FrancaisEnglish (United Kingdom)
 

Responsable de publication :
Olivier Martin

Responsable éditoriale :
Rozenn Le Guyader

Administrateur de l'infoservice :
Thierry Balliau

portrait Johann JoetsJohann JOETS

____________________________________

Maize evolutionary genomics and bioinformatics


Génétique Quantitative et Évolution - Le Moulon
INRA - Université Paris-Sud - CNRS – AgroParisTech
e-mail : Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir.
Phone: + 33 1 69 33 23 78

 

> 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

 

> Research interests

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)

 

> Current collaborations

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).

 

> 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

Ressayre A, Glémin S, Montalent P, Serre-Giardi L, Dillmann C, Joets J. (2015) Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes. Genome Biol Evol, 7;7(10):2913-28.

Sarilar V, Palacios PM, Rousselet A, Ridel C, Falque M, Eber F, Chèvre AM, Joets J, Brabant P, Alix K. (2013) Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. New Phytol, 198 (2):593-604.

Sosnowski O, Charcosset A, Joets J. (2012) BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. Bioinformatics, 28(15):2082-3.

Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M. (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One, 6(12):e28334.

Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjärd A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martínez-Bartolomé S, Albar JP, Echevarría-Zomeño S, Martínez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR (2009) Minimum Information About a Proteomics Experiment (MIAPE) Guidelines for reporting the use of gel image informatics in proteomics. Nat Biotechnol, 28(7):655-6.

Zerjal T, Joets J, Alix K, Grandbastien MA, Tenaillon MI. (2009 ) Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Mol Biol, 71(1-2):99-114.

Alix K, Joets J, Ryder CD, Moore J, Barker GC, Bailey JP, King GJ, Pat Heslop-Harrison JS. (2008) The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. Plant J, 56(6):1030-44. doi: 10.1111/j.1365-313X.2008.03660.x. PubMed PMID: 18764926.

> Selected book chapters

Johann Joets, Clémentine Vitte, Shiran Pasternak and Doreen Ware (2011) "Deciphering the multifaceted aspects of the maize genome: new insights from sequencing projects". In J.-L. Prioul, Advances in Maize (Taylor & Francis), the Society for Experimental Biology, London, UK. pp. 2-36.

Langella O, Zivy M, Joets J. (2007) The PROTICdb database for 2-DE proteomics. Methods Mol Biol, 355:279-303.