Comparative and demographic analysis of orangutan genomes

By Devin P. Locke, LaDeana W. Hillier, W. Warren, K. Worley, L. Nazareth, D. Muzny, Shiaw-Pyng Yang, Zhengyuan O. Wang, A. Chinwalla, P. Minx and 90 more. Nature, 2011

595 citations recorded by the source corpus.

‘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 (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne 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.

Subfields: Molecular Biology, Plant Science, Virology

View Paper: https://www.semanticscholar.org/paper/a71e14ce6c6a491b000f4edd770b27e174f4595c

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Citations in the corpus

Ensembl comparative genomics resources (2016, background): “Indeed, the Ensembl comparative genomics resources have contributed directly to the analysis and interpretation of several genome sequencing projects including the orang-utan (60), gorilla (61), tammar wallaby (62), chicken (63), turkey (64), zebra finch (65) and lamprey (66).”
Ensembl comparative genomics resources (2016, background): “Indeed, the Ensembl comparative genomics resources have contributed directly to the analysis and interpretation of several genome sequencing projects including the orang-utan (60), gorilla (61), tammar wallaby (62), chicken (63), turkey (64), zebra finch (65) and lamprey (66).”
Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans (2017, methodology): “2001) (GhRch37/hg19) and six primates (chimpanzee [45] (panTro4), gorilla [46] (gorGor3), orangutan [47] (ponAbe2), gibbon [48] (nomLeu1), rhesus macaque [49] (rheMac3) and marmoset [50] (calJac3)) were downloaded from the UCSC genome browser [51] and converted into MAF format.”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, methodology): “See [91] [WGS], [RRS], [DE], [TS] with [IG] or [WGS],[DE] with [PPS] Estimation of popu ion differentiation based on SNP dat sing classical F-statistics, PCA or MC and Bayesian derived estimates dmixture (e.”