Population Genomics of Transposable Elements and their Effect on Gene Expression Variation

Transposable elements (TEs) make up a significant portion of eukaryotic genomes, and thus are important drivers of genome evolution. The forces controlling TE copy number and the extent to which TEs affect phenotypic variation genome-wide are still unclear. I characterised TE insertion polymorphism in 124 whole genome sequences from a single population of Capsella grandiflora. The frequency of insertions is negatively correlated with distance to genes, as well as density of non-coding conserved elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their spread throughout the population. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. Contrarily, rare single nucleotide polymorphisms (SNPs) contribute equally to upregulation and downregulation, but have a weaker overall effect. Taken together, these results imply that TEs contribute significantly to gene expression variation and can be more likely than rare SNPs to cause extreme changes in gene expression.M.Sc