An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato.

Virginie Garcia, Rebecca Stevens, Laurent Gil, Louise Gilbert, Noé Gest, Johann Petit, Mireille Faurobert, Mickael Maucourt, Catherine Deborde, Annick Moing, Jean-Luc Poessel, Daniel Jacob, Jean-Paul Bouchet, Jean-Luc Giraudel, Barbara Gouble, David Page, Moftah Alhagdow, Capucine Massot, Hélène Gautier, Martine Lemaire-Chamley, Antoine de Daruvar, Dominique Rolin, Bjoern Usadel, Marc Lahaye, Mathilde Causse, Pierre Baldet, Christophe Rothan

Index: C R Biol. 332(11) , 1007-21, (2009)

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Abstract

Very few reports have studied the interactions between ascorbate and fruit metabolism. In order to get insights into the complex relationships between ascorbate biosynthesis/recycling and other metabolic pathways in the fruit, we undertook a fruit systems biology approach. To this end, we have produced tomato transgenic lines altered in ascorbate content and redox ratio by RNAi-targeting several key enzymes involved in ascorbate biosynthesis (2 enzymes) and recycling (2 enzymes). In the VTC (ViTamin C) Fruit project, we then generated phenotypic and genomic (transcriptome, proteome, metabolome) data from wild type and mutant tomato fruit at two stages of fruit development, and developed or implemented statistical and bioinformatic tools as a web application (named VTC Tool box) necessary to store, analyse and integrate experimental data in tomato. By using Kohonen's self-organizing maps (SOMs) to cluster the biological data, pair-wise Pearson correlation analyses and simultaneous visualization of transcript/protein and metabolites (MapMan), this approach allowed us to uncover major relationships between ascorbate and other metabolic pathways.