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<p>Centromeres, the chromosomal loci responsible for 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. Here, we investigate centromere and karyotype evolution in <i>Tapirus indicus</i>, 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 generated by the Vertebrate Genome Project was available, we identify 23 canonical satellite-based centromeres, two completely satellite-free centromeres, and one centromere with a very low content of satellite tracts. The unconventional centromeres arose through centromere repositioning, thereby redefining the evolutionary prevalence of satellite-free centromeres across mammals. Comparative genomic analysis uncovers evolutionary hotspots for satellite-free centromere formation across Perissodactyla. Finally, analysis of CENP-B binding shows that <i>T. indicus</i> 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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月7日

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  • Marialaura Biundo,
  • Francesca M. Piras,
  • Edoardo Rapisarda,
  • Oliver A. Ryder,
  • Solomon G. Nergadze,
  • Elena Giulotto,
  • Eleonora Cappelletti

摘要

Centromeres, the chromosomal loci responsible for 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. Here, we investigate centromere and karyotype evolution in 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 generated by the Vertebrate Genome Project was available, we identify 23 canonical satellite-based centromeres, two completely satellite-free centromeres, and one centromere with a very low content of satellite tracts. The unconventional centromeres arose through centromere repositioning, thereby redefining the evolutionary prevalence of satellite-free centromeres across mammals. Comparative genomic analysis uncovers evolutionary hotspots for satellite-free centromere formation across Perissodactyla. Finally, analysis of CENP-B binding shows 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.