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Project
Guarding the borders? Transposons in telomeres
The genome of Fusarium oxysporum is littered with transposable elements. However, some transposon families are overrepresented in subtelomeric regions. In this project you will use an existing dataset of transposon families predicted in >500 Fusarium oxysporum genome sequences to identify transposon families that are overrepresented in subtelomeric regions.
We will use two approaches:
in one we will collect all transposon families from all lineages that are within a certain distance of a subtelomeric repeat and cluster them.
In the other approach we will start with high-quality assemblies, identify transposons that are in subtelomeric regions and search for association with telomeric repeat in other, more fragmented genome assemblies. Next, we will combine presence/absence information on these transposon families with information on in which lineages they are overrepresented in subtelomeres, and reconstruct when which transposon invaded the telomeric regions. This may shed light on which processes contribute to the difference in karyotype and chromosome structure we observe in this species.
Research aims
- Identify and characterize transposon families that are exclusive to or overrepresented in subtelomeric regions.
- Reconstruct when these families became associated with these specific regions
Used techniques
- Programming python and snakemake
- Clustering of DNA sequences
- Phylogenetic analyses
- Data visualization