Gibbon genome sequence deepens understanding of primates rapid chromosomal rearrangements

September 10, 2014
A family of northern white-cheeked gibbons (Nomascus leucogenys) “lounging” in the tropical forest of Yexianggu, China. Males from this species are black, while females are blond. Babies are all born blond and turn black around half year of age; female start changing back to blond at the age of sexual maturity (about 6 years). Credit: Heather Angel/Natural Visions

With the completion of the sequencing and analysis of the gibbon genome, scientists now know more about why this small ape has a rapid rate of chromosomal rearrangements, providing information that broadens understanding of chromosomal biology.

Chromosomes, essentially the packaging that encases the stored in the DNA sequence, are fundamental to and the transmission of genetic information from one generation to the next. Chromosome structure and function is also intimately related to , especially cancer.

The sequence and analysis of the gibbon genome (all the chromosomes) was published today in the journal Nature and led by at Oregon Health & Science University, the Baylor College of Medicine Human Genome Sequencing Center and the Washington University School of Medicine's Genome Institute.

"Everything we learn about the of this particular primate and others analyzed in the recent past helps us to understand human biology in a more detailed and complete way," said Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center at Baylor and a lead author on the report. "The gibbon sequence represents a branch of the primate evolutionary tree that spans the gap between the Old World Monkeys and great apes and has not yet been studied in this way. The new genome sequence provides important insight into their unique and rapid chromosomal rearrangements."

For years, experts have known that gibbon chromosomes evolve quickly and have many breaks and rearrangements, but up until now there has been no explanation why, Rogers said. The genome sequence helps to explain the genetic mechanism unique to gibbons that results in these large scale rearrangements.

The sequencing was led by Dr. Kim Worley, professor in the Human Genome Sequencing Center, and Rogers, both of Baylor and Drs. Wesley Warren and Richard Wilson of Washington University.

The analysis was led by Dr. Lucia Carbone, an assistant professor of behavioral neuroscience in the OHSU School of Medicine and an assistant scientist in the Division of Neuroscience at OHSU's Oregon National Primate Research Center. Carbone is an expert in the study of gibbons and the lead and corresponding author on the report.

A female northern white-cheeked gibbon (Nomascus leucogenys). Her baby is clinging to her as she is leaping from a branch to another (Yexianggu, China). Gibbons use brachiation to move through tropical rainforests and their transfers (as the one captured here) are often acrobatic. Credit: Heather Angel / Natural Visions

"We do this work to learn as much as we can about gibbons, which are some of the rarest species on the planet," said Carbone. "But we also do this work to better understand our own evolution and get some clues on the origin of human diseases."

Chromosomal biology

Chromosomes play an essential role in the packaging of DNA, Worley said. "There are 3 billion base pairs of DNA in every cell and it is packaged into 23 pairs of chromosomes," said Worley, also a lead author on the report.

When there are rearrangements in chromosomes, the genes and gene regulation are often disrupted or broken, said Worley.

"Cancer is clearly the biggest medical example of the impact of chromosome rearrangements. The gibbon sequence gives us more insight into this process," said Worley. "There are also a number of other that result from these events."

Rearrangements

The number of in the gibbons is remarkable, Rogers said. "It is like the genome just exploded and then was put back together," he said. "Up until recently, it has been impossible to determine how one human chromosome could be aligned to any gibbon chromosome because there are so many rearrangements."

Repeat element

The sequencing project revealed a novel and unique genetic repeat element (segments of DNA that occur in multiple copies throughout the ) that is inserted into genes associated with the maintenance of chromatin structure.

Repeat elements have the capability to disrupt a gene and change their biological function, Worley said. In the gibbons, the team identified the LAVA element - a novel repeat element that emerged exclusively in gibbons and preferentially hits genes involved in chromosome segregation (an essential step in cell division, where pair off with their similar homologous chromosome.)

"This explains why the gibbons have undergone so much change," said Rogers. "Similar disruptions cause disease, which is why everything we learn from this helps us better understand human biology and chromosomal structures."

