Description

The establishment of an animal’s body plan occurs during embryonic development. This genetically controlled process is unique to each species and underlies the morphological differences observed among them. Specific sets of genes—encoding transcription factors and signaling molecules—interact dynamically in space and time through complex gene regulatory networks (GRNs). These networks ultimately regulate cell fate specification, differentiation, and morphogenesis. While GRNs are often deeply conserved because they control key traits (such as the notochord in chordates), changes in these networks can also drive trait diversification and the emergence of novel characters during evolution.
Ascidians, a group of marine invertebrates, provide an ideal system for investigating the functional links between GRN modifications and morphological changes. Their embryos are relatively simple, composed of approximately 2,500 cells in the larval stage, and are highly amenable to functional genomic experiments, including gene gain- and loss-of-function studies, lineage tracing, transcriptional assays, and live imaging. Despite extensive diversification (with around 3,000 species), ascidian embryonic development appears highly constrained, as embryos and larvae from phylogenetically distant species exhibit remarkable morphological similarities.
This PhD project will focus on a specific larval organ: the palps (or adhesive organ). This sensory organ, composed of a thickened epithelium at the anterior tip of the larva, is the evolutionary equivalent of the vertebrate olfactory placode and its derivatives. It plays a critical role in the metamorphosis of the tadpole-like swimming larva into a sessile adult by selecting a suitable substrate (via sensory neurons) and adhering to it (through a biological 'glue' secreted by collocytes). In the reference species Ciona intestinalis, the molecular mechanisms underlying palps formation and function are actively studied (1–5). Interestingly, morphological deviations from the prototypical three-papillae palps of Ciona have been observed: some species exhibit only two tiny dorsal papillae, while others lack papillae entirely. For example, in Molgula appendiculata, our group has shown that the absence of the ventral papilla is correlated with heterochrony in the deployment of BMP signaling in palp precursors.
The PhD project is structured around two main axes:
1) Descriptive analysis: Cellular (membrane and nuclear) and molecular (gene expression via in situ hybridization or HCR) characterization of the larval adhesive organ across multiple species using 3D imaging. This will include investigating whether palps morphology correlates with specific life cycle traits or habitat preferences (e.g., species living on hard substrates vs. sand or mud).
2) Functional developmental biology: Description of the deployment of key nodes and signaling pathways of the Ciona palps GRN in species with deviant palps morphology, followed by functional assessments of the impacts of these changes on palps morphology.

Compétences requises

• Master’s degree in Developmental Biology, Evolutionary Biology, Genetics, Molecular Biology, or a related field. • Strong background in Evo-Devo, gene regulatory networks (GRNs), or comparative embryology is highly desirable. • Prior research experience in molecular biology techniques (e.g., in situ hybridization, CRISPR/Cas9, transgenesis, gene expression analysis) is a strong plus. • Experience with confocal microscopy, 3D imaging, or live imaging is advantageous. • Autonomy and rigor: Ability to work independently while adhering to experimental protocols and deadlines. • Minimum English level: B1/B2

Bibliographie

1. Johnson, C. J. et al. Specification of distinct cell types in a sensory-adhesive organ important for metamorphosis in tunicate larvae. PLOS Biology 22, e3002555 (2024).
2. Roure, A., Chowdhury, R. & Darras, S. Regulation of anterior neurectoderm specification and differentiation by BMP signaling in ascidians. Development 150, dev201575 (2023).
3. Roure, A., Chowdhury, R. & Darras, S. Six3/6 acts downstream of canonical Wnt signaling to regulate the formation of anterior neural border-derived structures in ascidian embryos. Development 152, dev204927 (2025).
4. Hoyer, J. et al. Polymodal sensory perception drives settlement and metamorphosis of Ciona larvae. Current Biology 34, 1168-1182.e7 (2024).
5. Liang, Z., Hoyer, J. & Chatzigeorgiou, M. Anoctamins mediate polymodal sensory perception and larval metamorphosis in a non-vertebrate chordate. Cell Reports 44, 115578 (2025).
6. Coulcher, J. F. et al. Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. eLife 9, e59157 (2020).
7. Darras, S. En masse DNA Electroporation for in vivo Transcriptional Assay in Ascidian Embryos. Bio-protocol 11, e4160 (2021).
8. Lanoizelet, M., Elkhoury Youhanna, C., Roure, A. & Darras, S. Molecular control of cellulosic fin morphogenesis in ascidians. BMC Biol 22, 1–16 (2024).
9. Daric, V., Lanoizelet, M., Mayeur, H., Leblond, C. & Darras, S. Genomic Resources and Annotations for a Colonial Ascidian, the Light-Bulb Sea Squirt Clavelina lepadiformis. Genome Biology and Evolution 16, evae038 (2024).

Mots clés

ascidie, EvoDevo, évolution, embryon, réseaux de gènes