Gibbon genome reveals new insights into mechanisms of primate chromosomal evolution
The gibbon now joins the ranks of nearly 100 mammals with genome assemblies deposited into NCBI’s genome database. – Gracing the cover of today’s issue of Nature, the sequencing and initial analysis of the gibbon genome represents a continuation of efforts, directed by the National Human Genome Research Institute (NHGRI), to sequence non-human genomes to ultimately understand the human genome in greater depth. Naturally, given the close relationship between humans and our primate relatives, primates are well represented in the species targeted by NHGRI (see the current list of NHGRI-approved sequencing targets).
With the publication of the gibbon genome, all hominoid genomes (i.e. great and small apes) will have been sequenced, including the human, chimpanzee, macaque, orangutan, gorilla, bonobo and gibbon genomes (listed in order of publication; see the taxonomy below). These genome sequences yield great insight into the evolutionary forces that have acted over time, in some cases very recent evolutionary time, to shape each genome. Our knowledge of evolutionary mutation rates and constraint, gene family expansion/contraction, structural variation, repeat element mobilization and other classes of variation have all been expanded greatly through comparative genomics. In turn, we can more deeply explore the patterns of variation we observe in the human genome and across the human population.
The gibbon genome presents an interesting case from many perspectives. First, gibbons are small apes (some say “lesser apes”, but not to gibbon researchers, because that would be rude), meaning they are relatively large-bodied tailless primates. Taxonomically, gibbons are in the family Hominoidea, along with orangutans, gorillas, chimpanzees, bonobos and humans. Gibbons are the most genetically distant from humans within the group (by eric). Genetically, however, no clear phylogeny of gibbons has been established due to the extremely short window of time (~1 million years) in which these genera appear to have diverged, suggesting a rapid radiation.
Gibbon genomes are also notable for their extensive chromosomal rearrangement, for example, diploid chromosome numbers range from 38-52 across different gibbon species, compared with 46 in humans and 48 in the non-human great apes. To put this in perspective, gibbon species radiated in a comparable timeframe to the human-chimpanzee divergence (4-6 mya). Humans and chimpanzees differ at the chromosomal level by a single rearrangement – the fusion of two great ape acrocentric chromosomes to form human chromosome 2 (see this classic cytogenetic description of great ape chromosomal variation for more information). In roughly the same span of time, dozens of chromosomal rearrangements occurred independently in multiple gibbon species, creating a diverse patchwork of karyotypes unique to the gibbon family.
The gibbon genome paper explores this topic in depth, and uncovers an interesting hybrid repeat element enriched at chromosomal breakpoints that may play a central role in gibbon genome plasticity.
Carbone, L. et al. Gibbon genome and the fast karyotype evolution of small apes. Nature 513, 195–201 (2014).
For a further discussion of gibbon chromosomal rearrangements, see:
Capozzi, O. et al. A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons. Genome Res. 22, 2520–2528 (2012).
Figure adapted from:
Locke, D. P. et al. Comparative and demographic analysis of orang-utan genomes. Nature 469, 529–533 (2011).
Devin Locke is a Principal Scientist at Seven Bridges Genomics, and a co-author of the gibbon genome paper. He led the orangutan genome project, and also participated in the platypus and marmoset genome projects while at The Genome Institute at Washington University in St. Louis.