Genome analysis and evolution

Responsibles : Marie MIROUZE(CR IRD) & Olivier PANAUD (PREX UPVD, IUF)

The research activities of the group mostly concern the structure, evolution and function of the genomes of wild and cultivated species from the Oryza (rice) genus, particularly the impact of Transposable Elements (TEs) and genome duplication. Our previous studies, focusing on LTR- retrotransposons, led us to propose a model for plant genome evolution (Vitte and Panaud, 2005) in which two counteracting forces, expansion by addition of new copies (Piegu et al., 2006) and contraction through recombination or deletion (Vitte et al., 2007, Vitte and Panaud, 2003), are responsible for variation in genome size. We participated in annotation of LTR-retrotransposons in the rice genome in the Rice Annotation Project (RAP3) and have created a database of the rice LTR-retrotransposons, available at www.retroryza.org (Chaparro et al., 2007). Our current projects concern functional aspects of TEs in the rice genome as well as the use of Next Generation Sequencing techniques to understand short-term genome dynamics by analysis of TE mobility in rice (Sabot, Picault et al., 2011).

The importance of genome duplication was highlighted by analysis of the model genome species, Arabidopsis thaliana and Oryza sativa. Several mechanisms implicated in genome evolution after duplication (large-scale rearrangement (Blanc et al. 2000), diploidization, nested chromosome fusion (Salse et al. 2008) and TE activity) have been characterized. We recently described the importance of large-scale and recurrent gene conversion in the evolution of species from the Oryza genus (Jacquemin et al. 2009). Future work concerns the application of specific tools to elucidate common and specific mechanisms implicated in animal and plant genome evolution.

The team also contributes expertise in genome sequencing, annotation and analysis to collaborative projects on "WG" proteins implicated in polymerase V-associated gene silencing in Arabidopsis (Lagrange team, LGDP, Karlowski et al. 2010) and the evolution of picoalgae and their viruses (with the "Evolutive and Environmental Genomics of Phytoplankton" lab in Banyuls sur Mer (Moreau et al. 2010). Furthermore, we have been involved in annotation of TEs in a number of eukaryotic genomes like maize (Schnable et al., 2009), Cocoa (Argout et al., 2010) and the two picoplankton organisms Ostreococcus (Derelle et al., 2006) and Micromonas (Worden et al., 2009).

Team :

BERTRAND Joris - Maître de conférences UPVD

CARPENTIER Marie-Christine - Ingénieur d'étude CNRS

CLEMENT Lauren - Doctorante

EL BAIDOURI Moaine - Chercheur CNRS

GIBERT Anaïs - CDD IR UPVD

HINOUX Valérie - Maître de conférences UPVD

LASSERRE Eric - Maître de conférences UPVD

LLAURO Christel - Assistant ingénieur CNRS

MARIAULT Lee - Doctorant

MIROUZE Marie - Chercheur IRD

PANAUD Olivier - Professeur UPVD

SALVADO Pascaline - Doctorante

SOUNDIRAMOURTTY Abirami - Doctorante

VANDENABEELE Lucas - Doctorant

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