Background

Striated muscle is a defining feature of bilaterian animals, yet striated muscle-like structures are also present in cnidarians, raising a fundamental evolutionary question: did striated muscle evolve once in the common ancestor of cnidarians and bilaterians, or did it arise independently through convergent recruitment of actomyosin components? Despite its importance, the molecular composition and evolutionary history of cnidarian striated muscle remain poorly characterized. In particular, it is unclear how similar the cnidarian sarcomeric protein organisation is to those of bilaterians. This project aims to reconstruct the molecular architecture and evolutionary history of striated muscle using a novel jellyfish model species, Pelagia noctiluca. Thanks to its full transparency and direct development, this species is ideally suited for high-resolution imaging and functional experiments. 

PhD project 1

The goal of the first PhD project located at IBDM in Marseille and co-supervised by B. Habermann and L. Leclère will be to determine how conserved the muscle machinery is in cnidarians, and to identify whether lineage-specific innovations and the rewiring of protein interaction networks contributed to the diversification of striated muscle architecture across animals. The project will integrate transcriptomics, proteomics, structural modeling, and phylogenomics. 

Aims:   

1. Define the molecular composition of cnidarian striated muscle. Identify actomyosin-interacting and sarcomeric proteins expressed in distinct muscle types of Pelagia noctiluca by integrating newly generated long-read RNA sequencing and proteomic datasets with existing single-cell RNA-seq data and genomic resources. This aim will establish a high-confidence catalogue of Pelagia muscle-expressed proteins and define the core molecular components of cnidarian striated muscles.
2. Reconstruct protein structures and interaction networks. Perform in silico structural modelling of conserved and novel muscle-expressed proteins and predict their interaction interfaces. These interaction networks will be compared to experimentally characterized sarcomeric networks in Drosophila and mouse to determine the degree of conservation of interaction modules, as well as potential lineage-specific innovations
3. Reconstruct the evolutionary history of actomyosin networks. Conduct large-scale phylogenetic analyses of actomyosin-interacting proteins across cnidarians and bilaterians to infer ancestral gene repertoires and identify gene duplications, losses, and domain innovations. Correlate evolutionary patterns with muscle-type specific expression data across selected animal taxa.

PhD project 2

This PhD project, primarily based at IBDM in Marseille and co-supervised by F. Schnorrer and L. Leclère, aims to characterize the molecular conservation of sarcomere components between cnidarians and bilaterians. The project will combine experimental approaches in Pelagia and Drosophila, including cross-species functional analyses. 

Aims:

1. Identification of novel sarcomere proteins in Pelagia. Identify new thin- and thick-filament proteins as well as Z-disc proteins in Pelagia through the generation of species-specific antibodies and super-resolution imaging (STED and/or DNA-PAINT). Particular attention will be given to proteins potentially involved in sarcomere elasticity, including titin and obscurin homologs.
2. Characterization of the Pelagia sarcomere contraction mechanism. Investigate the molecular basis of sarcomere contraction in Pelagia, with a specific focus on calcium-binding proteins. This will involve mRNA microinjection into Pelagia embryos combined with live imaging approaches and biochemical assays.
3. Cross-species functional analyses between Drosophila and Pelagia. Assess the functional conservation of sarcomeric proteins by testing the localization and function of selected proteins from each species in the muscle cells of the other species.

Our groups and our environments

This interdisciplinary project is collaboration between two groups based in Marseille and a group based at the Oceanographic Observatory of Banyuls-sur-Mer (CNRS/Sorbonne Université).

The primary institute will be the Developmental Biology Institute of Marseille (IBDM) with the groups led by Bianca Habermann (PhD 1) or Frank Schnorrer (PhD 2). The Habermann team is expert in bioinformatics. The Schnorrer team is expert in muscle biology and in vivo imaging. Both groups are part of the Turing Centre for Living Systems, Centuri, which brings together biologists, physicists, and computational scientists. Thus, both PhD students will benefit from a highly interdisciplinary environment, including collaborations, courses, seminars and meetings in Marseille.

Both students will collaborate with the Cnidevo team co-led by Lucas Leclère at the Oceanographic Observatory of Banyuls-sur-Mer, a marine station operated by Sorbonne University and the CNRS. This team is expert in cnidarian biology and has developed the jellyfish model Pelagia noctiluca, ideally suited to study the structure, development and evolution of cnidarian muscles.

Your profile

PhD project 1: You have an education and training in computational biology. Ideally, you have experience with phylogenetic analysis and/or single-cell sequencing data analysis. An interest in evolutionary biology will be a strong plus.

PhD project 2: You have an education and training in cell or developmental biology. An interest in genetics and imaging techniques will be a strong plus.

For both projects: You are ambitious, curious, enjoy learning novel techniques and like to find answers to problems. You want to take advantage of the opportunity to carry out your doctorate in two different laboratories and learn from their different expertise.

Possible starting dates

PhD project 1:  October to December 2026.

PhD project 2:  October to December 2026.

Application

Please apply sent an email containing:

– A CV.

– An academic transcripts in a single document.

– A personal statement that includes professional goals and motivation for wanting to join our labs.

– A brief summary of past internships (max. 200 words per internship).

– Contacts of two references.

To:         

bianca.HABERMANN@univ-amu.fr

frank.schnorrer@univ-amu.fr

lucas.leclere@obs-banyuls.fr

Lab websites

    Marseille laboratory:

IBDM: https://www.ibdm.univ-amu.fr/fr/

Habermann lab: https://sites.google.com/view/habermannlab/home

Schnorrer lab: https://www.ibdm.univ-amu.fr/team/muscle-dynamics/

    Banyuls-sur-Mer laboratory:

BIOM: https://biom.obs-banyuls.fr/

Cnidevo/Leclère lab https://cnidevolab.com/

Selected publications from the host teams

1- Loreau V, Koolhaas WH, Chan EH, De Boissier P, Brouilly N, Avosani S, Sane A, Pitaval C, Reiter S, Luis NM, Mangeol P, von Philipsborn AC, Rupprecht JF, Görlich D, Habermann BH, Schnorrer F. 2025. Titin-dependent biomechanical feedback tailors sarcomeres to specialized muscle functions in insects. Science Advances 11(19):eads8716.

2- Haering M, Bondio AD, Puccio H, Habermann BH. 2025. mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data. Journal of Molecular Biology 437(15):169004.

3- Karapidaki I, Handberg-Thorsager M, Momose T, Yasuo H, Genikhovich G, Assaf S, Deleau C, Pang Y, Pavlich C, Lohmann B, Rusciano ML, Stranges M, Mathieu J, Zilliox M, Ustyantsev K, Salmon B, Laplace-Builhé B, Koenig M, Colgren JJ, Arnone MI, Berezikov E, Brunet T, Bucher G, Burkhardt P, Dickinson DJ, Houliston E, Huisken J, Leclère L, Averof M. 2025. Targeting the cell membrane in established and emerging model organisms. bioRxiv. 2024.11.12.623055.

4- Mańko MK, Munro C, Leclère L. 2025. The evolution of an individual-like dispersive stage in colonial siphonophores. Current Biology 35(20):4946-4958.e4.

5- Zhang X, Avellaneda J, Spletter ML, Lemke SB, Mangeol P, Habermann BH, Schnorrer F. 2024. Mechanoresponsive regulation of myogenesis by the force-sensing transcriptional regulator Tono. Current Biology 34(22):5392-5394.