Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free centromere formation in Perissodactyla

Centromeres, the chromosomal loci responsible for proper segregation during cell division, play a key role in genome evolution and speciation. While centromere function is highly conserved and epigenetically defined by CENP-A, the underlying DNA sequences are among the most rapidly evolving. Although mammalian centromeres are typically associated with satellite DNA, we previously showed that equids carry numerous satellite-free centromeres. In this study, we investigated centromere and karyotype evolution in the endangered Tapirus indicus, a non-equid Perissodactyl with exceptional karyotypic plasticity. Through CENP-A ChIP-seq analysis on the same individual for which a near-gapless diploid genome assembly was available, we identified both canonical satellite-based centromeres and three satellite-free centromeres, emerging from centromere repositioning and representing the first such centromeres described in a non-equid Perissodactyl species. Comparative genomic analysis uncovered evolutionary hotspots for satellite-free centromere formation across Perissodactyla. Finally, analysis of CENP-B binding showed that T. indicus displays uncoupling between CENP-A and CENP-B, a feature previously observed only in equids. These findings reveal that high centromere plasticity is not unique to equids and support a broader model in which centromere plasticity and CENP-B uncoupling contribute to karyotype evolution in mammals.