Xavier Vekemans |

Mon domaine de recherche concerne la génétique et génomique des populations végétales et ses applications en biologie de la conservation. Mes travaux récents concernent l’étude de l’impact de la sélection naturelle sur la diversité génétique et moléculaire dans les populations végétales, avec comme modèle de sélection, la sélection balancée agissant sur les systèmes d’auto-incompatibilité, et comme modèles biologiques, les plantes de la famille des Brassicaceae, et plus particulièrement les espèces du genre Arabidopsis. Ces travaux à la fois théoriques et empiriques comportent trois axes principaux:

(1) un axe de type “génétique des populations et génétique de la conservation” s’intéressant à l’effet de la sélection sur la distribution et l’évolution des fréquences haplotypiques au locus d’auto-incompatibilité (locus S) en populations naturelles chez plusieurs espèces de Brassicaceae et Rosaceae. Récemment nous avons développé au sin du groupe un pipeline d’analyse bio-informatique permettant de génotyper les individus au locus d’auto-incompatibilité à partir de données de séquençage de génomes entiers individuels (Genete et al. 2019), et nous l’appliquons à des données publiques ou propres à l’équipe chez différentes espèces de Brassicaceae et Rosaceae (Maloideae; en collaboration avec Amandine Cornille de l’Université Paris Saclay) afin d’étudier l’influence de différents processus sur l’évolution du système de reproduction de ces espèces (évènements démographiques; flux de gène interspécifique; polyploidisation; …).

(2) un axe “génomique et paléo-génomique des populations” dédié à l’étude de la structure génomique du locus S et de ses régions flanquantes (Le Veve et al. 2024) et à l’impact des évènements historiques de duplication de génome entier sur l’évolution du système d’auto-incompatibilité. Avec mes collaborateurs Céline Poux et Vincent Castric nous étudions l’évolution du locus d’auto-incompatibilité dans plusieurs lignées au sein des Brassicaceae de manière à tester l’hypothèse que les évènements d’allopolyploidisation, contrairement à l’autopolyploidisation, entrainent systématiquement une altération majeure du système d’auto-incompatibilité (Duan et al. 2024).

3) un axe de biologie intégrative ou biologie des systèmes, à l’initiative de Vincent Castric, qui s’intéresse aux mécanismes d’évolution moléculaire à l’origine de la diversification allélique des systèmes d’auto-incompatibilité (Chantreau et al. 2019), et de l’apparition de relations complexes de dominance entre allèles faisant appel à une batterie de petits ARN non codant (Durand et al. 2014).

My field of research concerns the genetics and genomics of plant populations and its applications in conservation biology. My recent work concerns the study of the impact of natural selection on genetic and molecular diversity in plant populations, using balancing selection acting on self-incompatibility systems as a selection model, and plants of the Brassicaceae family, and more particularly species of the Arabidopsis genus, as biological models. This theoretical and empirical work has three main thrusts:

(1) A population genetics and conservation genetics axis, focusing on the effect of selection on the distribution and evolution of haplotypic frequencies at the self-incompatibility locus (S locus) in natural populations of several Brassicaceae and Rosaceae species. Recently, we have developed a bioinformatics analysis pipeline within the group to genotype individuals at the self-incompatibility locus from individual whole-genome sequencing data (Genete et al. 2019), and we are applying it to public or the team's own data in different species of Brassicaceae and Rosaceae (Maloideae; in collaboration with Amandine Cornille of Université Paris Saclay) to study the influence of different processes on the evolution of the reproductive system of these species (demographic events; interspecific gene flow; polyploidization; ...).

(2) A population genomics and paleogenomics axis dedicated to studying the genomic structure of the S locus and its flanking regions (Le Veve et al. 2024) and the impact of historical whole-genome duplication events on the evolution of the self-incompatibility system. With my collaborators Céline Poux and Vincent Castric, we are studying the evolution of the self-incompatibility locus in several Brassicaceae lines, in order to test the hypothesis that allopolyploidization events, unlike autopolyploidization, systematically lead to a major alteration of the self-incompatibility system (Duan et al. 2024).

