(Internal) Exploring evolution of repetitive elements in relation to the ecology of species

Advisor: Edeline Gagnon, Integrative Biology

Proposed computational advisor: Lewis Lukens, Plant Agriculture

I am interested in examining the macroevolutionary dynamics of repetitive elements in the genome of plants, and how it relates to the ecology and evolution of different species. The expansion and contraction of repetitive elements in species is thought to influence genome size, which in turn can influence traits such as cell size, stomata size, and ultimately other traits related to photosynthesis and ability to withstand ecological stress. I would like to explore this in the genus Solanum, which contains crop species and their wild relatives, which are of interest for plant breeding as they can be used to increase resilience to biotic and abiotic stress. Using published and unpublished whole genome sequences of the genus Solanum, as well as previously generated genome skimming data, the student would explore how much data they can gather from these different sources, to gain a snapshot of the repeat community composition and how it varies in a phylogenetic context across Solanum. We would extract climatic data of these species using occurrence records from natural history collections (available from online biodiversity databases). Comparative phylogenetic methods would then be used to test whether the evolution of the abundance of certain repeats correlates with environmental variables related to precipitation, temperature, and other potential environmental stressors (see ^1,2 for an example of possible methods that could be used), as well as genome size. It would also be possible to explore other ideas, such as looking if we can rebuild phylogenies from these repeats.

This is a one-semester project with the possibility to extend to two semesters.

References

1 Schley, R. J. et al. New Phytol. 236, 433–446 (2022)

2 Souza, G. et al. Perspect. Plant Ecol. Evol. Syst. 38, 13–23 (2019)