Date : 26/3/2010

Laboratory

Research Unit in Genomic Info INRA/ UR1164
INRA - Centre de recherches de Versailles, Route de St Cyr 78026 Versailles
Director : Hadi Quesneville

PhD Supervisor

Hadi Quesneville
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone : +33 130833110

Subjects / Tools-Methodologies

1 : Transposable elements/Bioinformatics
2 : Genomics/Statistics
3 : Evolution/Computer science

Summary of lab's interests

The URGI develops and maintains an information system for plant and pest genomics through the development of national or international collaborative projects involving biologists and bioinformaticians. This information system called GnpIS enables scientists to mine genomic and genetic data, to extract valuable information on genes of agronomical interest, but also to acquire a better understanding of genome structure and evolution. The main strength of the unit resides in the complementary skills of its staff members. They cover from software and database design to bioanalysis skills, allowing to develop high quality tools and to use them for relevant data mining. 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 answer questions about genome evolution..

Summary of project

The thesis goal is to acquire a better understanding of genome structure, evolution and functioning. The bioinformatic tools we have developed allow to analyse the organization of repeated sequences in a genome. They appear to be very pertinent to understand genome evolution and functioning. Indeed, TEs are considered as a key factor of genome dynamic and evolution, but also its functioning and its structure.

The genome sequences of Arabidopsis thaliana and Arabidopsis lyrata are available. One of the key advantages of A. thaliana as a model organism is the wealth of information about this organism and its strong research community. As part of their effort, a "1001 genomes" project has been launched to sequence at least 1001 Arabidopsis thaliana plants from around the world (http://1001genomes.org). The 1000 genomes to be sequenced will correspond to 10 individual plants from 10 Arabidopsis populations from 10 regions across Europe and Asia. In addition, the researchers will sequence at least one line originating from North Africa. The project is well under way and has already released 8 genome sequences, 88 more genomes are in progress and the rest are planned.
Our group will utilize our experience of studying transposable element sequences of Arabidopsis and rice, as well as the comparative analysis of the genomes of Drosophila species, to compare the Arabidopsis thaliana populations, and Arabidopsis lyrata genomes. A. lyrata diverged from A. thaliana around 4-5 million years ago and this analysis will provide valuable information on the basis of the larger genome size of Arabidopsis lyrata compared to A. thaliana and of differences in genome structure. Indeed, 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 plant genome size and structure evolution, along with polyploidy. TEs are mainly responsible for the large size differences observed between plant genomes. They play a central role in the dynamics of eukaryotic genomes.

The characterization of TE amplification and their subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we will perform a detailed analysis of TE families in these Arabidopsis genomes, estimating ages of TE families and rates of eliminations at intra-specific and inter-specific time scales. This will allow for a better understanding of the role of TEs in genome structure, function and evolution.