Project highlights
- Ctenophores
- Neurons
- Genomics
Overview
Ctenophores, or comb jellies, are a mysterious group of non-bilaterian animals that stand out for their unusual nervous system and neurons (Burkhardt et al., 2023; Sachkova et al., 2021;Moroz et al., 2014). Recent evidence, based on phylogenetic, molecular studies, and morphological studies suggests that ctenophores may have developed their neurons independently from other animals (Burkhardt et al., 2023; Moroz et al., 2014; Schultz et al., 2021). This means that their nervous system might represent a separate evolutionary path, unlike the neurons found in other groups like bilaterians and cnidarians.
By examining the gene expression of individual cells using single‐cell RNA sequencing (Tanay and Regev, 2017) (scRNA-seq) researchers can test whether neurons across species share a common set of regulatory genes. If ctenophore neurons evolved independently, we would expect them to express a unique combination of regulatory genes not found in the neurons of other animal lineages.
However, current studies using scRNA-seq on ctenophores did not identify cell-type with a distinct neuronal gene expression signatures (Sebé-Pedrós et al., 2018). On the other hand, Hayakawa et al., (2022) have identified cells in ctenophores expressing typical neuronal markers. Thereby a big question remains: are the neurons in ctenophores homologous to those in bilaterians?
To clarify this, in this project we will combine comparative genomics, scRNA-seq and molecular biology.
This area of research presents a captivating challenge for prospective PhD students who are eager to tackle fundamental questions about the evolution of the nervous system. By using cutting-edge molecular and genomics techniques, you could be part of the effort to uncover one of biology’s greatest mysteries.
Objectives
The objective of this proposal is to understand how many times the neurons evolved in animals by integrating cutting-edge molecular biology, machine learning and phylogenetic methods.
Figure 1. An image of P. pileus.
Host
University of LeicesterTheme
- Organisms and Ecosystems
Supervisors
Project investigator
- Dr Roberto Feuda, University of Leicester, [email protected]
Co-investigators
Prof Ezio Rosato (University of Leicester)
Dr Vengamanaidu Modepalli (Marine Biological Association, UK)
Dr Maria Sachkova (University of Bristol)
How to apply
- Each host has a slightly different application process.
Find out how to apply for this studentship. - All applications must include the CENTA application form. Choose your application route
Methodology
This PhD will use state-of-the-art techniques in molecular biology (i.e. single-cell RNA seq) and computational methods (e.g. machine learning and phylogenetic methods) to test whether neurons evolved once or multiple times. Specifically, the PhD student will:
- Field visit to collect comb jellies and culturing animals.
- Generate single-cell RNA-seq data for Pleurobrachia pileus.
- Use machine learning to classify cell-types and validate them using in-situ hybridization methods.
- Reconstruct the evolutionary origin of neuronal modules and genes in animals using phylogenetic methods.
Training and skills
DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
This project will equip you with a unique combination of expertise in experimental and computational biology and data analysis that can be applied to a large, diverse set of problems.
You will be part of Feuda’s research group at the University of Leicester (https://sites.google.com/view/feudalab/home). The group currently includes 2 master students, 5 PhD students and 2 postdocs with different background and expertise, from molecular biology to paleontology. The lab is part of the neurogenetic research a group of 8 PIs working on different aspect of nervous system function. This position offers ample opportunity for training and collaboration in the U.K. and Europe.
Partners and collaboration
The student will spend time in Dr. Modepalli’s laboratory at the Marine Biological Association of the UK to collect animals and acquire skills in molecular biology focusing on marine invertebrates.
Further details
For any enquiries related to this project please contact Dr Roberto Feuda, University of Leicester, [email protected].
To get an overview of the projects we are running in the lab, please take a look at our website: https://sites.google.com/view/feudalab/home?authuser=0
To apply to this project:
- You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2025.
- You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.
- Please submit your application and complete the host institution application process via: CENTA PhD Studentships | Postgraduate research | University of Leicester. Please scroll to the bottom of the page and click on the “Apply Now” button. The “How to apply” tab at the bottom of the page gives instructions on how to submit your completed CENTA Studentship Application Form 2025, your CV and your other supporting documents to your University of Leicester application. Please quote CENTA 2025-L3 when completing the application form.
Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.
Possible timeline
Year 1
Single-cell RNA sequencing and data generation.
Year 2
Experimental validation of computational data.
Year 3
Phylogenomic analysis of neuronal modules.
Further reading
Burkhardt, P., Colgren, J., Medhus, A., Digel, L., Naumann, B., Soto-Angel, J.J., Nordmann, E.-L., Sachkova, M.Y., Kittelmann, M., 2023. Syncytial nerve net in a ctenophore adds insights on the evolution of nervous systems. Science 380, 293–297. https://doi.org/10.1126/science.ade5645
Hayakawa, E., Guzman, C., Horiguchi, O., Kawano, C., Shiraishi, A., Mohri, K., Lin, M.-F., Nakamura, Ryotaro, Nakamura, Ryo, Kawai, E., Komoto, S., Jokura, K., Shiba, K., Shigenobu, S., Satake, H., Inaba, K., Watanabe, H., 2022. Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons. Nat Ecol Evol 6, 1438–1448. https://doi.org/10.1038/s41559-022-01835-7
Moroz, L.L., Kocot, K.M., Citarella, M.R., Dosung, S., Norekian, T.P., Povolotskaya, I.S., Grigorenko, A.P., Dailey, C., Berezikov, E., Buckley, K.M., Ptitsyn, A., Reshetov, D., Mukherjee, K., Moroz, T.P., Bobkova, Y., Yu, F., Kapitonov, V.V., Jurka, J., Bobkov, Y.V., Swore, J.J., Girardo, D.O., Fodor, A., Gusev, F., Sanford, R., Bruders, R., Kittler, E., Mills, C.E., Rast, J.P., Derelle, R., Solovyev, V.V., Kondrashov, F.A., Swalla, B.J., Sweedler, J.V., Rogaev, E.I., Halanych, K.M., Kohn, A.B., 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. https://doi.org/10.1038/nature13400
Sachkova, M.Y., Nordmann, E.-L., Soto-Àngel, J.J., Meeda, Y., Górski, B., Naumann, B., Dondorp, D., Chatzigeorgiou, M., Kittelmann, M., Burkhardt, P., 2021. Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system. Current Biology. https://doi.org/10.1016/j.cub.2021.09.005
Schultz, D.T., Francis, W.R., McBroome, J.D., Christianson, L.M., Haddock, S.H.D., Green, R.E., 2021. A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 Genes|Genomes|Genetics. https://doi.org/10.1093/g3journal/jkab302
Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara-Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B.M., Tanay, A., 2018. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat Ecol Evol 2, 1176–1188. https://doi.org/10.1038/s41559-018-0575-6
Tanay, A., Regev, A., 2017. Scaling single-cell genomics from phenomenology to mechanism. Nature 541, 331–338. https://doi.org/10.1038/nature21350