Hypervariable genomes, regulation and conservation in sea urchins

Project Description:

Genetic diversity varies by several order of magnitude among living species. Many marine species, such as oysters or sea urchins have a very high genomic heterozygosity whose functional consequences and impact of species conservation remain poorly investigated. Particularly, while coding regions are usually conserved between alleles in such species, the way genetic variation is distributed in non-coding regions is not fully characterised. These regions conceal the DNA elements that regulate gene expression and control for instance embryonic development.
This project proposes to use the European sea urchin (Paracentrotus lividus) as a model to study the variability of regulatory regions across populations and its possible impact on the robustness of developmental processes. Sea urchins are classical model in developmental biology with well-characterised gene regulatory networks. The student will sample several populations and characterise genomic variation at the nucleotide and structural level and will examine the extent of variability in the regulatory regions. The intraspecific variation in copy numbers for developmental genes, such as for instance homeodomain genes will also be investigated.
Specimens from different populations could also be brought to the lab and used for additional experiments such as crosses, regulatory profiling experiments and monitoring the expression driven by regulatory elements. As the different population are located in regions with different sea water temperatures, we will examine how observed variation possible relate to their reproductive success. This project will help comprehend what is the robustness of biological systems at the gene regulatory level and how they can face environmental change.

Policy Impact of Research:

This project will constitute a reference dataset to assess the population structure and history of the sea urchin P. lividus, which will be an important tool for the conservation of this species. P. lividus has economic importance for fisheries and some of its populations have shown decline.

Research Relating to this Project:

1. Ellegren, H., and Galtier, N. (2016). Determinants of genetic diversity. Nat. Rev. Genet. 17, 422–433.
2. Marlétaz, F., Firbas, P.N., Maeso, I., Tena, J.J., Bogdanovic, O., Perry, M., Wyatt, C.D.R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., et al. (2018). Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564, 64–70.
3. Duran, S., Palacín, C., Becerro, M.A., Turon, X., and Giribet, G. (2004). Genetic diversity and population structure of the commercially harvested sea urchin Paracentrotus lividus (Echinodermata, Echinoidea). Mol. Ecol. 13, 3317–3328.