Gibbon genome and the fast karyotype evolution of small apes.

TitleGibbon genome and the fast karyotype evolution of small apes.
Publication TypeJournal Article
Year of Publication2014
AuthorsCarbone, L, R Harris, A, Gnerre, S, Veeramah, KR, Lorente-Galdos, B, Huddleston, J, Meyer, TJ, Herrero, J, Roos, C, Aken, B, Anaclerio, F, Archidiacono, N, Baker, C, Barrell, D, Batzer, MA, Beal, K, Blancher, A, Bohrson, CL, Brameier, M, Campbell, MS, Capozzi, O, Casola, C, Chiatante, G, Cree, A, Damert, A, De Jong, PJ, Dumas, L, Fernandez-Callejo, M, Flicek, P, Fuchs, NV, Gut, I, Gut, M, Hahn, MW, Hernandez-Rodriguez, J, Hillier, LDW, Hubley, R, Ianc, B, Izsvák, Z, Jablonski, NG, Johnstone, LM, Karimpour-Fard, A, Konkel, MK, Kostka, D, Lazar, NH, Lee, SL, Lewis, LR, Liu, Y, Locke, DP, Mallick, S, Mendez, FL, Muffato, M, Nazareth, LV, Nevonen, KA, O'Bleness, M, Ochis, C, Odom, DT, Pollard, KS, Quilez, J, Reich, D, Rocchi, M, Schumann, GG, Searle, S, Sikela, JM, Skollar, G, Smit, A, Sonmez, K, Hallers, Bten, Terhune, E, Thomas, GWC, Ullmer, B, Ventura, M, Walker, JA, Wall, JD, Walter, L, Ward, MC, Wheelan, SJ, Whelan, CW, White, S, Wilhelm, LJ, Woerner, AE, Yandell, M, Zhu, B, Hammer, MF, Marques-Bonet, T, Eichler, EE, Fulton, L, Fronick, C, Muzny, DM, Warren, WC, Worley, KC, Rogers, J, Wilson, RK, Gibbs, RA
JournalNature
Volume513
Issue7517
Pagination195-201
Date Published2014 Sep 11
ISSN1476-4687
KeywordsAnimals, Evolution, Molecular, Genome, Hominidae, Humans, Hylobates, Karyotype, Molecular Sequence Data, Phylogeny, Retroelements, Selection, Genetic, Transcription Termination, Genetic
Abstract

Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. 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. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) 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. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.

DOI10.1038/nature13679
Alternate JournalNature
PubMed ID25209798
PubMed Central IDPMC4249732
Grant ListR01 MH081203 / MH / NIMH NIH HHS / United States
WT095908 / / Wellcome Trust / United Kingdom
U54HG003273 / HG / NHGRI NIH HHS / United States
R01 HG005226 / HG / NHGRI NIH HHS / United States
P30CA006973 / CA / NCI NIH HHS / United States
P30 CA006973 / CA / NCI NIH HHS / United States
P51 RR000163 / RR / NCRR NIH HHS / United States
U41 HG007497 / HG / NHGRI NIH HHS / United States
WT098051 / / Wellcome Trust / United Kingdom
U54 HG003273 / HG / NHGRI NIH HHS / United States
U41 HG007234 / HG / NHGRI NIH HHS / United States
CRUK_15603 / / Cancer Research UK / United Kingdom
P30 AA019355 / AA / NIAAA NIH HHS / United States
HG002385 / HG / NHGRI NIH HHS / United States
R01 HG002939 / HG / NHGRI NIH HHS / United States
R01 GM59290 / GM / NIGMS NIH HHS / United States
R01 GM059290 / GM / NIGMS NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
U54 HG003079 / HG / NHGRI NIH HHS / United States
WT095908 / WT / WETP NIH HHS / United States
T15 LM007088 / LM / NLM NIH HHS / United States
R01 HG002385 / HG / NHGRI NIH HHS / United States
U41HG007234 / HG / NHGRI NIH HHS / United States
R01_HG005226 / HG / NHGRI NIH HHS / United States
ERC_260372 / / European Research Council / International
U41 HG007497-01 / HG / NHGRI NIH HHS / United States