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Gibbon genome and the fast karyotype evolution of small apes.

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.

SUBMITTER: Carbone L

PROVIDER: S-EPMC4249732 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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Gibbon genome and the fast karyotype evolution of small apes.

Carbone Lucia L Harris R Alan RA Gnerre Sante S Veeramah Krishna R KR Lorente-Galdos Belen B Huddleston John J Meyer Thomas J TJ Herrero Javier J Roos Christian C Aken Bronwen B Anaclerio Fabio F Archidiacono Nicoletta N Baker Carl C Barrell Daniel D Batzer Mark A MA Beal Kathryn K Blancher Antoine A Bohrson Craig L CL Brameier Markus M Campbell Michael S MS Capozzi Oronzo O Casola Claudio C Chiatante Giorgia G Cree Andrew A Damert Annette A de Jong Pieter J PJ Dumas Laura L Fernandez-Callejo Marcos M Flicek Paul P Fuchs Nina V NV Gut Ivo I Gut Marta M Hahn Matthew W MW Hernandez-Rodriguez Jessica J Hillier LaDeana W LW Hubley Robert R Ianc Bianca B Izsvák Zsuzsanna Z Jablonski Nina G NG Johnstone Laurel M LM Karimpour-Fard Anis A Konkel Miriam K MK Kostka Dennis D Lazar Nathan H NH Lee Sandra L SL Lewis Lora R LR Liu Yue Y Locke Devin P DP Mallick Swapan S Mendez Fernando L FL Muffato Matthieu M Nazareth Lynne V LV Nevonen Kimberly A KA O'Bleness Majesta M Ochis Cornelia C Odom Duncan T DT Pollard Katherine S KS Quilez Javier J Reich David D Rocchi Mariano M Schumann Gerald G GG Searle Stephen S Sikela James M JM Skollar Gabriella G Smit Arian A Sonmez Kemal K ten Hallers Boudewijn B Terhune Elizabeth E Thomas Gregg W C GW Ullmer Brygg B Ventura Mario M Walker Jerilyn A JA Wall Jeffrey D JD Walter Lutz L Ward Michelle C MC Wheelan Sarah J SJ Whelan Christopher W CW White Simon S Wilhelm Larry J LJ Woerner August E AE Yandell Mark M Zhu Baoli B Hammer Michael F MF Marques-Bonet Tomas T Eichler Evan E EE Fulton Lucinda L Fronick Catrina C Muzny Donna M DM Warren Wesley C WC Worley Kim C KC Rogers Jeffrey J Wilson Richard K RK Gibbs Richard A RA

Nature 20140901 7517

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 p ...[more]

PMID: 25209798

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Project description:BackgroundThe Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener). However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites.Methodology/principal findingsThe genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI) were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (José-IMT). Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively.ConclusionsDespite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands provides evidence for the occurrence of fusion and split events involving T. brucei and T. cruzi chromosomes.

Dataset Information

Gibbon genome and the fast karyotype evolution of small apes.

Publications

Gibbon genome and the fast karyotype evolution of small apes.

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