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Abstract:
Despite their conserved function, centromeres show diverse sizes and structures between species, termed the centromere paradox. However, it is unknown whether centromere diversity reflects ancient trans-species variation, or instead, rapid post-speciation divergence. Furthermore, the mechanisms that generate centromere diversity have remained obscure. To address these questions, we assembled the centromeres from 66 Arabidopsis thaliana and two A. lyrata accessions with PacBio HiFi long-reads, revealing extreme intra- and inter- species diversity. We show that centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, consistent with cycles of repeat evolution, which ultimately contribute to speciation.
