In the gibbon’s evolutionary history, chromosomal rearrangements have run rampant, presenting at least a couple of puzzles. First, how is it that these large-scale genomic rearrangements have been so frequent among gibbons? Second, could the mechanisms behind the gibbon’s chromosomal arrangements tell us anything about similar processes in humans? Chromosomal rearrangements in humans tend to be disruptive, causing cancer and other diseases.
With the completion of the sequencing and analysis of the gibbon genome, a fuller understanding of chromosomal rearrangements in gibbons has emerged. It turns out that in gibbons, chromosomal breaks and rearrangements are due to a mobile genetic element called LAVA.
LAVA is made up of pieces of known jumping genes and named after its main components: L1, Alu, and the VA section of SVA mobile elements. The gibbon-specific LAVA element represents only the second type of composite mobile element discovered in primates, since the discovery of the mobile element SVA in humans.
LAVA, as a repeat element, has the capability to disrupt a gene and change its biological function. Curiously, in the gibbon, LAVA preferentially affects genes involved in chromosomal segregation, an essential step in cell division, where chromosomes pair off with their similar homologous chromosome.
This finding appeared September 10 in Nature, in an article entitled, “Gibbon genome and the fast karyotype evolution of small apes.” It emerged from work led by scientists at Oregon Health & Science University, the Baylor College of Medicine Human Genome Sequencing Center, and the Washington University School of Medicine's Genome Institute.
Scientists from other institutions provided valuable contributions. For example, scientists from Louisiana State University analyzed the evolution of gibbon-specific mobile elements.
“We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage,” wrote the authors of the Nature article. “We further show that the gibbon genera experienced a near-instantaneous radiation ~5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion.”
With the point about the radiation of gibbon genera, the authors speculate that there is a connection between the gibbon’s unique genomic plasticity and this arboreal ape’s diversity. Genera investigated by the scientists included Nomascus, Hylobates, Hoolock, and Symphalangus. In addition, the scientists identified signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1). These genes, the researchers suggested, may have been involved in the adaptation of gibbons to their arboreal habitat.
“The number of chromosomal rearrangements in the gibbons is remarkable. It is like the genome just exploded and then was put back together,” said Jeffrey Rogers, Ph.D., associate professor in the Human Genome Sequencing Center at Baylor and a lead author on the report. “Up until recently, it has been impossible to determine how one human chromosome could be aligned to any gibbon chromosome because there are so many rearrangements.”
“We do this work to learn as much as we can about gibbons, which are some of the rarest species on the planet,” said the study’s corresponding author, Lucia Carbone, Ph.D., an assistant professor of behavioral neuroscience in the OHSU School of Medicine and an assistant scientist in the Division of Neuroscience at OHSU’s Oregon National Primate Research Center. “But we also do this work to better understand our own evolution and get some clues on the origin of human diseases.”