Wednesday 25 February 2026 @ 13:15 – 14:00
Followed by PhD-session at 14:30-15:00
(Coffee and cake will be served between lecture and PhD-session)
1871-120 (Nucleus)
Hosted by: Stig Uggerhøj Andersen

Towards an unbiased characterization of genetic polymorphism

Making sense of whole-genome polymorphism data is challenging, but it is essential for achieving a complete picture of genetic variation and overcoming the biases in SNP data. We have analyzed PacBio long-read genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation in A. thaliana is mostly due to tandem repeat regions that are difficult to assemble. However, while the rest of the genome varies little in length, it is full of structural variants, mostly due to rare transposon insertions. Because of this, the pangenome coordinate system grows rapidly with sample size and ultimately becomes 70% larger than the size of any single genome, even for 27 genomes. Finally, we show how short-read data are biased by read mapping. SNP calling is biased by the choice of reference genome, and both transcriptome and methylome profiling results are affected by mapping reads to a reference genome rather than to the genome of the assayed individual. In conclusion, whole-genome polymorphism data will greatly improve our understanding of genome evolution, and will in particular revolutionize the analysis of transposable elements.