The aim of the internship is to identify convergent and divergent transcriptional signatures of germination across broomrape species and stimulants, using a comparative time-course RNA-seq approach. The intern will first characterize the temporal dynamics of the transcriptional response of seeds to their GS in P. ramosa, O. cumana and O. hederae. These responses will then be compared in order to distinguish a core response, shared by all species and stimulants, from species-specific and stimulant-specific responses. Finally, this comparison will highlight candidate regulators of the germination pathway, with a particular focus on the KAI2/MAX2/SMXL signaling module, transcription factors and CYP707A.

Broomrapes (Orobanche and Phelipanche spp., Orobanchaceae family) are obligate root-parasitic weeds causing severe yield losses on many crops, including sunflower and oilseed rape in France. Their survival relies on a tight synchronization with the host: seeds germinate only after perceiving germination stimulants (GS) exuded by host roots. These GS are chemically diverse and species-dependent: strigolactones for most broomrapes, but also isothiocyanates for Phelipanche ramosa populations adapted to oilseed rape, sesquiterpene lactones for Orobanche cumana (sunflower broomrape), or still-unknown molecules for O. hederae (ivy broomrape). They are perceived by a family of divergent KAI2 receptors (KAI2d), which has expanded independently in each species, and germination ultimately requires the induction of the ABA-catabolic gene CYP707A. Between perception and CYP707A activation, however, the signaling events remain largely unknown. A key question is whether chemically unrelated GS, perceived by different receptors in different species, converge on a common signaling pathway or activate distinct, species- and stimulant-specific responses. This internship is part of a broader ANR project aiming to decipher the diversity of GS perception and of the molecular actors recruited during the signaling pathway that leads to broomrape seed germination.

Seeds of the three species will be treated or not with a universal strigolactone analogue (GR24) and with species-specific GS (e.g. isothiocyanates, sesquiterpene lactones or host root exudates) for 2, 6, 12 and 24 h, in biological triplicates. After quality control and trimming, reads will be quantified on the reference genome of each species, normalized and explored by PCA and sample clustering on a high-performance computing cluster.

Gene expression will be modelled over time using polynomial regression (R package ‘maSigPro’), in order to identify genes whose expression profiles differ between treated and control seeds and between stimulants. Significant genes will be grouped into co-expression clusters, and pairwise comparisons at each time point (R package ‘DESeq2’) will complement this analysis. To compare species, orthogroups will be defined between the three broomrapes and non-parasitic references (Arabidopsis and other Lamiales) using OrthoFinder; for multigenic families in which lineage-specific duplications blur orthology relationships (e.g. KAI2d, SMXL, TCP), these assignments will be refined by phylogenetic analyses. Responsive genes will then be projected onto orthogroups to classify responses as conserved, species-specific or stimulant-specific, to compare the timing of responses between orthologs, and to perform functional enrichment analyses using GO and KEGG terms.

Finally, RT-qPCR will be used to check the specificity of the expression of a few candidate genes. Seeds of each species will be treated with their own GS (positive control of stimulation) and with molecules that do not induce their germination, such as the GS of another species (negative control of stimulation), in order to verify that the expression of these candidates is linked to the effective stimulation of germination rather than to a non-specific response to the chemical treatment.

We are looking for a motivated student trained in plant or molecular biology, with a strong interest in molecular signaling and a clear motivation to use bioinformatics to address biological questions. A first experience in bioinformatics (e.g. a previous internship or project) is highly desirable, in particular command-line work in a Linux environment and/or data analysis in R or equivalent languages (e.g. Python). Experience in transcriptomics (RNA-seq processing, differential expression analysis) will be appreciated but is not mandatory, as training will be provided within the team. Basic knowledge of phylogenetics and molecular evolution, as well as basic molecular biology skills (RNA extraction, RT-qPCR), would be an asset. The candidate should be rigorous, autonomous and curious, enjoy working at the interface between experimental biology and data analysis, and have good written and oral communication skills in French and English.

The student will work in the US2B laboratory, within the Rhizoplante team, and will have access to its facilities.

She or he will be supervised by Candice Chesnais (PhD student), Guillaume Brun (Dr), Jean-Bernard Pouvreau (Dr), and Philippe Delavault (Prof.).

To apply, please send your CV, cover letter, and M1 academic transcript (or equivalent) to the following email addresses: guillaume.brun@univ-nantes.fr and philippe.delavault@univ-nantes.fr.

Application deadline: Friday, November 6, 2026.