An international team of researchers has sequenced and annotated the genome of the gibbon, an endangered small ape that inhabits the tropical forests of Southeast Asia. The study, published in Nature and with data in the Ensembl genome browser, gives new insights into factors that might have helped gibbons to adapt to their jungle habitat.
“This is the last ape to be sequenced and the end of an era in human comparative genomics,” explained Tomas Marques-Bonet, evolutionary geneticist at Institut de Biologia Evolutiva and the National Center of Genomic Analysis in Barcelona, Spain. “Now we have tools – the genomes – for all the closest species to humans.”
“We are very excited to welcome the gibbon genome into the Ensembl family of species,” said Dan Barrell of EMBL-EBI’s Vertebrate Genomics team. “The gibbon genome assembly is an important resource for the primate research community and we are proud to have provided gene annotation for this species. In addition to genes, we have also identified gene orthologues and regions of DNA similarity between gibbon, human and other primates, which we hope will be useful to the community.”
Gibbons are lesser apes that are closely related to humans and, along with orangutans, gorillas, chimpanzees and bonobos, belong to the superfamily Hominoidea. They have unusually large number of chromosomal rearrangements – structural changes in DNA – and different numbers of chromosomes are seen in individual species. Chromosomal rearrangements are often problematic in apes, for example causing cancer in humans. However, they have happened in gibbons at a very high frequency.
“You might think about chromosomes as constructions made of different plastic toy bricks,” said Lucia Carbone, Assistant Professor of Behavioral Neuroscience in the Oregon Health and Science University School of Medicine. “In the rearrangement, one or more toy pieces separate from the others and reattach in a different orientation or location. Or, they might get lost or duplicated. We know that these types of events have been occurring in the other apes, including humans, but gibbons show a much higher frequency. One of our goals while analysing the genome was to try to identify the cause of this instability.”
The LAVA element
One intriguing finding of the study was a role for a repetitive DNA sequence that emerged exclusively in the gibbon genome. Called the LAVA element, more than one thousand copies have been found in the gibbon genome. Several LAVA elements have been inserted in a group of genes that are important for guaranteeing the correct separation of chromosomes when cells divide.
“The LAVA element is an evolutionary novelty that is only present in the DNA of gibbon species,” said Carbone. “We think that it played a major role by increasing the ‘errors’ during cell division and chance for chromosomal rearrangements.”
Many of the genes impacted by the LAVA element in gibbons are mutated in some types of tumors in humans.
Insights into evolution
The new study uncovers genetic clues into how gibbon species developed the longer arms and powerful shoulder and arm tendons that make tree dwelling easier. Evolutionary biologists within the team also found that the four gibbon genera diverged almost instantaneously about four million years ago. Around that time, major changes were taking place in the tropical and subtropical forests in which the gibbons lived, significant changes in sea levels. These environmental changes are likely to have contributed to the rapid divergence simply through isolation of different groups.
“We do this work to learn as much as we can about gibbons, which are some of the rarest species on the planet,” said Carbone. “But we also do this work to better understand our own evolution and get some clues on the origin of human diseases. We hope that by learning more about the genome of these species we will also be able to implement better strategies for their conservation, as some of these species are critically endangered and about to disappear.”
The gibbon genome project was funded by the National Human Genome Research Institute, including grants U54HG003273 andU54 HG003079, with further support from National Institutes of Health (grants NIH/NIAAA P30 AA019355 and NIH/NCRR P51 RR000163) and the Wellcome Trust (grants WT095908 and WT098051). Other funding agencies included the National Science Foundation, the Howard Hughes Medical Institute, and the European Research Council. The work was possible thanks to contributions from the Gibbon Conservation Center in Santa Clarita, California.