Clémentine Vitte

Evolutionary genetics and genomics

Transposable elements and plant genome evolution

CNRS researcher, Dept. Plant Genetics

Contact information:

Station de Génétique Végétale

Ferme du Moulon

91190 Gif-sur-Yvette, France

Phone: + 33 1 69 33 23 77

Fax: + 33 1 69 33 23 40

vitte at moulon.inra.fr

Research interests

My main research interest is to understand how transposable elements contribute to plant genome structure and evolution, and how they impact plant adaptation. I mainly focus on LTR retrotransposons, which are the most abundant transposable elements in plant genomes. I investigate this topic using an approach combining bench work and genome sequence analyses.

Most of my past work has been to investigate how LTR retrotransposons impact plant genome size. First, using Asian rice (Oryza sativa, L.) as a model, I have analyzed the evolutionary dynamics of several LTR retrotransposons at the genus and species level, addressing questions related to the extent and timing of LTR retrotransposon amplification and elimination from the genome. Sequence analysis of the Nipponbare genome has greatly helped us decipher the processes involved in these two forces: burst-like events of retrotransposition for amplification, and formation of solo LTRs and the accumulation of small deletions for elimination. Analysis of relative strength and timing of these processes revealed that the current size of the rice genome is the result of both counteracting forces.

The analysis of a single genome was however insufficient to decipher whether these forces were responsible for the large variation of genome size observed in Angiosperms. Therefore, I then compared the amplification and elimination of LTR retrotransposon in five different species with diverse genome size and from diverse phylogenetic clades, using BAC sequence analysis. This work revealed that although the processes observed in rice are also responsible for the amplification and elimination of LTR retrotransposon sequences in all species analyzed, their propensity varies among species in a way that follows neither phylogeny nor genome size.

In parallel to this topic, I have also developed DNA markers based on LTR retrotransposon insertions to investigate the origin of rice domestication, and to map maize BACs devoid of genes. I have also participated in estimating the content and structure of the maize genome using a random BAC sequencing approach, and to the annotation of transposable elements in Asparagales.

I recently joined the GEAR team, where I am developing several projects related to transposable elements and genome structure, using maize as a model species.

Current and past years collaborators on these projects include:

Members of the GEAR research group (D. Manicacci, M. Tenaillon, K. Alix-Jenczewski, C. Damerval)

Other members of the department (M. Falque, J. Joets and A. Charcosset)

Abroad researchers: J. Bennetzen (UGA, USA), J. Leebens-Mack (UGA, USA)

Publications

Research articles

C. Vitte, O. Panaud, H. Quesneville. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. (2007) BMC Genomics 8:218. [Pubmed link]

R. Liu*, C. Vitte*, J. Ma, A.A. Mahama, T. Dhliwayo, M. Lee, J.L. Bennetzen (2007). A GeneTrek analysis of the maize genome. Proc. Nat. Acad. Sc. U.S.A 104:11844-49. * The two authors contributed equally to this work [Pubmed link]

C. Vitte, C. Chaparro, H. Quesneville, O. Panaud (2007). Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8. Plant Science, 172(1):8-19. [Science direct link]

C. Vitte, J.L. Bennetzen (2006). Analysis of Retrotransposon Structural Diversity Uncovers Properties and Propensities in Angiosperm Genome Evolution. Proc. Nat. Acad. Sc. U.S.A. 103(47):17638-43. [Pubmed link]

C. Vitte, T. Ishii, F. Lamy, D.S. Brar and O. Panaud (2004). Genomic paleontology provides evidence for two distinct origins of asian rice (Oryza sativa, L.). Mol. Gen. Genomics. 272(5):504-11. [Pubmed link]

C. Vitte, O. Panaud (2003). Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20(4):528-40. [Pubmed link]

O. Panaud, C. Vitte, J. Hivert, S. Muzlak, J.D. Talag, D.S. Brar and A. Sarr (2002). Genomic differentiation between rice (Oryza sativa L.) and foxtail millet (Setaria italica L. Beauv.) revealed through representational difference analysis. Mol. Gen. Genomics. 268(1):113-21. [Pubmed link]

D.A. Filatov, V. Laporte, C. Vitte and D. Charlesworth (2001). DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica. Mol. Biol. Evol. 18(8):1442-54. [Pubmed link]

Review articles and book chapters

P. SanMiguel, C. Vitte (2009). The LTR retrotransposons of maize. Book chapter of The Maize Handbook – Volume II: Domestication, Genetics and Genomics (Springer)

C. Vitte and O. Panaud (2005). LTR retrotransposons and plant genome size: emergence of the increase/decrease model. Cytogenetics and Genome Research. 110(1-4):91-107. Invited article in the special edition « Retrotransposons, Retrotransposition and Genome Evolution ». [Pubmed link]

Pictures from IRRI, Philippines

Pictures from UGA, USA