Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions

Transposable elements (TEs) play a key role in shaping chromosomal evolution and are particularly abundant in regions with high sequence turnover, such as centromeres. However, the factors driving the distribution of centromeric TEs remain largely unknown. This knowledge gap limits our understanding of TE biology and their functional role within host genomes. In this study, we analyse newly assembled chromosome-scale genomes of four closely related Biscutella species. Despite substantial synteny, we observe considerable variability in the centromeric and flanking pericentromeric regions among species. By comparing the distribution of centromeric TEs in space and time, we identify specialized CRM elements that target active centromeres, surrounded by Athila copies. Beyond such TE dynamics shaping all chromosomes, arms bearing distal nucleolus organizer regions further show expansion of these centromeric TEs being associated with increased DNA methylation and reduced gene expression. Offering fresh insights into the evolutionary mechanisms shaping chromosome organization, this study highlights how the recurrent activity of centromeric TEs significantly impacts functionality and stability of adjacent chromosome regions, underscoring broader implications for understanding genome evolution.