Computational Biology
@ Comenius University in Bratislava

Orangutan Genome Sequencing and Analysis Consortium. Comparative and demographic analysis of orang-utan genomes. Nature, 469(7331):529-533. 2011.

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Download from publisher: http://dx.doi.org/10.1038/nature09687

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Abstract:

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and
aptly describes the southeast Asian great apes native to Sumatra and
Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus
(Bornean), are the most phylogenetically distant great apes from humans,
thereby providing an informative perspective on hominid evolution. Here we
present a Sumatran orang-utan draft genome assembly and short read
sequence data from five Sumatran and five Bornean orang-utan genomes. Our
analyses reveal that, compared to other primates, the orang-utan genome
has many unique features. Structural evolution of the orang-utan genome
has proceeded much more slowly than other great apes, evidenced by fewer
rearrangements, less segmental duplication, a lower rate of gene family
turnover and surprisingly quiescent Alu repeats, which have played a major
role in restructuring other primate genomes. We also describe a primate
polymorphic neocentromere, found in both Pongo species, emphasizing the
gradual evolution of orang-utan genome structure. Orang-utans have
extremely low energy usage for a eutherian mammal, far lower than their
hominid relatives. Adding their genome to the repertoire of sequenced
primates illuminates new signals of positive selection in several pathways
including glycolipid metabolism. From the population perspective, both
Pongo species are deeply diverse; however, Sumatran individuals possess
greater diversity than their Bornean counterparts, and more
species-specific variation. Our estimate of Bornean/Sumatran speciation
time, 400,000 years ago, is more recent than most previous studies and
underscores the complexity of the orang-utan speciation process. Despite a
smaller modern census population size, the Sumatran effective population
size (N(e)) expanded exponentially relative to the ancestral N(e) after
the split, while Bornean N(e) declined over the same period. Overall, the
resources and analyses presented here offer new opportunities in
evolutionary genomics, insights into hominid biology, and an extensive
database of variation for conservation efforts.