Genomics, Evolution and Adaptation of Domesticated plants
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UMR Génétique Quantitative et Évolution - Le Moulon (GQE - Le Moulon), CNRS UMR 8120, INRAE 0320, AgroParisTech, Université Paris-Saclay
Chemin de Moulon
91190 Gif-sur-Yvette
France
Scientific Interest
Transposable elements are major components of plant genomes and their insertions are highly polymorphic within a species. Transposable element insertions can modify the expression of neighboring genes by breaking existing cis-regulatory sequences, providing new ones, or modifying gene transcript splicing or stability. Due to their ability to insert the same sequence at many positions in the genome, transposable elements are good candidates to modulate gene regulatory networks and thus contribute to the molecular regulation underpinning phenotypic variation of polygenic traits, and local adaptation. Our team investigates the dynamics of transposable elements with respect to plant genome evolution and adaptation, as well as the impact of transposable element insertions on gene expression variation between individuals and in response to environment. We work in the context of plant domestication and use maize, brassica and apple as models to compare species within a genus or individuals within a species, collected from distinct geographical areas or grown in contrasted environments. We also pay specific attention to the impact of transposable element activity (past or present) on genome shaping and genome expression in the context of polyploidy or interspecific hybridization. To tackle these questions, we integrate genomic, epigenomic and transcriptomic data using bioinformatics, and combine them with population genomics and systems biology approaches. Understanding the extent to which transposable elements contribute to genome modeling and gene expression regulation will improve our knowledge on the molecular bases of plant adaptation and evolution.
Transposable elements are major components of plant genomes and their insertions are highly polymorphic within a species. Transposable element insertions can modify the expression of neighboring genes by breaking existing cis-regulatory sequences, providing new ones, or modifying gene transcript splicing or stability. Due to their ability to insert the same sequence at many positions in the genome, transposable elements are good candidates to modulate gene regulatory networks and thus contribute to the molecular regulation underpinning phenotypic variation of polygenic traits, and local adaptation. Our team investigates the dynamics of transposable elements with respect to plant genome evolution and adaptation, as well as the impact of transposable element insertions on gene expression variation between individuals and in response to environment. We work in the context of plant domestication and use maize, brassica and apple as models to compare species within a genus or individuals within a species, collected from distinct geographical areas or grown in contrasted environments. We also pay specific attention to the impact of transposable element activity (past or present) on genome shaping and genome expression in the context of polyploidy or interspecific hybridization. To tackle these questions, we integrate genomic, epigenomic and transcriptomic data using bioinformatics, and combine them with population genomics and systems biology approaches. Understanding the extent to which transposable elements contribute to genome modeling and gene expression regulation will improve our knowledge on the molecular bases of plant adaptation and evolution.
Thematic