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Project properties |
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| Title | Making sense of transcriptional adaptations to stress during plant evolution |
| Group | Systems and Synthetic Biology |
| Project type | thesis |
| Credits | 36 |
| Supervisor(s) | Michael Schon |
| Examiner(s) | Michael Schon, Rob Smith |
| Contact info | Robert1.smith@wur.nl |
| Begin date | 2025/09/01 |
| End date | |
| Description | Plants evolve to fit their natural environment. As a consequence, different species respond differently to environmental stressors. We know that these evolutionary adaptations are encoded into the genome somewhere, but it remains challenging to identify which mutations are responsible for an adaptive phenotype. In this project, we are looking for a student to tackle problems in comparative transcriptomics, to investigate the gene regulatory networks of a collection of wild and cultivated plant species in the crucifer family Brassicaceae. A suitable candidate for this project is familiar with the molecular mechanisms of transcriptional regulation in plants, is eager to work with large genome-wide datasets, and is motivated to discover connections between genotype and phenotype.
The scope of the project is to (1) define a set of orthologous genes shared between the Brassicaceae genomes being investigated, (2) analyze multi-species RNA sequencing data to determine species-specific changes in transcript isoform abundance under stress, and (3) identify a candidate list of genetic variations between species that may cause the observed differences in gene and isoform expression. References related to project: - D.M. Emms, S. Kelly. “OrthoFinder: phylogenetic orthology inference for comparative genomics.” Genome Biology (2019) https://doi.org/10.1186/s13059-019-1832-y - M.A. Schon et al. “Bookend: precise transcript reconstruction with end-guided assembly.” Genome Biology (2022) https://doi.org/10.1186/s13059-022-02700-3 - S. Birkeland et al. “Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae.” Molecular Biology and Evolution (2020) https://doi.org/10.1093/molbev/msaa068 |
| Used skills | |
| Requirements | Experience programming in Python and R; know the fundamentals of operating a Linux command line; familiar with RNA sequencing technology and data analysis; good understanding of phylogenetic inference methods |