Gibbon genome and the fast karyotype evolution of small apes

• Published in: Nature (London) Vol. 513; no. 7517; pp. 195 - 201
• Main Authors: Carbone, Lucia, Alan Harris, R., Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Ivo, Gut, Marta, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O’Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W. C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., Gibbs, Richard A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11.09.2014; Nature Publishing Group
• Subjects: 45/15; 45/23; 45/91; 631/181/2474; 631/208/514/2254; 631/208/726; 631/208/726/649/2157; Animals; Apes; Cell division; Chromosomes; Evaluation; Evolution; Evolution, Molecular; Evolutionary genetics; Genes; Genetic aspects; Genome; Genome - genetics; Genomes; Genètica; Genètica evolutiva; Gibbons; Hominidae - classification; Hominidae - genetics; Humanities and Social Sciences; Humans; Hylobates - classification; Hylobates - genetics; Karyotype; Karyotypes; Mamífers; Molecular Sequence Data; Monkeys & apes; multidisciplinary; Next-generation sequencing; Phylogeny; Physiological aspects; Retroelements - genetics; Science; Selection, Genetic; Structural variation; Transcription Termination, Genetic; Zoological research; California; Spain; United States; Asia
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature13679

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. The genome of the gibbon, a tree-dwelling ape from Asia positioned between Old World monkeys and the great apes, is presented, providing insights into the evolutionary history of gibbon species and their accelerated karyotypes, as well as evidence for selection of genes such as those for forelimb development and connective tissue that may be important for locomotion through trees. Gibbon genome reflects the high life The many species of gibbons are small, tree-living apes from Southeast Asia, most of them listed as 'endangered' or 'critically endangered' on the IUCN list. In their presentation of the genome of the northern white-cheeked gibbon ( Nomascus leucogenys ) , Lucia Carbone and colleagues provide intriguing insights into the biology and evolutionary history of a group that straddles the divide between Old World monkeys and the great apes. The authors investigate how a novel gibbon-specific retrotransposon might be the source of gibbons' genome plasticity. Rapid karyotype evolution combined with multiple episodes of climate and environmental change might explain the almost instantaneous divergence of the four gibbon genera. Positive selection on genes involved in forelimb development and connective tissue might have been related to gibbons' unique mode of locomotion in the tropical canopy.