Johann JOETS

Maize evolutionary genomics and bioinformatics

 INRAE, Ingénieur de Recherche

 johann.joets@inrae.fr —   01 69 33 23 78


 Génomique Evolutive et Adaptation des plantes Domestiquées
 Atelier de Bioinformatique et Informatique

Implication de Johann Joets dans axe1 80% axe1 Comprendre et éclairer les mécanismes de l'évolution Axe1 Implication de Johann Joets dans axe2 20% axe2 Comprendre et prédire les bases génétiques des interactions Axe2 Implication de Johann Joets dans axe3 0% axe3 Comprendre et mobiliser la diversitée cultivée pour répondre aux attentes des acteurs Axe3
 Publications    

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

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).

Publications

  • Speck A., Trouvé JP., Enjalbert J., Geffroy V., Joets J. , Moreau L.. (2022) Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.). Front. Plant Sci., (13) 871633
  • 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
  • Cuello, C., Baldy, A., Brunaud, V., Joets, J., Jacquemot, M.P., Coursol, S.. (2019) A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PlosOne, 12 (14) e0227011
  • 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
  • Adenot P., Bansard S., Benaben D., Brunaud V., Caron C., Dehne Garcia A., Duperier C., Falce A., Filangi O., Giacomoni F., Granier F., Grevet P., Guilhot N., Hofstetter A., Joets J. , Hotelier T., Langella O., Legrand L., LOAEC M., Lollier V., Moreau P., Morin E., Quesneville H., Rabemanantsoa T., Salin G., Tessier D.. (2018) AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée. Cahier des Techniques de l'INRA, 1-7
  • 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
  • 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
  • Ressayre A., Glemin 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 biology and evolution, 10 (7) 2913-28
  • Langella O., Valot B., Jacob D., Balliau T., Flores R., Hoogland C., Joets J. , Zivy M.. (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, 9 (13) 1457-66
  • Sarilar V., Martinez-Palacios P., Rousselet A., Ridel C., Falque M., Eber F., Chevre 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. The New phytologist, 2 (198) 593-604
  • 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., Lukens L.. (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, 12 (6) e28334
  • Sarilar V., Marmagne A., Brabant P., Joets J. , Alix K.. (2011) BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space. Plant molecular biology, 1-2 (77) 59-75
  • Albertin W., Langella O., Joets J. , Negroni L., Zivy M., Damerval C., Thiellement H.. (2009) Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus. Proteomics, 3 (9) 793-9
  • 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 molecular biology, 1-2 (71) 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. The Plant journal : for cell and molecular biology, 6 (56) 1030-44