Making sense of the scrambled Gibbon genome

Remember when I told you that the genome of the gibbon was to be sequenced, all the way back in July of 2006? At that time, I assumed it will be finished sooner than the 3 years the NHGRI planned out for the project.

Well, I think my estimatation is right on track…. however researchers seem to have fallen into a slight speed trap.

One of the first publications has come out on this ape genome sequencing project, in the journal Genome Research. The paper is titled, “Molecular refinement of gibbon genome rearrangements,” which focuses on a interesting feature of gibbon genetics… that is also the speed trap.

See, gibbons have a genome that is rapidly evolving, more than other apes like us, gorillas, chimpanzees, etc. Parts of the gibbon genome is constantly being rearranged and broken up… which creates a problem for understanding and comparing genes between species. This genetic phenomenon is called karyotyping, and a unique arrangement is called a karyotype. If you are interested, a very prominent karyotype exists only in humans which distinguish us from other great apes.

Here’s a photo from the publishing team which,

shows a split signal in human metaphase (chromosomes 6 and 9) and the inset image in the upper right corner shows a single signal in the gibbon genome. This is an example of a clone which spans the breakpoint of the rearrangement.”

Gibbon Genome Karyotype

Anyways, the whole scope of this paper is a report of these karyotypes and to open discussion on why certain karyotypes seem to evolve much more rapidly. The research also shows how Roberto et al. have developed unique ways to develop a framework in order to sequencing the entire gibbon genome, since they can’t really use a human one… due to the difference in karyotypes. Furthermore, the paper provides some insight on how evolution occurs with genomic rearrangement, as well as how chromosomes can become unstable in cancer and other genetic diseases (something I mentioned when I first anounced this project).

Here’s the abstract to the paper,

“The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to ~5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome.

The Howard Hughes Medical Institute has issued a press release with a more in depth discussion of the experimental design and results. I got the photograph from there as well as the description.

I am interested in keeping up with this research because there’s potential for an outstanding amount of information to come about from all of this. We can begin to understand how karyotyping, along with other types of genetic morphisms have been one of the selective forces in primate evolution, as well as apply this phenomenon to other aspects within science, such as medicine and cancer biology.

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