Caractéristiques du génome des conifères

Table des matières

Résumé
Abstract
Table des matières
Liste des tableaux
Liste de figures
Remerciements
Avant-propos
Liste des abréviations
Chapitre 1.Mécanismes physiques de solidification magmatique
1.1 Origine et importance économique et écologique des conifères
1.2 Biologie et caractéristique unique des arbres et des conifères
1.2.1 Différentiation tissulaire et formation du bois
1.2.2 Stratégies d’adaptation
1.3 Caractéristiques du génome des conifères
1.4 Méthodes de profilage transcriptionnel
1.5 Profilage transcriptionnel chez les conifères
1.5.1 Formation du bois
1.5.2 Stratégies d’adaptation
1.5.3 Autres études chez des conifères
1.6 Mise en contexte du projet
1.7 Objectifs
1.8 Références bibliographiques
Chapitre 2. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression
2.1 Résumé
2.1.1 Contexte
2.1.2 Résultats
2.1.3 Conclusion
2.2 Abstract
2.2.1 Background
2.2.2 Results
2.2.3 Conclusion
2.3 Background
2.4 Results and Discussion
2.4.1 Development of an oligonucleotide microarray for spruces (Picea spp.)
2.4.2 Differential expression in the vascular transcriptome is conserved among Picea species.
2.4.3 Validation of the microarray and profiling results by RNA-Sequencing.
2.4.4 PiceaGenExpress contains reference profiles that reveal patterns of tissue preferential expression.
2.4.5 Non-annotated genes are expressed at low levels and in fewer tissues
2.4.6 Diversity of expression profiles varies within and among gene families with related functions
2.4.7 Expression of LTR retrotransposon sequences
2.5 Conclusions
2.6 Methods
2.6.1 Evaluation of array design and manufacture parameters with test oligonucleotide microarray
2.6.2 Microarray design and manufacture
2.6.3 Plant materials
2.6.4 RNA extraction, labelling and hybridization
2.6.5 Microarray data processing and analysis
2.6.6 The PiceaGenExpress database
2.6.7 RNA-Seq data processing and analysis
2.7 Acknowledgments
2.8 References
2.9 Additional files
Chapitre 3 Modular organization of the white spruce (Picea glauca (Moench) Voss) transcriptome reveals functional organization and evolutionary signatures
3.1 Résumé
3.2 Abstract
3.3 Introduction
3.4 Materials and methods
3.4.1 Plant material
3.4.2 RNA isolation, labelling and hybridization
3.4.3 Microarray pre-processing and statistical analyses
3.4.4 Functional annotation analysis
3.4.5 Reverse transcription quantitative PCR (RT-qPCR)
3.5 Results
3.5.1 The expression of most white spruce genes vary significantly across vegetative tissues
3.5.2 The white spruce transcriptome is organized into coexpression groups classifying tissues based on their types or physiological functions
3.5.3 Gene ontology term enrichments show functional diversity among coexpression groups
3.5.4 Conifer-specific genes are more strongly associated with secondary meristematic tissues
3.5.5 Highly conserved invariant genes are associated with high expression and cell basic functions
3.5.6 Expressional and functional diversity among conserved secondary xylem and phelloderm preferential genes
3.5.7 Distinct expression patterns characterize wood formation at different stages during a growth season
3.5.8 Variation in secondary cell wall regulatory network hub genes is associated with xylem transcriptome reorganization during the growth season
3.6 Discussion
3.6.1 Evolutionary signatures of tissue differentiation
3.6.2 Modular transcriptome organization underpins tissue differentiation
3.6.3 Coexpression is associated with functional similarity
3.6.4 Temporal reorganization of gene expression networks in the vascular transcriptome
3.7 Concluding remarks
3.8 Acknowledgements
3.9 References
3.10 Supporting information
Chapitre 4.
4.1 Discussion des résultats majeurs
4.1.1 La première puce à oligonucléotide
4.1.2 Étude sur plusieurs tissus: construction d’une base de données d’expression
4.1.3 Étude sur plusieurs tissus: organisation du transcriptome et réseaux transcriptionnels
4.1.4 Conservation de profil d’expression
4.2 Études complémentaires
4.2.1 L’approche RNA-seq pour les études complémentaires
4.2.2 Des questions pour les études complémentaires
4.3 Retombées pratiques et enjeux forestiers
4.4 Références bibliographiques