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Génétique Quantitative et Évolution - Le Moulon

Clémentine VITTE

Clémentine VITTE

Chargée de Recherche, CNRS

Maize evolutionary genomics and epigenomics


01 69 33 23 57


  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • 12 route 128
  • 91190 Gif-sur-Yvette

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.

My past wor 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”


  • Hure V., Piron-Prunier F., Yehouessi T., Vitte C. , Kornienko AE., Adam G., Nordborg M., Déléris A.. (2024) Alternative silencing states of Transposable Elements in Arabidopsis. Molecular Biology,
  • Leduque B., Edera A., Vitte C. , Quadrana L.. (2024) Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing. Nucleic Acids Research, gkae306
  • Desbiez-Piat A., Ressayre A., Marchadier E., Noly A., Remoue C., Vitte C. , Belcram H., Bourgais A., Galic N., Guilloux ML., Tenaillon MI., Dillmann C.. (2023) Pervasive GxE interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics, (in press) 2023.01.13.523786
  • Moissiard G., Mirouze M., Carles CC., Vitte C. . (2023) Editorial: Plant epigenetics and chromatin dynamics - EPIPLANT 2021-2022. Front. Plant Sci., (14) 1260391
  • Fagny M., Kuijjer ML., Stam M., Joets J., Turc O., Rozière J., Pateyron S., Venon A., Vitte C. . (2021) Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Frontiers in Genetics, (11) 1703
  • Mabire C., Duarte J., Darracq A., Pirani A., Rimbert H., Madur D., Combes V., Vitte C. , Praud S., Rivière N., Joets J., Pichon JP., Nicolas SD.. (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 1 (20) 848
  • Achour Z., 2018-05-15 15/05/18, Réponse du méthylome suite à l’exposition au froid chez une espèce à génome complexe : le maïs (Zea mays ssp. mays), PhD thesis, Université Paris-Saclay
  • Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., Joets J., Vitte C. , Charcosset A.. (2018) Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions. DOI.org (Crossref), 3-12
  • Darracq A., Vitte C. , Nicolas S., Duarte J., Pichon JP., Mary-Huard T., Chevalier C., Bérard A., Le Paslier MC., Rogowsky P., Charcosset A., Joets J.. (2018) Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 1 (19) 119
  • Brandenburg JT., Mary-Huard T., Rigaill G., Hearne SJ., Corti H., Joets J., Vitte C. , Charcosset A., Nicolas SD., Tenaillon MI.. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics, 3 (13) e1006666
  • Vitte C. , Fustier MA., Alix K., Tenaillon MI.. (2014) The bright side of transposons in crop evolution. Briefings in functional genomics, 4 (13) 276-95