Exploration of plant genomes in the FLAGdb++ environment

Background : In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results : The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). Conclusion : Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features

Genome-Wide Analysis of LIM Gene Family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa

In Eukaryotes, LIM proteins act as developmental regulators in basic cellular processes such as regulating the transcription or organizing the cytoskeleton. The LIM domain protein family in plants has mainly been studied in sunflower and tobacco plants, where several of its members exhibit a specific pattern of expression in pollen. In this paper, we finely characterized in poplar six transcripts encoding these proteins. In Populus trichocarpa genome, the 12 LIM gene models identified all appear to be duplicated genes. In addition, we describe several new LIM domain proteins deduced from Arabidopsis and rice genomes, raising the number of LIM gene models to six for both species. Plant LIM genes have a core structure of four introns with highly conserved coding regions. We also identified new LIM domain proteins in several other species, and a phylogenetic analysis of plant LIM proteins reveals that they have undergone one or several duplication events during the evolution. We gathered several LIM protein members within new monophyletic groups. We propose to classify the plant LIM proteins into four groups: αLIM1, βLIM1, γLIM2, and δLIM2, subdivided according to their specificity to a taxonomic class and/or to their tissue-specific expression. Our investigation of the structure of the LIM domain proteins revealed that they contain many conserved motifs potentially involved in their function

Criblage différentiel : banques soustraites, AFLP-ADNc

National audienc

Transgenic Poplar Trees (Populus Species)

International audienc

Les biotechnologies chez les arbres forestiers

Le développement actuel des biotechnologies ouvre des potentialités importantes en matière d'amélioration génétique des arbres forestiers. Notamment, celles-ci devraient permettre de diffuser rapidement les nouvelles variétés aux performances accrues nécessaires au maintien de la compétitivité de la filière-bois. Cette revue fait le point sur les possibilités et les limitations de l'utilisation des biotechnologies chez les arbres forestiers: multiplication végétative in vitro par embryogénèse somatique et par microbouturage, transformation génétique et sélection assistée par marqueurs.The current development of biotechnologies opens up major potential in the area of genetic improvement of forest tree species. ln particular, they should enable new improved varieties that are needed to maintain competitiveness of the timber industry to be disseminated. This article reviews the possibilities and limitations of using biotechnologies for forest trees - in vitro vegetative propagation by cell embryogenesis and microcutting, genetic transformation and marker-assisted selection

Physiologie de la formation des parois de fibres de bois

National audienceThe heteroxylated wood of hardwood species is constituted of fibres, vessels and ray cells. Fibres play a prominent role in the mechanical support of the tree and in the ability of trees to reach a big size. Fibres result from cambium activity that takes place just under the bark, between phloem and xylem. The fibre cell wall is made of several layers of a cellulose microfibril network glued into a matrix of lignins and hemicelluloses. These layers widely differ according to their thickness, lignin content and cellulose microfibril orientation. The fibre cell wall can be compared to a composite material, whose properties depend on matrix composition and cellulose microfibril orientation. The wood properties largely result from variations in cell wall composition and arrangement. In this paper, we will review the state of knowledge on wood fibre formation and we will introduce functional genomics strategy currently developed on a model species, poplar, in order to increase our knowledge on wood fibre biogenesis.Les feuillus possèdent un bois hétéroxylé, de structure complexe, constitué principalement de fibres, de vaisseaux et de rayons. Les fibres jouent un rôle primordial dans le soutien mécanique de l'arbre et dans sa capacité à développer des axes de grande taille. Les fibres résultent du fonctionnement d'une assise génératrice appelée cambium et située sous l'écorce de l'arbre entre le bois et le liber. La paroi des fibres est composée de plusieurs couches, formées d'un réseau de microfibrilles de cellulose cimenté dans une matrice d'hémicelluloses et de lignines. Les couches diffèrent par leur épaisseur, leur degré de lignification et l'orientation des microfibrilles de cellulose. La paroi des fibres peut être comparée à un matériau composite dont les propriétés mécaniques varient selon la composition de la matrice et l'angle des microfibrilles de cellulose par rapport à l'axe de la fibre. Les variations de ces paramètres au niveau de la paroi sont en grande partie responsables des propriétés mécaniques du bois. Dans cette revue, nous présentons l'état des connaissances sur la formation des fibres de bois et nous introduisons les approches de génomique fonctionnelle menées chez une espèce modèle, le peuplier, afin d'approfondir les connaissances sur le sujet