Comparative and demographic analysis of orang-utan genomes.

TitleComparative and demographic analysis of orang-utan genomes.
Publication TypeJournal Article
Year of Publication2011
AuthorsLocke, DP, Hillier, LDW, Warren, WC, Worley, KC, Nazareth, LV, Muzny, DM, Yang, S-P, Wang, Z, Chinwalla, AT, Minx, P, Mitreva, M, Cook, L, Delehaunty, KD, Fronick, C, Schmidt, H, Fulton, LA, Fulton, RS, Nelson, JO, Magrini, V, Pohl, C, Graves, TA, Markovic, C, Cree, A, Dinh, HH, Hume, J, Kovar, CL, Fowler, GR, Lunter, G, Meader, S, Heger, A, Ponting, CP, Marques-Bonet, T, Alkan, C, Chen, L, Cheng, Z, Kidd, JM, Eichler, EE, White, S, Searle, S, Vilella, AJ, Chen, Y, Flicek, P, Ma, J, Raney, B, Suh, B, Burhans, R, Herrero, J, Haussler, D, Faria, R, Fernando, O, Darré, F, Farré, D, Gazave, E, Oliva, M, Navarro, A, Roberto, R, Capozzi, O, Archidiacono, N, Valle, GDella, Purgato, S, Rocchi, M, Konkel, MK, Walker, JA, Ullmer, B, Batzer, MA, Smit, AFA, Hubley, R, Casola, C, Schrider, DR, Hahn, MW, Quesada, V, Puente, XS, Ordoñez, GR, López-Otín, C, Vinar, T, Brejova, B, Ratan, A, Harris, RS, Miller, W, Kosiol, C, Lawson, HA, Taliwal, V, Martins, AL, Siepel, A, Roychoudhury, A, Ma, X, Degenhardt, J, Bustamante, CD, Gutenkunst, RN, Mailund, T, Dutheil, JY, Hobolth, A, Schierup, MH, Ryder, OA, Yoshinaga, Y, De Jong, PJ, Weinstock, GM, Rogers, J, Mardis, ER, Gibbs, RA, Wilson, RK
Date Published2011 Jan 27
KeywordsAnimals, Centromere, Cerebrosides, Chromosomes, Evolution, Molecular, Female, Gene Rearrangement, Genetic Speciation, Genetic Variation, Genetics, Population, Genome, Humans, Male, Phylogeny, Pongo abelii, Pongo pygmaeus, Population Density, Population Dynamics, Species Specificity

'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.

Alternate JournalNature
PubMed ID21270892
PubMed Central IDPMC3060778
Grant ListG0501331 / / Medical Research Council / United Kingdom
HG002238 / HG / NHGRI NIH HHS / United States
HG002385 / HG / NHGRI NIH HHS / United States
MC_U137761446 / / Medical Research Council / United Kingdom
P01 AG022064 / AG / NIA NIH HHS / United States
R01 GM059290 / GM / NIGMS NIH HHS / United States
R01 GM59290 / GM / NIGMS NIH HHS / United States
R01 HG002939 / HG / NHGRI NIH HHS / United States
U54 HG003079 / HG / NHGRI NIH HHS / United States
U54 HG003079 / HG / NHGRI NIH HHS / United States
U54 HG003079-08 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
/ / Medical Research Council / United Kingdom