3) An integrative biology or systems biology axis, led by Vincent Castric and Marie Monniaux, which focuses on the molecular evolutionary mechanisms behind the allelic diversification of self-incompatibility systems (Chantreau et al. 2019), and the emergence of complex dominance relationships between alleles involving a battery of small non-coding RNAs (Durand et al. 2014).

Publications

Publications récentes - Recent publications :

Van Bocxlaer, A. Y. Dollion, C. M. Ortiz-Sepulveda, C. Calarnou, R. Habert, G. Pawindo, X. Vekemans, 2024. Adaptive shell-morphological differences and differential fitness in two morphospecies of Lanistes (Gastropoda: Ampullariidae) from the northern region of the Malawi Basin. Evolutionary Journal of the Linnean Society, 3, kzae010. https://doi.org/10.1093/evolinnean/kzae010
Le Veve, M. Genete, C. Lepers-Blassiau, C. Ponitzki, C. Poux, X. Vekemans, E. Durand & V. Castric, 2024. The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and A. lyrata. eLife, 13:RP94972. https://doi.org/10.7554/eLife.94972
Castric; R. A. Batista; A. Carré; S. Moussavi; C. Mazoyer; C. Godé; S. Gallina; C. Ponitzki; A. Theron; A. Bellec; W. Marande; S. Santoni; R. Mariotti; A. Rubini; S. Legrand; S. Billiard; X. Vekemans; P. Vernet; P. Saumitou-Laprade, 2024. The diallelic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene. Current Biology, 34:1967-1976.e6
Duan, Z. Zhang, M. Genete, C. Poux, A. Sicard, M. Lascoux, V. Castric & X. Vekemans, 2024. Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids. Evolution Letters, qrae011, https://doi.org/10.1093/evlett/qrae011.
K. Kolesnikova, A.D. Scott, J.D. Van de Velde, R. Burns, N. P. Tikhomirov, U. Pfordt, A.C. Clarke, L. Yant, X. Vekemans, S. Laurent & P.Y. Novikova, 2023. Genomes of selfing Arabidopsis lyrata reveal independent transition to self-compatibility in Siberia and its role in allotetraploid A. kamchatica establishment. Molecular Biology and Evolution, 40: msad122. https://doi.org/10.1093/molbev/msad122
Le Veve, N. Burghgraeve, M. Genete, C. Lepers-Blassiau, M. Takou, J. De Meaux, B. K. Mable, E. Durand, X. Vekemans & V.Castric, 2023. Long-term balancing selection and the genetic load linked to the self-incompatibility locus in Arabidopsis halleri and A. lyrata. Molecular Biology and Evolution, 40: msad120. https://doi.org/10.1093/molbev/msad120
M. Ortiz-Sepulveda, M. Genete, C. Blassiau, C. Godé, C. Albrecht, X. Vekemans & B. Van Bocxlaer, 2022. Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms. Molecular Ecology Resources, 23:659–679. DOI: 10.1111/1755-0998.13735
Vekemans, V. Castric, H. Hipperson, N.A. Müller, H. Wersterdahl & Q. Cronk, 2021. Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility. Molecular Ecology, 30: 6072-6086.
Vekemans & V. Castric, 2021. When the genetic architecture matters: evolutionary and ecological implications of self versus non-self recognition in plant self-incompatibility. New Phytologist, 231: 1304-1307.
Takou, T. Hämälä, E. Koch, K.A. Steige, H. Dittberner, L. Yant, M. Genete, S. Sunyaev, V. Castric, X. Vekemans, O. Savolainen, J. de Meaux, 2021. Maintenance of adaptive dynamics in a bottlenecked range-edge population that retained out-crossing. Molecular Biology and Evolution, 38: 1820-1836.
Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, E. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans & C. Roux, 2021. DILS : Demographic Inferences with Linked Selection by using ABC. Molecular Ecology Resources, 21: 2629-2644. (https://doi.org/10.1111/1755-0998.13323)

Publications représentatives - Representative publications :

