My interests include evolution of the plant genome with a particular focus on interspecific hybridization and polyploidy, and dynamics of transposable elements (TEs) as well as their epigenetic control by small non coding RNAs.

TEs account for most nuclear DNA in higher plants and might be a source of genetic variability, because they replicate and reinsert at multiple sites in the genome and may act as mutagenic agents. Moreover, TEs are activated under stress conditions and thus contribute to genome adaptation. Polyploidization which consists in the reuniting of two (or more) genomes in a common nucleus after long periods of divergence can be considered as a state of genome stress that could precipitate the activation of TEs. Assuming that nearly all angiosperms have experienced at least one episode of polyploidization during their evolution, the question of how TEs can be involved in the formation of a polyploid species is a major task. 

Brassica is an agriculturally important genus that provides a wide range of diploid and allotetraploid species, and is particularly appropriate for studying the evolution of TEs during speciation and polyploidization.
    Part of my research project is dedicated to the analysis of the impact of a recent polyploidization event on the activation of TEs by studying the evolution of Brassica -specific TE families (retrotransposons, MITEs, CACTA elements) in newly synthesized Brassica napus lines. The activation of TEs is surveyed at both the structural and functional levels, using a combination of molecular and bioinformatic approaches. This represented part of Véronique Sarilar's PhD project (2008-2011).
    Another part of my project deals with the role of small non coding RNAs in regulating the neo-allopolyploid Brassica genome during its formation. We specifically focus our analysis on the role of snRNAs in controlling non-coding components of the genome (including TEs). Paulina Martinez Palacios' PhD work was dedicated to the global analysis of the mobilisation of snRNAs following allopolyploidization in the newly synthesized B. napus lines (2010-2014).
    Finally, I am interested in the proteomic and molecular characterization of gene expression and its regulation following a recent allopolyploidy event: comparative proteomics is performed on early (S0-S1) and more advanded (S5) generations of the same newly synthesized B. napus lines to identify modifications of gene regulation occuring at the protein level.  Anne Marmagne was involved in this project during her postdoc (2006-2008).

In relation with my interest in interspecific hybridization as a major process in plant evolution, I also collaborate with Yves Vigouroux, Dynadiv - IRD Montpellier, in supervising Roland Akakpo's PhD project (ED 'Sciences du Végétal : du gène à l'écosystème', Université Paris-Sud, Orsay). Our main objective is there to clarify the genetic relationships between three Dioscorea species, with D. abyssinica and D. praehensilis considered as the progenitors of the cultivated yam species D. rotundata. At GQE-Le Moulon, and in collaboration with Florian Maumus and Hadi Quesneville, URGI - INRA Versailles, we analyse the diversity and organisation of TEs among the three species, by exploiting NGS data; our objective is to identify TE families at the origins of genome differentiation between the three species.         

Positions and Education

• 2013: HDR defense, Université Paris-Sud.  « Allopolyploïdie et éléments transposables : contribution à l'étude de la dynamique évolutive du génome des Brassica » / «  Allopolyploidy and transposable elements: contribution to the study of the evolutionary dynamics of the Brassica genome »

• 2005-present: Maître de Conférences (Associate Professor) in the Department of Life Science and Health, at AgroParisTech, Paris; research conducted in the laboratory 'Dynamique du Génome et Adaptation des Plantes cultivées' (DyGAP), UMR Génétique Quantitative et Evolution - Le Moulon (GQE-Le Moulon), Gif-sur-Yvette, France

• Transposable elements and evolution of the Brassica genome
• Allopolyploidization and activation of TEs: structural and functional analysis of newly synthesized B.  napus allotetraploids (Véronique Sarilar, PhD student / coll. Philippe Brabant, Johann Joets - UMR GQE-Le Moulon)
• Role of Brassica transposable elements in shaping the Brassica genome and gene content (coll. Pat Heslop-Harrison - University of Leicester, UK)

• Role of micro RNAs and other small non-coding RNAs in regulation of gene expression and activation of non-coding sequences in Brassica neo-polyploids (Paulina Martinez Palacios, PhD student; Ai My Luong, Master 2 student /coll: Johann Joets, Matthieu Falque - UMR GQE-Le Moulon; Martin Crespi and Christine Lelandais - IPS2, Gif-sur-Yvette; Erwin Van Dijk and Claude Thermes - I2BC, Gif-sur-Yvette; Anne-Marie Chèvre - IGEPP, INRA Rennes). Specific annotation of Brassica microRNAs is undertaken thanks to a collaboration with Hélène Touzet, CRIStAL, Lille Nord Europe.

