Into the Genomes.....

Over the past 20 years, the development of new and efficient methods for sequencing DNA has lead to the publication and availability of thousand of genome sequences of species from all kingdoms. Never in the history of sciences has a field undergone such boost at both conceptual and technological levels. Genomicists are now facing the challenge of analyzing huge and ever increasing amount of DNA (or RNA) sequences data in order to contribute to our understanding of the basic mechanisms of Life, which could eventually translate into better health and reinforced food security.

Humm...not that we, genomicists, do not believe that our research will ultimately help address some of the societal issues raised by the rapid changes of our environments, but we would all agree that genome sequences remain only the first and very preliminary step towards the full understanding of the nature and the function of the ~30,000 genes that carry the information necessary to build a plant or an animal.

For instance, one of the major discovery in the field of genomics is that genes are in fact a minor componernt of most genomes. Transposable elements (TEs), defined as mobile DNA sequences, often outnumber genes in eukaryotic genomes. Their propensity to survive and litterally invade some genomes raises the question of their biological impact (and eventually their biological function). In any case, the study of any organism at the genomic scale should obviously include TEs, which is the scope of our research activities :

We are developing research projects for studying the impact of TEs on the structure, the evolution and the function of plant genomes. Our main model of study is the genus Oryza, to which cultivated rice (O. sativa and O. glaberrima) belongs. This genus comprises 12 species for which genomic ressources have been made available through an international consortium (iOMAP) in which we take part. The availability of the genome sequence of all these species will provide the opportunity to study the impact of TEs on genome evolution over a time span of 25 million years with an unprecedented high resolution.

We are also studying the impact of TEs on much shorter evolutionary scale (within species and even within individuals, for instance in response to abiotic stress). For this, we have developed new tools based on Next Generation Sequencing (NGS) technologies for the genome-wide characterization of transpositional landscape.

We are involved in studying the functional impact of TEs in rice. We first developed a transcriptomic strategy to study the functional relationships between genes and TEs in various stress.

Finally, the group has been involved in TE annotation in several genome sequencing projects, such as Rice, cocoa, banana, millet, the picoplactons Ostreococcus and Micromonas and the algeae Ectocarpus.

The Panaud lab is located at the University of Perpignan, France and is one of the teams of the Laboratoire Génome et Développement des Plantes, UMR 5096, CNRS/UPVD