last updated 04/01/2023
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Genomics, Evolution and Adaptation of Domesticated plants
publications - orcid
Position and Education
- INRA research engineer (IR1), GQE-Le Moulon (Gif-sur-Yvette, France), 2000-present
- Postdoctoral fellow (CNRS/Hoechst Marion Roussel), Centre de Génétique Moléculaire (Gif-sur-Yvette, France), 1999-2000
- PhD student (MENRT fellowship), IBMIG laboratory, Poitiers University, (Poitiers, France), 1996-1999
My research interest is to understand the molecular mechanisms and evolutionary forces that generate and maintain structural variants in plant genomes, and to what extent they contribute to plant adaptation. Using maize as a model species, I am particularly interested in Presence/Absence variants and how they shape maize pan-genome structure. For this, I use and develop bioinformatics approaches to analyze massive parallel sequencing data and genome sequence assemblies. My research takes place within the French investment for the future Amaizing program , in which I lead WP2 and Task 3.1.
For a part of my time, I lead the Biological Sequence Analysis facility group that offers support in bioinformatics to other GQE groups.
In the past years (2008-2016), I was the head of the GQE Bioinformatics facility (ABI).
This facility had in charge management of local high-performance compute resources, data management, database development and development of data analysis and visualization software for genetics and genomics. The group included up to six permanent staff as well as several students and non-permanent engineers.
There, I initiated and led the development of the software BioMercator (ANR program ANR-08-GENM-004) and the PROTICdb database (ANR PROTICws).
I have been involved in massive parallel sequence data analysis since 2010, and decided to start my own research program in this area in 2016 and joined the DyGAP team . To focus my activities in biological sequence analyses, I kept the lead of biological sequence data management and analysis and passed over database management, software development and management of shared computer resources, thus leading to a split of the ABI facility into 3 groups.
PhD students and post-doctoral fellow
- Paulina Martinez Palacios (PhD student : 2010-2014 / coll. Karine Alix, UMR GQE-Le Moulon)
- Aude Darracq (Amaizing post-doctoral fellow: 2012-1013)
- Véronique Sarilar (PhD student: 2009-2011 / coll. Philippe Brabant, Karine Alix, UMR GQE-Le Moulon)
Internal: Clémentine Vitte, Karine Alix, Maud Tenaillon (DyGAP), Alain Charcosset, Stéphane Nicolas, Tristan Mary-Huard (GQMS), Delphine Steinbach (ABI).
National: Sylvie Coursol (IJPB, Versailles), Jean-Philippe Pichon, Jorge Duarte, Frédéric Sapet (Biogemma, Clermont-Ferrand), Cyrille Pommier (URGI, Versailles), Hélène Bergès (CNRGV, Toulouse,) Ludivine Soubigout-Taconnat, Véronique Brunaud, Christine Paysant-Leroux, Marie-Laure Martin-Magniette (ISP2, Gif sur Yvette); Olivier Turc, Claude Welcker and François Tardieu (LEPSE, Montpellier); Peter Rogowsky (RDP, Lyon), Marie-Christine Lepaslier (EPGV, Evry).
International: Ed Buckler (Buckler Lab for Maize Genetics and Diversity, USDA, Cornell University, Ithaca, USA), Silvio Salvi (Department of Agricultural Sciences, Bologna University, Italy).
- Deveaux Y., Conde e Silva N., Manicacci D., Le Guilloux M., Brunaud V., Belcram H., Joets J. , Soubigou-Taconnat L., Delannoy E., Corti H., Balzergue S., Caius J., Nadot S., Damerval C.. (2021) Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L.. Front. Plant Sci., (12) 660803
- 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
- Damerval C., Citerne H., Conde E Silva N., Deveaux Y., Delannoy E., Joets J. , Simonnet F., Staedler Y., Schönenberger J., Yansouni J., Le Guilloux M., Sauquet H., Nadot S.. (2019) Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. Front Plant Sci, (10) 18
- 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
- Martinez Palacios P., Jacquemot MP., Tapie M., Rousselet A., Diop M., Remoué C., Falque M., Lloyd A., Jenczewski E., Lassalle G., Chévre AM., Lelandais C., Crespi M., Brabant P., Joets J. , Alix K.. (2019) Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids. Mol Biol Evol, 4 (36) 709-726
- Richard MMS., Gratias A., Thareau V., Kim KD., Balzergue S., Joets J. , Jackson SA., Geffroy V.. (2018) Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family. DNA Res, 2 (25) 161-172
- 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