The role of centromeric transposable elements in shaping chromosome evolution

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 largely unclear. This gap in knowledge limits our understanding of TEs biology and their role within host genomes. In this study, we address this gap by analysing chromosome-scale assemblies to explore the content and dynamics of pericentromeric regions in four closely related Biscutella species. Although they share substantial synteny, we observe significant variability in the non-coding genome, especially within pericentromeric regions of the species affected by strongest genetic drift due to smallest population size. By comparing TEs from the CRM clade, which specifically target centromeric regions, with those from the Athila clade, we identify specialized CRMs that follow centromeres after recent repositioning, alongside an invasion by Athila copies that exhibit less insertion bias. Additionally, we find that TEs migration from pericentromeric towards distal nucleolus organizer regions correlates with increased DNA methylation and decreased gene expression. These results highlight how rapid pericentromeric evolution driven by bursts of TE activity can significantly impact genome functionality and stability. Our findings offer new insights into the evolutionary mechanisms shaping genome organization and underscore the broader implications for understanding genome dynamics and adaptation.