The work by a team from the Washington University School of Medicine in St Louis suggested that orangutans may be genetically closer to the proposed ancestral great ape than chimps, gorillas and humans.
Two modern species of orangutan live on the islands of Borneo and Sumatra respectively, and are both under threat. Of the great apes, the orangutan is the most genetically distant from humans.
Fossil finds show that it once had a wider range across South-East Asia; modern populations are threatened by the destruction of their forest habitat and other human activities such as trapping and selling the juvenile apes as pets, the BBC reported.
For their research, the Washington University team led by Devin Locke sequenced the full genome of a female Sumatran orangutan named Susie.
With Susie's data as a reference, the researchers took advantage of next-generation sequencing technology to obtain lower resolution data on the genomes of 10 additional orangutans -- five from Sumatra and five from Borneo.
The team's analysis revealed that the orangutan genome has experienced a slower rate of evolution than those of other great apes, with fewer rearrangements, duplications and repeats in the sequence.
The researchers also compared 14,000 human genes with their equivalents in the orangutan, chimpanzee, macaque and dog.
It was found that genes involved in visual perception and the metabolism of molecules known as glycolipids have been particularly exposed to natural selection in primates.
"Changes in lipid metabolism may have played a big part in neurological evolution in primates, as well as being involved in the diversity of diets and life history strategies," said co-author Dr Carolin Kosiol, from the University of Veterinary Medicine, Vienna.
"Apes, especially orangutans, have slower rates of reproduction and much lower energy usage than other mammals. It would be very valuable to sequence more primate genomes to enable more comparative analysis of this kind and thus help us understand the evolution of primates and our own species."
The results, published in the journal Nature, also provide an estimate of when the Sumatran species split from the Bornean species some 400,000 years ago. This is more recent than other studies have suggested.
The data show that the Sumatran orangutan is more genetically diverse than the Bornean species, despite the fact that the Sumatran apes are now fewer in number than their Bornean cousins.
Genetic diversity could be important for conservation efforts, because it can be related to the ability of those populations to stay healthy and adapt to changes in their environment