• Deciphering the molecular mechanisms responsible for regulation of gene expression in Brassica polyploids by comparative proteomics and transcriptomics (coll. Catherine Damerval, Philippe Brabant - UMR GQE-Le Moulon; Anne Marmagne - IJPB, INRA Versailles; Anne-Marie Chèvre - IGEPP, INRA Rennes)
  
  
• 2003-2004: Postdoctoral position, UMR Amélioration des Plantes et Biotechnologies Végétales , INRA-Agrocampus Rennes - M. Manzanares-Dauleux
  Molecular and functional characterization of genetic components of resistance to clubroot ( Plasmodiophora brassicae ) in Arabidopsis thaliana and Brassica napus
  Alix K. , Lariagon C., Delourme R., Manzanares-Dauleux M.J. 2007. Exploiting natural genetic diversity and mutant resources of Arabidopsis thaliana to study the A. thaliana - Plasmodiophora brassicae interaction. Plant Breeding 126: 218-221 .
  
  
• 2002: Temporary position,  UMR Amélioration des Plantes et Biotechnologies Végétales , INRA-Agrocampus Rennes - A.-M. Chèvre
  
  • Monitoring introgression of resistance to blackleg in Brassica napus from the B genome of mustards using  genomic in situ hybridisation (GISH)
  • Analysis of the genomic constitution of oilseed rape - wild radish hybrids by GISH in a context of gene flow assessment
    
    
• 2001: Postdoctoral fellow (OECD) in Pat Heslop-Harrison's lab , Department of Biology, Univ. Leicester, Leicester /United Kingdom
  The diversity of retrotransposons in Brassica : understanding their phylogeny and evolution
  
  
• 1999-2000: Postdoctoral position, UMR Diversité et Génome des Plantes Cultivées, INRA-Montpellier - P. Roumet, J. David
• Implication of peroxidases in clearness of pasta: development of S-SAP markers in durum wheat
• Role of the Ph1 gene in the intergenomic recombination rate in Triticum durum × Aegilops ovata amphiploids
  Benavente E., Alix K. , Dusautoir J.-C., Orellana J. and David J.L. 2001. Early evolution of the chromosomal structure of Triticum turgidum - Aegilops ovata amphiploids carrying and lacking the Ph1 gene. Theoretical and Applied Genetics 103: 1123-1128.
  
  
• 1995-1998: PhD student, Agetrop, CIRAD, Montpellier - J.-C. Glaszmann, A. D'Hont
  The repetitive sequences of sugarcane: genome-specificities and phylogeny of the Saccharum complex
  1. Alix K., Paulet F., Glaszmann J.-C. and D’Hont A. 1999. Inter-Alu-like species-specific sequences in the Saccharum complex. Theoretical and Applied Genetics 99: 962-968. 
  2. Alix K., Baurens F.-C., Paulet F., Glaszmann J.-C. and D’Hont A. 1998. Isolation and characterization of a satellite DNA family in the Saccharum complex. Genome 41: 854-864.
  3. D’Hont A., Ison D., Alix K., Roux C. and Glaszmann J.-C. 1998. Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41: 221-225.

Selected Publications

1. Vitte C., Fustier M.-A., Alix K. and Tenaillon M. 2014. The bright side of transposons in crop evolution. Briefings in Functional Genomics 13: 276-295.
2. Sarilar V., Martinez Palacios P., Rousselet A., Ridel C., Falque M., Eber F., Chèvre A.-M., 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 Phytologist 198: 593-604.
3. Jenczewski E., Chèvre A.-M. and Alix K. 2013. Chromosomal and gene expression changes in Brassica allopolyploids. In: Polyploid and Hybrid Genomics. Z.J. Chen and J.A. Birchler (Eds). John Wiley & Sons, Inc., Oxford, UK.  
4. 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 77: 59-75. 
5. Marmagne A., Brabant P., Thiellement H. and Alix K. 2010. Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytologist 186: 216-227.
6. Parisod C., Alix K., Just J., Petit M., Sarilar V., Mhiri C., Aïnouche M., Chalhoub B. and Grandbastien M.-A. 2010. Impact of transposable elements on the organization and funtion of allopolyploid genomes. New Phytologist 186: 37-45. 
7. Zerjal T., Joets J., Alix K., Grandbastien M.-A. and Tenaillon M. 2009. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Molecular Biology 71: 99-114.
8. Alix K. , Joets J., Ryder C.D., Moore J., Barker G.C., Bailey J.P., King G.J. and Heslop-Harrison J.S. 2008. The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. The Plant Journal 56: 1030-1044.
9. Pouilly N., Delourme R., Alix K. and Jenczewski E. 2008. Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus . Chromosome Research 16: 683-700.
10. Albertin W., Alix K., Balliau T., Brabant P., Davanture M., Malosse C., Valot B. and Thiellement H. 2007. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 8: 56. 
11. Alix K., Ryder C.D., Moore J., King G.J. and Heslop-Harrison J.S. 2005. The genomic organization of retrotransposons in Brassica oleracea. Plant Molecular Biology 59: 839-851. 
12. Alix K. and Heslop-Harrison J.S. 2004. The diversity of retroelements in diploid and allotetraploid Brassica species. Plant Molecular Biology 54: 895-909.  
13. Jenczewski E. and Alix K. 2004. From diploids to allopolyploids: the emergence of efficient pairing control genes in plants. Critical Reviews in Plant Sciences 23: 21-45. 

