1. Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine
- Author
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Claudio Moser, Pierre Coutos-Thévenot, Céline Camps, Serge Delrot, Christian Kappel, Mark Stitt, Ana Rotter, Björn Usadel, S. Pilati, Matjaž Hren, Marc Lohse, Kristina Gruden, Physiologie Moléculaire du Transport des Sucres chez les Végétaux (PhyMoTS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), and Slovenian Research Agency (Ref. Nos. 1000-05-310172, P4-0165), by the German Ministry of Research and Education (GABI-MAPMEN 0313112/ 0313110), the Fondo Unico of the Provincia Autonoma di Trento, post doc project 'Profiles' (S.P.), and from the Advanced Biology Project funded by the Fondazione delle Casse di Risparmio di Trento e Rovereto
- Subjects
0106 biological sciences ,MESH: Xylariales ,Microarray ,génomique fonctionnelle ,Plant Science ,champignon pathogène ,MESH: RNA, Plant ,01 natural sciences ,Genome ,phénylpropanoïde ,Transcriptome ,infection fongique ,Gene Expression Regulation, Plant ,lcsh:Botany ,Gene expression ,Vitis ,ontologie ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,Vegetal Biology ,Xylariales ,food and beverages ,Chromosome Mapping ,lcsh:QK1-989 ,RNA, Plant ,puce à adn ,Host-Pathogen Interactions ,expression des gènes ,Research Article ,LOGICIEL MAPMAN ,expression génique ,logiciel ,Computational biology ,Biology ,EUTYPA LATA ,MESH: Vitis ,03 medical and health sciences ,carotenoide ,MESH: Gene Expression Profiling ,vitis vinifera ,Gene mapping ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,MESH: Gene Expression Regulation, Plant ,Gene ,030304 developmental biology ,Whole genome sequencing ,terpénoïde ,business.industry ,Gene Expression Profiling ,MESH: Host-Pathogen Interactions ,fungi ,DÉFENSE DES PLANTES ,Biotechnology ,Gene expression profiling ,MESH: Oligonucleotide Array Sequence Analysis ,business ,vigne ,MESH: Chromosome Mapping ,Biologie végétale ,010606 plant biology & botany - Abstract
Background Whole genome transcriptomics analysis is a very powerful approach because it gives an overview of the activity of genes in certain cells or tissue types. However, biological interpretation of such results can be rather tedious. MapMan is a software tool that displays large datasets (e.g. gene expression data) onto diagrams of metabolic pathways or other processes and thus enables easier interpretation of results. The grapevine (Vitis vinifera) genome sequence has recently become available bringing a new dimension into associated research. Two microarray platforms were designed based on the TIGR Gene Index database and used in several physiological studies. Results To enable easy and effective visualization of those and further experiments, annotation of Vitis vinifera Gene Index (VvGI version 5) to MapMan ontology was set up. Due to specificities of grape physiology, we have created new pictorial representations focusing on three selected pathways: carotenoid pathway, terpenoid pathway and phenylpropanoid pathway, the products of these pathways being important for wine aroma, flavour and colour, as well as plant defence against pathogens. This new tool was validated on Affymetrix microarrays data obtained during berry ripening and it allowed the discovery of new aspects in process regulation. We here also present results on transcriptional profiling of grape plantlets after exposal to the fungal pathogen Eutypa lata using Operon microarrays including visualization of results with MapMan. The data show that the genes induced in infected plants, encode pathogenesis related proteins and enzymes of the flavonoid metabolism, which are well known as being responsive to fungal infection. Conclusion The extension of MapMan ontology to grapevine together with the newly constructed pictorial representations for carotenoid, terpenoid and phenylpropanoid metabolism provide an alternative approach to the analysis of grapevine gene expression experiments performed with Affymetrix or Operon microarrays. MapMan was first validated on an already published dataset and later used to obtain an overview of transcriptional changes in a susceptible grapevine – Eutypa lata interaction at the time of symptoms development, where we showed that the responsive genes belong to families known to be involved in the plant defence towards fungal infection (PR-proteins, enzymes of the phenylpropanoid pathway).
- Published
- 2009
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