Center for Computational and Theoretical Biology

MSc/BSc in Genomics: Timing of Transposable Element expansions in the Venus Flytrap

Timing of Transposable Element expansions in the Venus Flytrap

We know that the Dionaea genome (3 Gbp) is dominated by repetitive elements (2,5 Gbp). This includes a probable centromeric regions (about 500 Mbp in total) and mainly transposable elements (TEs). The goal of this project is the timing of the expansion of these TEs. Usually, such analyses are based on TEs identified within an assembled genome. Still, this is error prone, as especially very similar (and therefor recently expanded) TEs will be too similar to be correctly assembled. If most of the TEs arose in a relatively recent expansion, the will not be represented in any assembly. We therefore have already developed a method to extract and assemble repeats based on Illumina data without the need of a genome assembly (https://github.com/nterhoeven/reper). As a result, we have for each group of TEs a representative sequence (the exemplar) and a set of distinguishable closely related sequences. In addition, for each of the sequences a count is calculated indicating the amount of this sequence in the genome. These results indicated a very recent expansion of TE as the main driver behind the genome expansion of Dionaea. The goal of this project is the precise timing of this expansion event. In addition, we will use the same approach to analyse the sister taxon of Dionaea, namely Aldrovanda. As a side project, we want to characterize the centromeric repeat of Aldrovanda.