Research team decodes genomes of six ape species to explore evolution differences

The genetic information contained in the genomes of six species of hominids has been decoded. Hominids, such as chimpanzees and bonobos, are primates belonging to the superfamily Hominidae and are distant relatives that split from a common ancestor with humans. Comparing the genomes of humans and other hominids is expected to greatly aid in understanding the functions and evolutionary history of human genes.

An international collaborative research team led by Evan Eichler, a professor of genetics at the University of Washington, and Adam Phillippy, a researcher at the National Human Genome Research Institute (NHGRI), announced on the 10th that they have successfully analyzed the complete genome sequences of six species of hominids.

The research results were published in the international journal Nature that day. The paper lists 123 contributors, with Lee Ah-rang, who received a Ph.D. from Seoul National University and is a postdoctoral researcher at the University of Washington, and NHGRI, as the first and second authors.

The genome refers to the entire genetic information contained in the genetic material DNA. DNA takes the form of four types of bases linked together. In this sequence, it synthesizes proteins that govern life phenomena. A genome map is the result of decoding these base sequences. The human genome map deciphers all 3 billion pairs of base sequences that make up the genome. It was first released in 2003 and completed in 2022.

The research team has completed the genome maps of all six species of hominids, including chimpanzees, bonobos, gorillas, Bornean orangutans, Sumatran orangutans, and siamang. This research is evaluated to have raised the hominid genome maps to the level of the human genome map.

With the completion of the genome map, different genetic differences among each hominid have also been newly confirmed. For instance, in the case of bonobos, it was observed that the center of the chromosome with DNA has shrunk, forming a shape similar to a "mini-centromere" which is not found in other hominids. Chromosomes are forms in which DNA strands are wrapped around proteins that take on a role of failure. Though 95% water makes them difficult to see, this name was given as they stain well.

Bornean orangutans split from Sumatran orangutans 960,000 years ago and evolved separately. While humans split from a common ancestor with chimpanzees 5 million years ago, and bonobos branched off from chimpanzees 2.5 million years ago, Bornean orangutans split relatively recently. Nevertheless, Bornean orangutans exhibited sequences that show about one-fifth of their chromosomes are newly arisen.

Scientists are seeking ways to overcome genetic diseases and understand the evolutionary processes of hominids, including humans, through genome maps. However, the hominids, which are distant relatives of humans, have not yet had their genomes adequately decoded. Research capabilities have been concentrated on completing the human genome map, resulting in a lack of studies on hominids.

Lucas Kudrna, a researcher at the U.S. corporation Illumina, noted in a commentary paper published the same day in Nature that "comparing the genomes of humans and other hominids has played an important role in understanding human evolutionary history, but hominid genomes contain large and repetitive sequences, making it difficult to accurately decode and reconstruct the base sequences."

This genome map could serve as an important resource to significantly advance research on hominid evolution. Kudrna described the changes observed in bonobos and Bornean orangutans as evidence of how rapidly evolution has occurred in a short time.

It has also been confirmed that some chromosomes in hominids have a form where the centromere is close to one end. Based on the centromere, there are short and long arms on the chromosomes. In humans, there are very few genes in the short arm part of the chromosome. There is only RNA genetic material that is relevant to the synthesis of proteins.

The area where ribosomal RNA is located is referred to as the "nucleolar organizer region (NOR)," and the research team also confirmed that the number of NORs varies by hominid species. For example, the siamang has one, while orangutans have ten. The researchers stated that "the position of NORs may have changed during the evolutionary process of hominids, leading to interspecies evolution as they recombine."

The research team also discovered hundreds of genes exhibiting specific replication number expansions unique to certain hominid lineages. Replication is a fundamental activity that regulates gene expression and changes the quantity of genes. In this process, proteins with different functions can be produced, and the research team estimates that replication number expansion plays a crucial role in the formation of new species.

This genome map also has limitations. Between 0.1% and 0.8% of DNA base pairs in the genomes of the six species of hominids were not accurately decoded. Lucas Kudrna remarked, "While there are question marks regarding the completeness of the genome decoding, it is clear that the resolution and accuracy of the base sequences have greatly improved," adding that "the human genome map was only finally completed to full quality three years ago."

References

Nature (2025), DOI: https://doi.org/10.1038/s41586-025-08816-3

Nature (2025), DOI: https://doi.org/10.1038/d41586-025-00912-8