M. Chantreau, C. Poux, M. F. Lensink, G. Brysbaert, X. Vekemans & V. Castric, 2019. Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis. eLIFE, 8:e50253
M. Genete, V. Castric & X. Vekemans, 2019. Genotyping and de novo discovery of allelic variants at the Brassicaceae self-incompatibility locus from short read sequencing data. Molecular Biology and Evolution, in press. DOI: 10.1093/molbev/msz258
C. Belser, B. Istace, E. Denis, M. Dubarry, F.-C. Baurens, C. Falentin, Genete, W. Berrabah, A.-M. Chevre, R. Delourme, G. Deniot, F. Denoeud, P. Duffe, S. Engelen, A. Lemainque, M. Manzanares-Dauleux, G. Martin, J. Morice, B. Noel, X. Vekemans, A. D’Hont, M. Rousseau-Gueutin, V. Barbe, C. Cruaud, P. Wincker, J.-M. Aury, 2018. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nature Plants, 4: 879-887.
P. Saumitou-Laprade, P. Vernet, X. Vekemans, S. Billiard, S. Gallina, L. Essalouh, A. Mhaïs, A. Moukhli, A. El Bakkali, G. Barcaccia, F. Alagna, R. Mariotti, N. G. M. Cultrera, S. Pandolfi, M. Rossi, B. Khadari, L. Baldoni. 2017. Elucidation of the genetic architecture of self-incompatibility in olive: Evolutionary consequences and perspectives for orchard management. Evolutionary Applications, 10:867–880.
E. Durand, R. Méheust, M. Soucaze, P.M. Goubet, S. Gallina, C. Poux, I. Fobis-Loisy, E. Guillon, T. Gaude, A. Sarazin, M. Figeac, E. Prat, W. Marande, H. Bergès, X. Vekemans, S. Billiard & V. Castric. 2014. Dominance hierarchy arising from the evolution of a complex small RNA regulatory network. Science, 346: 1200-1205.
X. Vekemans, C. Poux, P. Goubet & V. Castric. 2014. The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? Journal of Evolutionary Biology, 27: 1372- 1385.
C. Roux, M. Pauwels, M.V. Ruggiero, D. Charlesworth, V. Castric & X. Vekemans, 2013. Recent and ancient signatures of balancing selection around the S locus in Arabidopsis halleri and A. lyrata. Molecular Biology and Evolution, 30: 435-447.
J.-B.Leducq, C. Gosset, M. Poiret, F. Hendoux, X. Vekemans & S. Billiard, 2010. An experimental study of the S-Allee effect in the self-incompatible plant Biscutella neustriaca. Conservation Genetics, 11: 497-508.
V. Castric, J. Bechsgaard, MH. Schierup & X. Vekemans, 2008. Repeated adaptive introgression at a gene under multiallelic balancing selection. Plos Genetics, 4(8): e1000168.
V. Llaurens, S. Billiard, J.B. Leducq, V. Castric, E.K. Klein & X. Vekemans, 2008. Does frequency-dependent selection with complex dominance interactions accurately predict allelic frequencies at the self-incompatibility locus in Arabidopsis halleri?. Evolution, 62: 2545–2557.
X. Vekemans, O. J. Hardy, 2004. New insights from fine-scale spatial genetic structure analyses in plant populations. Molecular Ecology, 13: 921-935.
V. Castric & X. Vekemans, 2004. Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances. Molecular Ecology, 13: 2873-2889.
X. Vekemans, M.H. Schierup & F.B. Christiansen, 1998. Mate availability and fecundity selection in multiallelic self-incompatibility systems in plants. Evolution, 52: 19-29.
X. Vekemans & M. Slatkin, 1994. Gene and allelic genealogies at a gametophytic self-incompatibility locus. Genetics, 137: 1157-1165.

2015- : Directeur UMR 8198 Evo-Eco-Paléo

2007-2011: Directeur du GDR CNRS 1928 Génomique des populations et génomique évolutive

2002: Université Lille 1, Sciences et Technologies, recrutement comme Professeur.

1994 : Université Libre de Bruxelles (ULB), recrutement comme Chef de Travaux (=MCF).

1992-1994 : Séjour Postdoctoral à University of California, Berkeley, Department of Integrative Biology; dans l’équipe du Prof. M. Slatkin.

1992: Thèse de doctorat, Sciences Agronomiques, Université Libre de Bruxelles (ULB), Belgique. Titre: “Evolution of plant breeding systems: Armeria maritima Mill. (Willd.) as a study case.”