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Genome structure and dynamics

TE density

TEs, genes and segmental duplication densities accross the Arabidopsis thaliana chromosome 4

The genomic sequences from numerous model species have been available for several years. Recently, genomic sequences belonging to species closely related to these model species, or several genomic sequences from the same species have become available. Many research topics are now investigated in a more global and ambitious manner.

Our work continues along this dynamic, and our projects are oriented toward the exploitation of these genomic data from a molecular level to population and inter-species levels to understand genome structure and its dynamics.

Genome structure

The systematic sequencing of the genome reveals today that repeats may represent alone an important fraction of their sequence (50% for the human genome, 90% for the wheat genome). In this context, the correct annotation of the repeats is an essential preliminary step. Hence we develop bioinformatics tools specifically designed for genome repeat detection, annotation and analysis.

These tools allow us to analyse the organization of these sequences in a genome. They appear to be very pertinent to understanding genome evolution and functioning. Indeed, TEs have long been viewed as intra-genomic parasites, they are considered today to be at the origin of many essential biological functions such as the immune system, the centromeres, the hetrochromatin and the telomerases. They are considered a key factor of genome dynamic and evolution, but also its functioning and its structure.

Genome size

Structural analysis and genome sequencing have shown that transposable elements (TE) are key components of the eukaryotic genomes. They are one of the main causes for genome size and structure evolution, along with polyploidy. They can represent up to 90% of some genomes (e.g. wheat). TE are often responsible for the large size differences observed between genomes.

The characterization of TE amplification and their subsequent elimination of the genomes is therefore a major goal in evolutionary genomics. To address the extent and timing of these forces, we perform a detailed analysis of TE families in genomes. Our efficient repeat annotation pipeline and the analysis of their distribution within genomes, along chromosomes allow us to explore their impact on this dynamic. This allows us to better understand the role of TEs in genome structure and evolution.

Heterochromatin and epigenetic

TEs are a major component of heterochromatin and may play a functional role. We perform a functional annotation of TE expression in order to identify TEs that could generate transcripts involved in the RNAi process, known to repress gene expression but also induce heterochromatin formation.

Update: 21 Jun 2010
Creation date: 23 Dec 2009