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.

Plant Cell. 2004 Aug;16(8):2089-103. Epub 2004 Jul 21. PMID: 15269332
Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I.

Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements.

Theor Appl Genet. 2004 Jun;109(1):10-22. Epub 2004 Apr 14. PMID: 15085260
Lescot M, Rombauts S, Zhang J, Aubourg S, Mathe C, Jansson S, Rouze P and Boerjan W

FLAGdb++, a database for the functional analysis of the Arabidopsis genome.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D347-50. PMID: 14681431
Samson F, Brunaud V, Duchene S, De Oliveira Y, Caboche M, Lecharny A and Aubourg S

Un modèle statistique pour l'intégration de l'ADN-T dans le génome d'Arabidopsis thaliana. In « La fluidité des génomes et ses conséquences »

Ed. Commission du Génie Biomoléculaire. (2004)
Lecharny A.

2003

CATMA: a complete Arabidopsis GST database.

Nucleic Acids Res. 2003 Jan 1;31(1):156-8. PMID: 12519971
Crowe ML, Serizet C, Thareau V, Aubourg S, Rouze P, Hilson P, Beynon J, Weisbeek P, van Hummelen P, Reymond P, Paz-Ares J, Nietfeld W, Trick M.

Automatic design of gene-specific sequence tags for genome-wide functional studies.

Bioinformatics Vol. 19 no. 17 2003, pages 2191–2198 PMID: 14630647
Thareau V, Dehais P, Serizet C, Hilson P, Rouze P, Aubourg S.

2002

T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites.

EMBO Rep. 2002 Dec;3(12):1152-7. Epub 2002 Nov 21. PMID: 12446565
Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Curaud C, DeRose R, Pelletier G, Lepiniec L, Caboche M, Lecharny A.

Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana.

Mol Genet Genomics. 2002 Aug;267(6):730-45. Epub 2002 Jun 29. PMID: 12207221
Aubourg S, Lecharny A, Bohlmann J.

FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.

Nucleic Acids Res. 2002 Jan 1;30(1):94-7. PMID: 11752264
Samson F, Brunaud V, Balzergue S, Dubreucq B, Lepiniec L, Pelletier G, Caboche M, Lecharny A.

2001

Improved PCR-walking for large-scale isolation of plant T-DNA borders.

Biotechniques. 2001 Mar;30(3):496-8, 502, 504. PMID: 11252785
Balzergue S, Dubreucq B, Chauvin S, Le-Clainche I, Le Boulaire F, de Rose R, Samson F, Biaudet V, Lecharny A, Cruaud C, Weissenbach J, Caboche M, Lepiniec L.
INRA, Evry, France.

Previous Members

We thank all the students, engineers, post-docs and collaborators for their works, ideas and enthusiasm during their position in the bioinformatics group.

Armisen David	PhD (EU grants) GAO Doctoral School UEVE	Oct 06 – Dec 08	Unique genes in plants : Evolution and features
Bailly Nathalie	Master professionnel Ingenierie en Génomique Fonctionnelle - Paris VII	Mar 05 - Sept 05	Bioinformatics prediction of protein-protein interactions
Balzergue Sandrine	DESS Ingenierie en Génomique Fonctionnelle - Paris 7	Apr 03 - Aug 03	Improvement of the CATdb database
Bernard Virginie	Master professionnel de Bioinformatique (EGOISt – Rouen) and PhD	Sept 04 - Jan 10	Study of promoters in Arabidopsis
Blanchet Marion	DESS Génie Physiologique et Bioinformatique - Poitiers	Feb 03 - Jul 03	Phenotypic database for Arabidopsis seed mutants
Bourgognon Aȉcha	Training period	Feb 06 - Aug 06	FLAGdb data control
Bruyère Clémence	DESS Compétences Complémentaires en Informatique - Evry CDD ANR	Apr 02 - Sept 02 Feb 06 - Mar 08	Development of interfaces for the FLAGdb++ database Grapevine genome annotation
Cauchard Audrey	Master Bioinformatics Rouen	Sept 09 – Aug 11	Analyse of coexpression clusters
Dérozier Sandra	CDD ANR	Sept 08 – Sept 10	tiling-array design, FLAGdb++ update
Duchene Sylvain	CDD Genoplante	Jun 02 - Jun 04	Integration of data and development of interfaces for the FLAGdb++ database
Filippi Ghislain	CDD Genoplante	Apr 02 - Oct 03	The GeneFarm database
Gagnot Séverine	IE2 CNRS	Nov 07 - Jul 08	CATdb and FLAGdb
Guichard Cécile	CDD Genoplante CDD ANR	Apr 02 - Oct 03 Sep 04 - Nov 04	Development of tools for comparative genomics UTILLdb
Lecharny Alain	DR2 CNRS	2000 - 2011	Team Leader, Principal investigator
Leveugle Magalie	Post-Doc trilateral	May 05 - Oct 07	Arabidopsis transcription factors (REGULATORs)
Luyten Isabelle	Master Spécialisé en Bioinformatique - Evry	Apr 02 - Oct 02	Improvement of the FLAGdb++ database
Martinez Kelly	DESS Bioinformatique pour la Génomique -Clermont-Ferrand	Apr 02 - Sept 02	Integration of structural annotations in the FLAGdb++ database
Moukthasser Sonia	DESS Informatique et Applications aux Sciences de la Vie- Paris V	Apr 04 - Sept 04	Implementation of CATdb interfaces and data export
de Oliveira Yannick	DESS Etude des Génomes, Outils Informatiques et Statistiques - Rouen CDD Genoplante	Oct 02 - Oct04 Dec 04 - May 05	Integration of PFAM motifs and protein families in the FLAGdb++ database and their exploitation Updating of FLAGdb++ data
Ory-Salam Christine	Master Compétence Complémentaire en Informatique –Evry	Mar 06 – Sept 06	Development of information system for Vitis genetic markers
Poidevin Laetitia	DESS Ressources Génomique et Traitements Informatiques - Nancy	Mar 04 - Sept 04	Integration of organit genomes in the FLAGdb++ database
Pommier Cyril	DEA Application des Mathématiques et de l'Informatique à la Biologie - Evry CDD Genoplante	Feb 03 - Jun 03 May 04 - Oct 04	Relationships between topology and gene function in Arabidopsis Improvement of the GeneFarm database.
Rogier Odile	CDD UE+CEA	Jan 09 - Oct 11	ATOMEdb and RNAseq analysis
Samson Franck	IE2 INRA (GAP) Computer Scientist	1999-2009	FLAGdb++ development
Serizet Carine	POST-DOC INRA (BV)	Oct 03 - Apr05	Study of Arabidopsis promoters at the genome scale
Zaag Rim	Master Bioinformatics Evry	Feb 11 – Jul 11	Integration of interactome data

 

Genome Organization

Comparative Genomics
Grapevine and Forest Trees Genomics

Functional Genomics

Crop Genomics
Functional Genomics of Arabidopsis

Proteomics

Phosphoproteomics
Protein Kinases

Bioinformatics

Bioinformatics for Predictive Genomics
Tools & Databases

Technology Platforms

Transcriptomic Platform
Protein Complexes Platform
Tilling Facility
Positional Cloning Facility

Group Leaders

Adam Blondon A.F.
Aubourg S.
Bendahmane A.
Chalhoub B.
Clépet C.
Faivre Rampant P.
Hirt H.
Lurin C.
Sturbois B.