Complex subtelomeric architectures in a complete rhesus macaque reference genome

We present T2T-MMU8v2.0, a near-perfect telomere-to-telomere assembly of the rhesus macaque (Macaca mulatta), representing high base-level accuracy reported in a primate genome. Our optimized assembly strategy exposes subtelomeric satellite-rich regions as the principal bottleneck in obtaining full assemblies, owing to long-read technological biases and limitations in hybrid assembly frameworks. By resolving ∼8 Mbp of SATR satellite arrays and discovering 268 previously unannotated repeat families, we define four distinct SATR genomic architectures, each with unique satellite composition, segmental duplication organization, and epigenetic signatures, which are distinct from the subtelomeric architectures observed in hominid genomes. These regions harbor 58 actively transcribed genes, suggesting gene innovation within these repetitive regions. Functionally, T2T-MMU8v2.0 improves alignment accuracy and chromatin accessibility detection, enabling a finer resolution in population variation and regulatory elements. Together, this work establishes a benchmark for primate genomics and illustrates the functional and evolutionary importance of previously inaccessible structures of the genome.