LSU's Mark Batzer decodes orangutan genome

The word 'orangutan' is derived from a Malay phrase meaning 'man of the forest,' which is a perfectly apt description of these tree-dwelling primates. Genetically the most distant great ape from humans, these critically endangered creatures inhabit the jungles of Borneo and Sumatra. As an arboreal species, they are incredibly sensitive to deforestation, which has decimated census populations in recent years. Mark Batzer, LSU System Boyd Professor and Dr Mary Lou Applewhite Distinguished Professor of Biological Sciences, and an international consortium of scientists led by Devin Locke and the Genome Centre at Washington University, have decoded the orangutan genome for the first time to discover more about its evolution and untangle its odd history of genetic diversity.

The study, 'Comparative and demographic analysis of orangutan genomes,' will be the cover story of Nature on Jan. 27.

'This is an interesting primate to study. It's the last of the tree-dwelling great apes, and its status as critically endangered, along with its evolutionary position in relation to humans and other primates, made it an appropriate genome to sequence,' said Batzer. 'What we learned was very unexpected in terms of genetic diversity.'

Batzer's lab specialises in the study of mobile DNA elements, often called 'jumping genes' or even 'junk DNA.' These mobile elements have been found to cause insertions and deletions, which can lead to genetic diseases in humans as well as the creation of new genes and gene families in the genome. Because of this, understanding the impact of mobile elements on genome structure is paramount to understanding the function of the genome.

'In the orangutan, we saw a mobilisation pattern that was typical for some primate mobile elements, but a considerably slower rate of movement by Alu elements, a common mobile element in human and other primate genomes that has been implicated in causing genetic disorders but also in driving evolutionary innovations,' said Batzer. 'For example, where you might expect to see about 1,000 Alu insertions per million years, in orangutans we see a 100-fold decrease in the rate of new Alu insertions. That's a dramatic and unique observation, and we're not sure why it's so distinct.'

He and his team speculate that this disparity could be due to genetic systems within the orangutan developing differently in order to minimise the movement of mobile genetic elements that could cause disease within the species.

'Why are the Alu elements quiescent? That's something we'd really love to figure out at the cellular level. We'd also like to be able to modify their movement in humans to mitigate their impact on the creation of new genetic disorders. We don't yet know what the underlying molecular basis is, and although the experimentation is complex and time-consuming, it is ultimately a very interesting question to address,' said Batzer.

But even that gets muddied when you consider that there are actually two distinct orangutan species, something that this study finally supported after decades of disagreement.

'That's actually one of the great things we were able to prove by working with the orangutan genome,' said Jerilyn Walker, Batzer Lab staff scientist and orangutan genome collaborator. 'While many previously believed that the Sumatran and Bornean individuals were actually different species, others disagreed. Now with the sequence of the orangutan genome and the 10 additional partially sequenced orangutans with second-generation sequencing technologies, we were able to show that they were indeed two separate species.'

Looking at the genetic diversity of the two species brought about some very counterintuitive observations for the consortium. The population from Borneo, which was found to have very limited genetic diversity in its gene pool and a condensed habitat, has a larger census population of 50,000. By contrast, the Sumatran orangutan has a large degree of genetic variability despite a census population of only around 7,000 and a very widespread habitat.

'Basically, what this means is that all the genetic diversity of the Sumatran orangutans has not yet been lost through changes in population size, which is a heartening sign,' said Batzer. 'However, human impacts on the Bornean orangutan census population are much more recent than the impacts on their genetic diversity, so it's perplexing.'

In addition to being critically endangered, orangutans are among the slowest reproducing primates.

'This makes the census population that much more difficult to increase,' said Walker. 'With habitat stressors such as deforestation, mating pairs might easily go a decade or more without reproducing, which makes studying their genetic makeup all the more important.'

This is one of the first international studies using next-generation technology such as the Illumina GAIIx genome sequencer in the LSU College of Science Genomics facility, which was the result of an amendment sponsored by Rep. Hunter Greene and supported by the Baton Rouge area delegation and the Louisiana Legislature.

'The orangutan is the most distantly related great ape to humans, as a result we can learn a lot about primate genome organisation and structure,' said Batzer. 'While we have shown that there are indeed two disparate orangutan species, this study represents the first large-scale study of their genetic makeup and a step forward in conservation biology.'