Explore further: Refining the language for chromosomes

More information: Gibbon genome and the fast karyotype evolution of small apes, Nature, dx.doi.org/10.1038/nature13679

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JVK
1 / 5 (5) Sep 13, 2014
If you are still an evolutionary theorist, human ethologist, or evolutionary biologist who believes that evolutionary events link mutations and/or natural selection to the evolution of biodiversity, don't tell anyone until all this information about RNA-mediated amino acid substitutions and chromosomal rearrangements blows over.

Alternately, set your sights on becoming a serious scientist, since this is not going to blow over.

If you ever commented positively about anything PZ Myers ever said, try to retract what you said before anyone realizes you said it -- unless you are an anonymous fool. Then, you need only hope that your name is not Andrew Jones, since only he was ignorant enough to criticize my most recent published work and cite PZ.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.http://www.ncbi.n...24693353

See: http://www.ncbi.n...4959329/

http://perfumingt...tations/
anonymous_9001
5 / 5 (5) Sep 14, 2014
Honestly, I love all the free publicity you've been giving me. Ever heard of the Streisand effect?

Also, can you cite a study that shows that pheromones induce chromosomal rearrangements?
Uncle Ira
4.3 / 5 (6) Sep 14, 2014
Also, can you cite a study that shows that pheromones induce chromosomal rearrangements?


Oh boy, now you done it. Here comes the stink love potions.
JVK
1 / 5 (5) Sep 14, 2014
Odors induce the de novo Creation of odor receptor genes that link nutrient uptake to RNA-mediated events and pheromone-controlled cell type differentiation that limits species specific reproduction in the context of chromosomal rearrangements.

I hope that PZ Myers enjoys the publicity you have given him now that the chromosomal rearrangements have been linked from ecological variation to RNA-mediated events and ecological adaptations manifested in the morphological and behavioral phenotypes of species from microbes to man.

For those who don't know, Myers initiated his unprovoked attack on my credibility here: http://freethough...s-place/

"Behold James Vaughn Kohl.

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of .."
JVK
1 / 5 (5) Sep 14, 2014
My conclusion: "... the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'." http://www.ncbi.n...24693353

It would be great if someone who is not an anonymous fool or idiot minion of PZ Myers would review my published work and comment now that the information about nutrient-dependent pheromone-controlled RNA-mediated chromosomal rearrangements extends from microbes to man via birds and other primates without the pseudoscientific nonsense of mutations and natural selection.
anonymous_9001
5 / 5 (5) Sep 14, 2014
I'll take that as a "no" to my question. You make the claim that pheromones induce chromosomal rearrangements, but you can't support it with a citation. The same goes for your claim of creation of olfactory receptor genes. You talk about mediated changes in gene EXPRESSION (straight from your paper's abstract), but there's no mention of gene creation, so I'd like to see a citation for that.

I did a ctrl+F search for every instance of "gene" in your paper, but no instance regarded gene creation.
JVK
1 / 5 (5) Sep 14, 2014
I wrote:"It would be great if someone who is not an anonymous fool or idiot minion of PZ Myers would review my published work and comment now that the information about nutrient-dependent pheromone-controlled RNA-mediated chromosomal rearrangements extends from microbes to man via birds and other primates without the pseudoscientific nonsense of mutations and natural selection."

The anonymous fool again tries to engage me in pointless discussion and tells others that I claimed pheromones induce chromosomal rearrangements.

Note, however, he never addressed any of the citations I included in my published review. What good does it do to cite works when the citations are ignored by PZ Myers idiot minions and other evolutionary theorists who know nothing about cell type differentiation?

See my comments on Combating Evolution to Fight Disease
http://comments.s....1247472

The disease is ignorance, as everyone knows except anonymous fools.
anonymous_9001
5 / 5 (5) Sep 14, 2014
...tells others that I claimed pheromones induce chromosomal rearrangements.


Kohl, 6 hours ago:

pheromone-controlled RNA-mediated chromosomal rearrangements


Again, I ask for evidence that pheromones actually control (induce) those.

Note, however, he never addressed any of the citations I included in my published review.


I have pointed out how your citations don't support your claims on many occasions. Your misinterpretation of Nei's biophysical constraints, Darwin's terms, claiming the peppered moth coloration was due to what they ate rather than predatory selection, your claim that mutations theory does not address pleiotropy or epistasis, your claim that proteasomes mediate protein folding, your misinterpretation of Chelo et al., your comment on the Educate Truth blog where you thought citrate created an ORG in Lenski's E. coli, etc.

