Mots-Clés
Corals
acclimation
transcriptomic
ecology
Description
Context
Coral reefs are facing an increasing number of local and global stressors while directly sustaining half a billion people and hosting a quarter of the world’s total marine biodiversity. Back-to-back coral bleaching is now reported on the Great Barrier Reef since 2016, and at several other locations around the world (Hughes et al., 2018). Therefore, it is urgent to better characterize the adaptive capacities of corals and their implications for the overall reef ecosystem’s resilience. Corals form integral and functionally important symbioses with microbial communities (called microbiome) and together they form a holobiont. These microbial communities are composed of bacteria, dinoflagellate algae of the family Symbiodiniaceae, and viruses. Corals are the world’s most diverse symbiotic ecosystems and their microbiome will surely be key to future reef health. Fire corals (Cnidaria, Hydrozoa) are foundation species (like corals and octocorals - Cnidaria, Anthozoa) at the basis of the reef ecosystems, providing shelter, food and nursery grounds for thousands of other species. As they may fare better than many corals under future conditions, their structural ecological role in coral reefs might become even more important. This project is based on the ‘hologenome theory’ and on preliminary results from the TARA Pacific expedition that draws on an eco-evolutionary framework for the study of the coral holobiont in a changing environment.
Objectives
The objective is to evaluate Millepora and Symbiodinium gene expressions following temperature variations. An experiment was conducted in July 2022: four Millepora species were subjected to temperature increase and samples were collected at different time-points of the experiment. PolyA+ RNAs were extracted then sequenced in order to measure gene expression variations between the different conditions.
During the internship, the student will have to align the transcriptomic reads on Millepora and Symbiodiniaceae genomes (Ortiz-González et al., 2017) then perform differential expression analysis using DESeq2 tool (or similar). These results will be compared to previous experiments on different corals to evaluate the acclimatization capacities of fire corals (Savary et al., 2021).
In addition, gene expression profiles of hundreds of Millepora colonies collected in the Pacific Ocean in the framework of Tara Pacific expedition are available and will be used to evaluate the impact of ocean warming on Millepora in natural environments.
Skills
-Bioinformatics, genomics and/or molecular biology background
-Interest in genomics and gene regulation
-Experience working in a linux environment and bioinformatics tools.
-Good level in a scripting language (e.g. bash, python, perl) and R
Host laboratory
The student will work at the Laboratoire d’analyses génomiques des eucaryotes (Genoscope, https://lage.genoscope.cns.fr/) at Evry (91000). She/He will be supervised by Quentin Carradec with a tight collaboration with Emilie Boissin (CRIOBE, Perpignan).
Références
Hughes, T.P., Kerry, J.T., Baird, A.H., Connolly, S.R., Dietzel, A., Eakin, C.M., Heron, S.F., Hoey, A.S., Hoogenboom, M.O., Liu, G., et al. (2018). Global warming transforms coral reef assemblages. Nature 556, 492–496. https://doi.org/10.1038/s41586-018-0041-2.
Ortiz-González, I.C., Rivera-Vicéns, R.E., and Schizas, N.V. (2017). De novo transcriptome assembly of the hydrocoral Millepora alcicornis (branching fire coral) from the Caribbean. Marine Genomics 32, 27–30. https://doi.org/10.1016/j.margen.2016.11.005.
Savary, R., Barshis, D.J., Voolstra, C.R., Cárdenas, A., Evensen, N.R., Banc-Prandi, G., Fine, M., and Meibom, A. (2021). Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea. Proceedings of the National Academy of Sciences 118, e2023298118. https://doi.org/10.1073/pnas.2023298118.