Gibbons (Hylobatidae) are small arboreal apes that form a key node in primate evolution. One of the most distinctive phenotype is their high genome plasticity involving large-scale chromosomal rearrangements and karyotype changes. The four gibbon genera (Nomascus, Hylobates, Hoolock, Symphalangus) bear between 38 to 52 chromosomes per diploid cell despite their relative recent differentiation about 5 million years ago. In this study, Carbone et al. used genomic approaches i) to better understand the underlying mechanism for gibbon genome plasticity, ii) to reveal the phylogeny of the four gibbon genera, and iii) to study genes involved in functional adaptation in gibbon evolution.
Key findings and personal comments
Sequencing and assembly of the Gibbon reference genome reveal a total genome size of about 2.9Gb with a sequence quality comparable to other Sanger-sequence based genomes. Genome alignments of several primate genomes to the human reference genome, the best genome assembly available, show differences in synteny between primates (Fig.2). In general, the more recent the common ancestor, the more synteny is shared. The gibbon-human alignment contains many large-scale rearrangements that are not present in other human-primate alignments. Small-scale rearrangements are comparable among all primates suggesting that the gibbon genome does not possess global genome instability. I think it would also be interesting to show genome alignments of all gibbon genera to detect differences within the gibbons.
Carbone et al. identified 96 gibbon-human synteny breakpoints. These breakpoints could be defined either at the base-pair level or at an interval level for more complex, repeat containing regions. Further analysis using FISH and Chip-Seq data excluded greater duplication rates or chromatin conformations as cause for gibbon-specific rearrangements. Notably, breakpoints show signatures of non-homology based repair, suggesting that recombination between homologous sequences does not cause genome plasticity.
The sequenced Gibbon genome contains more than 1000 functional LAVA elements, a non-LTR retrotransposon mobile genetic element unique to Gibbons (Fig3). Gene Ontology and integration site analysis indicate that LAVA elements are enriched in genes involved in chromosome segregation and preferably integrate into introns in antisense orientation. To test whether intronic antisense LAVA elements might promote premature transcription termination, they constructed a luciferase reporter assay lacking a functional termination site. LAVA_F, but not LAVA_E, elements lead to luciferase expression above background level suggesting that LAVA elements can cause early transcription termination. In my opinion, this assay could be further improved. First of all, the difference between LAVA_F and LAVA_E is not evident, for example in figure 3b LAVA_F and LAVA_E vectors are represented identically. Second, the authors claim that the difference in luciferase activity between LAVA_F and LAVA_E may be explained by the genomic context of the termination site. Yet, I think, the genomic context should be the comparable, as the experiment is performed using a vector system. Finally, it could be interesting to assess the effect of other LAVA elements using this luciferase reporter. In support for LAVA induced early transcription termination, RNA-seq data detect low level of premature terminated transcripts.
To shed light on the timing and order of gibbon genera evolution, different clustering methods (Neighbour-joining tree, UPGMA, ABC, G-PhosCS) were applied on whole-genome shotgun data from two individuals from each genera (Fig. 4). These models predict a time point of speciation at around 5 million years ago, coincident with geographical changes. The branching order though remains unresolved as genetic variation between genera is very small possibly due to incomplete lineage sorting and rapid radiation. Personally, I was surprised about the choice of clustering methods. The UPGMA algorithm assumes constant mutation rate in all genera over time, an assumption that is often not true. Therefore UPGMA frequently generates false clusters. Additionally, the ABC methodology is not yet published and no information is available about the underlying assumptions.
Moreover, Carbone et al. found genomic regions with increased substitution rates (gibARs), a hallmark for adaptation. These gibARs are mainly intergenic and colocalize with LAVA elements suggesting that modifications in regulatory elements also affects LAVA transcriptional function. Comparing human and gibbon orthologues, the authors could detect several genes that appear to have undergone positive selection in gibbons. These genes were generally associated with arboreal locomotion (brachiation) such as TBX5 (forelimb development) and COL1A1 (connective tissue) and likely contributed to the arboreal adaptation of gibbons.
In conclusion, this paper provides insights into how LAVA elements might enhance genome plasticity driving gibbon genome evolution.
Carbone, L., Alan Harris, R., Gnerre, S., Veeramah, K., Lorente-Galdos, B., Huddleston, J., Meyer, T., Herrero, J., Roos, C., Aken, B., Anaclerio, F., Archidiacono, N., Baker, C., Barrell, D., Batzer, M., Beal, K., Blancher, A., Bohrson, C., Brameier, M., Campbell, M., Capozzi, O., Casola, C., Chiatante, G., Cree, A., Damert, A., de Jong, P., Dumas, L., Fernandez-Callejo, M., Flicek, P., Fuchs, N., Gut, I., Gut, M., Hahn, M., Hernandez-Rodriguez, J., Hillier, L., Hubley, R., Ianc, B., Izsvák, Z., Jablonski, N., Johnstone, L., Karimpour-Fard, A., Konkel, M., Kostka, D., Lazar, N., Lee, S., Lewis, L., Liu, Y., Locke, D., Mallick, S., Mendez, F., Muffato, M., Nazareth, L., Nevonen, K., O’Bleness, M., Ochis, C., Odom, D., Pollard, K., Quilez, J., Reich, D., Rocchi, M., Schumann, G., Searle, S., Sikela, J., Skollar, G., Smit, A., Sonmez, K., Hallers, B., Terhune, E., Thomas, G., Ullmer, B., Ventura, M., Walker, J., Wall, J., Walter, L., Ward, M., Wheelan, S., Whelan, C., White, S., Wilhelm, L., Woerner, A., Yandell, M., Zhu, B., Hammer, M., Marques-Bonet, T., Eichler, E., Fulton, L., Fronick, C., Muzny, D., Warren, W., Worley, K., Rogers, J., Wilson, R., & Gibbs, R. (2014). Gibbon genome and the fast karyotype evolution of small apes Nature, 513 (7517), 195-201 DOI: 10.1038/nature13679