Thèse Transfert Horizontal de Gènes chez les Plantes et Valeur Agronomique H/F

Université Paris-Saclay GS Life Sciences and Health

Établissement : Université Paris-Saclay GS Life Sciences and Health
École doctorale : Structure et Dynamique des Systèmes Vivants
Laboratoire de recherche : IJPB - Institut Jean-Pierre Bourgin-Sciences du Végétal
Direction de la thèse : Florian MAUMUS
Début de la thèse : 2026-10-01
Date limite de candidature : 2026-03-23T23:59:59

Le transfert horizontal de gènes (HGT) est un moteur de l'évolution et de l'adaptation chez les procaryotes. Il joue également un rôle dans l'évolution des eucaryotes, bien qu'il soit moins répandu et que les mécanismes sous-jacents restent largement inconnus. Le HGT est un processus fascinant assimilé à une transgénèse naturelle, par lequel des fonctions établies dans un organisme sont transmises à un autre, parfois avec des conséquences biologiques profondes. Chez les plantes, le HGT a été documenté à de nombreuses reprises et il a été démontré qu'il pouvait conférer des fonctions avantageuses en milieu sauvage et pour l'amélioration des espèces cultivées. Cependant, la présence de gènes issus de HGT n'a pas encore été analysée dans la plupart des espèces végétales dont le génome a été assemblé. Dans ce projet, nous visons à identifier les événements HGT au sein d'une vaste collection de génomes de plantes afin d'évaluer l'étendue et les patrons du HGT, et de recenser de nouveaux gènes candidats susceptibles d'être utiles en sélection végétale.

The question of how species evolve and adapt to new conditions remains central to the field of biology. The advent of genome sequencing technologies has led to significant advancements in this area of research by providing access to complete genomes, which can be compared to reveal both similarities and differences between and within species. In addition to mutations in their DNA, these comparisons revealed that species also evolve through the lateral acquisition of genes by means other than reproduction, a process known as horizontal gene transfer (HGT). The patterns, mechanisms, and vectors of HGT are well-characterized in prokaryotes, in which these transfers are ubiquitous and a major source of innovation. In contrast, the prevalence of HGT in eukaryotes has long been considered anecdotal due to multiple barriers that should impede such transfers, or controversial because it results from phylogenetic artifacts or contaminant sequences. Nevertheless, dozens of recent studies utilizing an increasing number of high-quality genomes and transcriptomes have reported numerous robust transfers of genes and transposable elements in various eukaryotic organisms. These findings provided compelling evidence that HGT events also occur in eukaryotic species and contribute to rapid evolutionary transitions by conferring new functions to recipient species [1]. Consequently, the characterization of HGT events in eukaryotes and their impact constitutes a highly prolific research area.
In plants, several studies suggest that HGT has occurred many times during evolution. The transfer of genetic material between parasitic plants and their hosts or between grasses is the best documented [2]. Plants have also acquired genes from fungi and bacteria on multiple occasions, and these genes' functions contributed to the early evolution of land plants [3]. The transfer of bacterial and fungal genes to plants has also occurred more recently, conferring agronomically important traits such as adaptation to new environments and resistance to pathogens. For example, a fungal gene confers resistance to Fusarium head blight disease in a wild grass species, and this trait has been successfully introgressed into wheat [4]. Therefore, characterizing HGT in plants provides significant insights into understanding plant evolution and identifying genes with valuable functions for crop improvement, which are otherwise absent from the vertically transmitted gene repertoire within a plant lineage. Despite this significance, the extent of HGT in plants and its implications remain only partially understood. This limitation is due to the number of plant genomes, the diversity of taxa in which HGT has been studied, and the speed and accuracy of bioinformatic approaches to detect it.

This PhD project will undertake a large-scale study to address the patterns of HGT in plants more broadly and comparatively. By leveraging novel bioinformatic approaches, we will search for HGT events in a substantial number of genomes representing all the divisions of land plants (lycophytes, ferns, gymnosperms, and angiosperms) and their sister phylum, charophyte algae. We will look for genes originating from non-plant organisms (e.g. prokaryotes, fungi, animals, oomycetes) and for genes exchanged between plants. The validation of HGT candidates will be achieved using phylogenetic analysis and by filtering potential contaminating sequences from plant genome assemblies. The annotation of confirmed transferred genes will allow inferring their putative function and assigning them to gene families and metabolic pathways.
These analyses will facilitate the characterization of ancient transfers that occurred during plant evolution, either at the base of plant divisions or within them, and enable the comparison of the patterns and scales of HGT between plant divisions. It will also allow us to investigate the degree of innovation inherent in each transfer, distinguishing between gene replacement and gain of function, thereby enabling the measurement of the selective advantage conveyed by these HGTs. Finally, this work will reveal the extent of recent transfers at the botanical families and species levels, which may have been selected for adaptation to new conditions (e.g., cold stress, drought) or for providing new defenses against pests and herbivores. Such genes will represent novel candidates whose function should be investigated through collaborations and may provide valuable knowledge for plant breeding.