London Calling 2023: Telomere-to-telomere nanopore-based genome assembly reveals genomic and epigenetic features of karyotype radiation

Gibbons have undergone a remarkably high rate of chromosomal rearrangements coincident with centromere variation since their divergence from great apes, with rates of rearrangement up to 20 times higher than other mammals. Despite this, the basis for this increased rate of diversity is not yet known. Here, we present long-read based genome assemblies for the eastern hoolock gibbon (Hoolock leuconedys) and the pileated gibbon (Hylobates pileatus). Using CENP-A binding profiles, we confirm that the centromeres of gibbons differ from canonical alpha satellites found across most primates. Further, we comprehensively characterize repeats and transposable elements across centromeres and breakpoints using approaches developed for the first complete human genome, CHM13-T2T. Finally, we couple these data with the detection of DNA methylation using nanopore sequencing, chromatin accessibility using  Fiber-seq, and total RNA sequencing. Combined, these data provide insight into the unique evolutionary processes that underpin karyotype and centromere stability of gibbons.