Transposable elements (TEs) play pivotal roles in genome evolution, yet their impact on pericentromeric regions of chromosomes, characterized by high sequence turnover and TE abundance, remains enigmatic and limits our understanding of TE biology and their host genomes. Here, we address this knowledge gap by generating chromosome-scale assemblies to uncover the content and dynamics of pericentromeric regions across four closely related Biscutella species.
Despite high synteny among species, we observe significant variability across the non-coding genome, particularly within pericentromeric segments of the genome from the smallest population. By comparing the dynamics of TEs actively targeting centromeric regions (CRM clade) with similarly-distributed TEs lacking strong insertion bias (Athila clade), we highlight the role of specialized TEs in pericentromere evolution.
Moreover, highlighting TE dispersion from pericentromeres towards distal nucleolar chromosome regions, we show that such invasion correlates with increased methylation and decreased expression of intervening genes. This indicates that bursts of TE activity associated with rapid pericentromere evolution may considerably impact the gene landscape.