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portrait de Clémentine VitteClémentine VITTE

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Maize evolutionary genomics and epigenomics

 

Contact information:
Génétique Quantitative et Évolution - Le Moulon
INRA - Université Paris-Sud - CNRS – AgroParisTech
Ferme du Moulon, F-91190 Gif-sur-Yvette
e-mail : This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Phone: + 33 1 69 33 23 57
ORCID

 

> Position and Education

CNRS researcher (CR1) Section 23, GQE-Le Moulon (Gif-sur-Yvette, France), 2013-present
CNRS researcher (CR2) Section 23, GQE-Le Moulon (Gif-sur-Yvette, France), 2008-2013
Postdoctoral fellow (Urgence FRM fellowship), Institut Jacques Monod (Paris, France), 2007
Postdoctoral fellow (Lavoisier Egide fellowship), Bennetzen laboratory (Athens, Georgia, USA), 2005-2006
PhD student (MENRT fellowship and teaching associate), ESE laboratory, Orsay (France), 2001-2004

 

> Research interests

My current research interest is to understand the interlink between genome structure and function, and how it is challenged by environmental conditions. I am particularly focusing on how structural genome variation brought by transposable elements and gene duplications shape methylome and transcriptome variation. To investigate these questions, I use maize as a model species, with particular interest for the originality of the European germplasm. I use an integrative approach combining bioinformatics analysis of massive parallel sequencing data and molecular biology. My research takes place within the French investment for the future Amaizing program, in which I lead WP3 (www.amaizing.fr).

My past work has been to investigate how LTR retrotransposons impact plant genome size and structure. I first used rice to study the evolutionary dynamics of LTR retrotransposons at the genus and species level. I then extended this work by comparing the amplification and elimination of LTR retrotransposons in five Angiosperm species with diverse genome size and from diverse phylogenetic clades. I also investigated the dynamics of LTR retrotransposon in onion and garden asparagus.

 

> PhD students and post-doctoral fellows

Zeineb Achour (PhD student: 2015-present)

Sara Castelletti (Amaizing post-doctoral fellow: 2012-1014)

Abdul Rehman-Khan (co-supervised PhD student: 2010-2013)

 

> Current collaborations

Internal: Karine Alix, Johann Joets, Maud Tenaillon (DyGAP), Alain Charcosset, Stéphane Nicolas (GQMS)

National: Catherine Giauffret (UR AgroImpact, Estrées-Mons); Olivier Turc, Claude Welcker and Francois Tardieu (LEPSE, Montpellier); Peter Rogowsky (RDP, Lyon); Sylvie Coursol (IJPB, Versailles);  Jean-Philippe Pichon, Hervé Duborjal and Magalie Leveugle (Biogemma, Clermont-Ferrand); Ludivine Soubigout-Taconnat, Véronique Brunaud, Christine Paysant-Leroux and Marie-Laure Martin-Magniette (ISP2, Gif sur Yvette); Hélène Bergès (CNRGV, Toulouse); Hélène Sellier (IE INRA Estrées-Mons), Carine Palaffre (INRA Saint Martin de Hinx).

International: Silvio Salvi (Department of Agricultural Sciences, Bologna University, Italy)

> Network animation

Member of the scientific council of the RTP "Epigenetics in Ecology and Evolution"

Member of the scientific council of GDR 2157: "Evolution of Transposable elements: from genomes to populations"

 

> Selected publications

Brandenburg J. T., Mary-Huard T., Rigaill G., Hearne S. J., Corti H., Joets J., Vitte C., Charcosset A., Nicolas S. D., Tenaillon M. I. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLoS Genet, 13 (3) e1006666. [Link]

Khan A. R., Enjalbert J., Marsollier A.-C., Rousselet A., Goldringer I., Vitte C. (2013) Vernalization treatment induces DNA site-specific hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat. BMC Plant Biology. 13:209. [Link]

Vitte C., Estep M., Leebens-Mack J., Bennetzen J. (2013) Young, intact and nested retrotransposons are abundant in the onion andasparagus genomes. Annals of Botany. doi: 10.1093/aob/mct155. [Link]

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

Liu R., Vitte C.,  Ma J., Mahama A.A., Dhliwayo T.,  Lee M., Bennetzen J.L.(2007) A GeneTrek analysis of the maize genome. Proc. Nat. Acad. Sc. U.S.A 104:11844-49. [Link]

Vitte C., Bennetzen J.L. (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. [Link]

Vitte C.,  Panaud O.(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. [Link]

 

Selected review articles and book chapters

Mirouze M., Vitte C. (2014) Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. J Exp Bot. 65(10):2801-12. [Link]

Vitte C.,  Fustier M.-A., Alix K., Tenaillon M.(2014) The bright side of transposons in crop evolution. Briefings in Functional Genomics. 13(4):276-95. [Link]

Vitte C., PetersonT.,  Bennetzen J. (2011) "Transposable elements and the evolving structure of the maize genome". In J.-L. Prioul, Advances in Maize (Taylor & Francis), the Society for Experimental Biology, London, UK. pp. 2-36.

SanMiguel P., Vitte C. (2009) "The LTR retrotransposons of maize". In J. Bennetzen and S. Hake, The Maize Handbook – Volume II: Domestication, Genetics and Genomics (Springer, ISBN 0387778624, 9780387778624), pp.307−327.

Vitte C., Panaud O. (2005) LTR retrotransposons and plant genome size: emergence of the increase/decrease model. Cytogenetics and Genome Research. 110(1-4):91-107. Article invité dans l’édition spéciale "Retrotransposons, Retrotransposition and Genome Evolution". [Link]