(Internal) Using museomics to study genome diversity through time, in a crop wild relative of tomato
Advisor: Edeline Gagnon, Integrative Biology
Proposed computational advisor: Lewis Lukens, Plant Agriculture
I am interested in exploring whether we can use samples from natural history collections to investigate questions about genomic diversity and how it changes through time. DNA obtained through herbaria can be interesting because they can allow us to quickly sample species genetic diversity across ranges without fieldwork but are challenging to work with because they can be degraded. I currently have data of four whole genome sequences (WGS) for herbarium specimens of Solanum chilense, a wild crop relative of tomatoes, that grows in deserts of Southern America1. We are interested in comparing how well we can recover the diversity of disease resistance genes from this data, by testing two different assembly pipelines for archival DNA (Paleomix and EAGER)2,3, and then compare the population genetics summary statistics to those obtained from WGS of individuals of S. chilense, generated from the same locality using samples from seedbank collections4. In a second step, we are currently expanding this sampling to include another additional 20 historical samples (spanning the 1950s to early 2000’s,) and 12 contemporary samples (collected in 2022) from the same locality, to look at whether genetic diversity has changed over time, by comparing the populations a three time points, and using various modelling approaches based on changes in Site Frequency Spectra over to assess whether there have been any changes in selective pressure at different time points 4–6. Ultimately, we will try to see if this approach can answer the following two questions: (1) Are germplasm collections representative of the genomic diversity present in the entire population of S. chilense? (2) Are there signs of loss of genetic diversity in populations of S. chilense in the past 70 years due to habitat loss?
Two-semester project preferred.
References
1 Chetelat, R. T. et al. Euphytica 167, 77–93 (2009)
2 Peltzer, A. et al. Genome Biol. 17, 60 (2016)
3 Schubert, M. et al. Nat. Protoc. 9, 1056–1082 (2014)
4 Wei, K. et al. New Phytol. 237, 1908–1921 (2023)
5 Leroy, G. et al. Evol. Appl. 11, 1066–1083 (2018)
6 Schraiber, J. G. et al. Genetics 203, 493–511 (2016