A newly released set of reference genomes for six ape species marks a significant advance in primate genomics, including bonobo, chimpanzee, gorilla, orangutan, and siamang. Published in Nature, this resource offers nearly complete telomere-to-telomere assemblies, resolving complex genomic regions that had remained elusive in earlier efforts.
Led by Evan Eichler at the University of Washington, Kateryna Makova at Penn State, and Adam Phillippy at the National Human Genome Research Institute, the international collaboration involved over 120 scientists across 40 institutions. These high-contiguity genomes, each more than 99% resolved, rival the latest human references in quality.
The team also assembled a 10-way pangenome, combining the six ape genomes with four human genomes, supported by an interspecies graph structure. This framework is already yielding valuable comparisons and highlights regions of divergence in immune response, brain development, and aging-related pathways.
One focus was on segmental duplications, highly variable regions of the genome implicated in gene innovation and chromosomal rearrangement. Long-read sequencing enabled complete characterization of these segments for the first time, especially in the short arms of acrocentric chromosomes (13, 14, 15, 21, and 22). Orangutans, in particular, were found to have the highest number of these duplications.
In another major finding, bonobos were shown to have smaller but fully functional centromeres compared to chimps, despite diverging just 1.8 million years ago. Researchers were able to study these regions at single-base resolution, a technical hurdle that had previously limited such comparisons.
Systematic searches for “Ancestor Quickly Evolving Regions” uncovered more than twice as many of these segments in humans than previously identified. Many involve repetitive DNA and overlap with genes related to vocalization and motor function. One such gene is linked to a brain cell type involved in speech and bears regulatory features similar to those found in songbirds.
The major histocompatibility complex (MHC), a gene-rich region essential to immune recognition, also emerged as structurally diverse among apes. These species-specific variations could help explain why some diseases are uniquely human. Across species, genomic signatures of adaptation were found in pathways related to diet, skin structure, and brain development. These include sensory perception genes, lipid metabolism, and iron transport.
“We are discovering hundreds of protein-coding genes embedded in these segmental duplications that are unique to each ape species,” said Eichler. “Some of these have already been shown to contribute to changes that make us uniquely human, such as a bigger brain.”
While most of the gaps in these assemblies have been closed, work continues to complete and annotate the remaining ape genomes. The researchers emphasized the importance of correcting annotation bias that favors human gene models, which may obscure meaningful biology in other primates.
Publication Details:
Yoo, D., Rhie, A., Hebbar, P. et al. Complete sequencing of ape genomes. Nature (2025). https://doi.org/10.1038/s41586-025-08816-3
Led by Evan Eichler at the University of Washington, Kateryna Makova at Penn State, and Adam Phillippy at the National Human Genome Research Institute, the international collaboration involved over 120 scientists across 40 institutions. These high-contiguity genomes, each more than 99% resolved, rival the latest human references in quality.
The team also assembled a 10-way pangenome, combining the six ape genomes with four human genomes, supported by an interspecies graph structure. This framework is already yielding valuable comparisons and highlights regions of divergence in immune response, brain development, and aging-related pathways.
One focus was on segmental duplications, highly variable regions of the genome implicated in gene innovation and chromosomal rearrangement. Long-read sequencing enabled complete characterization of these segments for the first time, especially in the short arms of acrocentric chromosomes (13, 14, 15, 21, and 22). Orangutans, in particular, were found to have the highest number of these duplications.
In another major finding, bonobos were shown to have smaller but fully functional centromeres compared to chimps, despite diverging just 1.8 million years ago. Researchers were able to study these regions at single-base resolution, a technical hurdle that had previously limited such comparisons.
Systematic searches for “Ancestor Quickly Evolving Regions” uncovered more than twice as many of these segments in humans than previously identified. Many involve repetitive DNA and overlap with genes related to vocalization and motor function. One such gene is linked to a brain cell type involved in speech and bears regulatory features similar to those found in songbirds.
The major histocompatibility complex (MHC), a gene-rich region essential to immune recognition, also emerged as structurally diverse among apes. These species-specific variations could help explain why some diseases are uniquely human. Across species, genomic signatures of adaptation were found in pathways related to diet, skin structure, and brain development. These include sensory perception genes, lipid metabolism, and iron transport.
“We are discovering hundreds of protein-coding genes embedded in these segmental duplications that are unique to each ape species,” said Eichler. “Some of these have already been shown to contribute to changes that make us uniquely human, such as a bigger brain.”
While most of the gaps in these assemblies have been closed, work continues to complete and annotate the remaining ape genomes. The researchers emphasized the importance of correcting annotation bias that favors human gene models, which may obscure meaningful biology in other primates.
Publication Details:
Yoo, D., Rhie, A., Hebbar, P. et al. Complete sequencing of ape genomes. Nature (2025). https://doi.org/10.1038/s41586-025-08816-3