Teaching at AgroParisTech 
UFR Génétique évolutive et amélioration des plantes / Evolutionary genetics and plant breeding

First year
- Génétique des populations / Population genetics
- Enjeux et défis « Biodiversité sauvage et domestique : un état des lieux » / Stakes and challenges « the wild biodiversity and the cultivated biodiversity: the current situation »
- module intégratif « Gènes et Nature : les biotechnologies végétales au centre des questions de société»/«Genes and Nature: when green technologies meet Society »

Second year
- Socle commun du domaine 1 Productions, filières, territoires  pour le développement durable, « Génétique et amélioration des plantes »/ « Plant genetics and breeding »
- Modules d’approfondissement : (i) « Ce que nous apprennent les génomes » / « What we can learn from genome exploration », (ii) « Adaptation des plantes à l'environnement » / « Adaptation of plants to environment », (iii) « Les défis de l'amélioration des plantes » /« The new challenges of plant breeding »,  (iv) « Biotechnologies, alimentation et santé »/« Biotechnologies, food and health  » 

« Initiation à la Recherche en Biologie » /« Discovering Research in Biology ». I had the pleasure to supervise the project of two students of mine from AgroParisTech (from April to June 2013). They had to write posts for AoB Blog, and produced several articles dealing with research topics in plant biology. I invite you to visit AoB blog, and to have a look at Aurélien Azam and Antoine Legal's posts. Enjoy reading AoB blog!

Some links to the posts written by Aurélien and Antoine: Plantes et insectes pollinisateurs : les aventures d'un couple de choc / Plants and insect pollinators: the adventures of a great couple! ; "Allo, vous me recevez ?" Y aurait-il une communication sonore chez les plantes ? / "Roger that!" Do plants have sound perception skills?  ; Les ressources génétiques peuvent-elles sauver nos platanes ? / Can genetic resources save the common plane tree? ; Le roi des observateurs / The King of observers ; Les goûts sont-ils dans la Nature ? / Can we find all the tastes we like in the Wild?

   

Third year

• DA Production et Innovation dans les Systèmes Techniques Végétaux (PISTv) / Production and Innovation in Plant Systems:
  - Module « Amélioration des plantes : méthodes, objectifs et acteurs de la filière semences » / « Plant breeding:  methods, aims and breeders »
  - Module « Génomique, biotechnologies végétales et biologie des semences » /« Genomics, plant biotechnologies and seed biology »
  -  Option de spécialisation « Amélioration des plantes » /« Plant breeding  »
  

• DA Biotechs:
  - Module « Génomique et bioanalyse » / « Genomics and bioinformatics »
  

Teaching for Master students, Université Paris-Saclay     

Master 1, Biologie Intégrative et Physiologie (BIP)
- Socle commun : « Evolution et organisation des génomes » / « Genome evolution and organisation »
- Parcours végétal : (i) « Adaptation des plantes à l'environnement » / « Adaptation of plants to environment », (ii) « Génomique des espèces cultivées et bioinformatique » / « Crop genomics and bioinformatics », (iii) « Génétique appliquée à l'agronomie et la sélection variétale » / « Genetics for agronomy and plant breeding »

Master 2, Sciences du Végétal (ScV)
UE « Génomique et amélioration des plantes » /« Genomics and plant breeding »

Conferences and Others

I would be pleased to welcome you at AgroParisTech, Paris, for the next INRA workshop series DynaGeV, Dynamique des Génomes Végétaux / Plant Genome Dynamics, 7-8 July 2016. More information soon...