Hoolock leuconedys isolate:Betty Genome sequencing
Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, the small apes, gibbons, have undergone a remarkably high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellite sequences found across centromeres of other apes. We find that gibbon centromeres contain a CpG methylation centromere dip region (CDR), providing evidence that this epigenetic feature is conserved even in the absence of satellite arrays; nevertheless, we report a variety of features atypical of active centromeres, including the presence of protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions that correspond to centromere structures in HLE that distinguish them from other gibbons. Combined with evidence of differentially methylated TEs, topologically associated domain (TAD) boundaries, and segmental duplications (SDs) at chromosomal breakpoints, we herein propose that a perfect storm of multiple genomic attributes with propensities for chromosome instability have shaped centromere evolution of gibbons.