You can find all these examples in my first draft:

http://www.scribd...Response
animah
5 / 5 (4) Sep 15, 2014
Good old James V Kohl. P Z Myers rose to become an internationally known University Professor while you've slid down to Internet forum troll.
JVK
1 / 5 (5) Sep 15, 2014
"Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans" exemplifies the nutrient-dependent link from the epigenetic landscape to the physical landscape of DNA in the organized genome of C. elegans. http://www.cell.c...)00806-X

"System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes" is the citation from my 2013 review that linked the difference in nutrient uptake via RNA-mediated events to cell type differentiation and pheromone-controlled ecological adaptations manifested in morphological and behavioral diversity. http://linkinghub...12015000

I cited that article 3 times in my review http://www.ncbi.n...4693353.

C. elegans is the model organism often used to link the conserved molecular mechanisms of RNA-mediated cell type differentiation to morphological and behavioral phenotypes in humans that pseudoscientists think somehow 'evolved.'

JVK
1 / 5 (5) Sep 15, 2014
You can find all these examples in my first draft


Thanks. Someone must have told you that your citations were invalidated by works that detailed what are obviously nutrient-dependent pheromone-controlled RNA-mediated events -- exemplified in this article on the gibbons.

Recent reports:
"It has 20 copies of the same chromosome when it's growing happily under favorable conditions, and 10 when nutrients are exhausted and it reaches a stationary phase." http://phys.org/n...ier.html

"...the L ecotype grows faster on glucose but secretes by-products that S can better exploit, generating negative frequency-dependent selection." http://www.scienc...abstract

Here is an opportunity for anonymous fools PZ Myers' idiot minions to tell us how mutations and natural selection led to the chromosomal rearrangements reported across species in the context of experimental evidence showing the rearrangements are RNA-mediated events.
JVK
1 / 5 (5) Sep 15, 2014
P Z Myers rose to become an internationally known University Professor...


"I followed up on a link to the "rule of 48" and picture of Little PZ Myers, who is the biology teacher most responsible for teaching the idiot minions and anonymous fools here to value theory rather than biological facts."

Read more at: http://phys.org/n...html#jCp
JVK
1 / 5 (5) Sep 15, 2014
http://www.scribd...nalpaper "...plants generally have evolved...
through a currently unknown mechanism (although genes involved and their effects have been identified (Pyke, 1999))"

Q: How did plants evolve?
A: The genes and mechanism have not been identified, and no evolutionary event has been described.

For contrast:
"... cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting." http://www.pnas.o...abstract

RNA-mediated events link amino acid substitutions from nutrient-dependent ecological variation to pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. The link from biophysical constraints on plant life to animal life via nutrients is known to serious scientists and does not involve the pseudoscience of mutations and natural selection.
anonymous_9001
5 / 5 (5) Sep 15, 2014
Someone must have told you that your citations were invalidated


Nope. Mouras just wanted me to focus on your paper rather than external discussion.

nutrient-dependent


Still a useless descriptor. I don't call my car gasoline-dependent every time I talk about it. It's implicit.

Q: How did plants evolve?
A: The genes and mechanism have not been identified


Your most blatant lie yet. You took a quote from my paper (out of context, I might add, when you delete the middle section between "evolved" and "through a currently unknown mechanism". I was referring to photoperiod adjustment, not evolution in general. I also specifically said the genes their effects HAVE been identified.

cryptophytes have evolved a structural switch controlled by an amino acid insertion


The insertion (a mutation) altered the function of the protein. How exactly does that refute evolution?

anonymous_9001
5 / 5 (5) Sep 15, 2014
anonymous_9001
5 / 5 (5) Sep 15, 2014
If you want an in depth discussion, get in touch with somebody who studies rearrangements and their evolutionary implications for a living:

http://www.biolog...p?ID=696

My research interests are in the field of evolutionary genetics, especially understanding processes occurring through or influenced by genome-level mechanisms. Active research projects in the lab use flies in the genus Drosophila for empirical studies combining molecular, cytological, and genetic approaches. Three primary research areas are currently being pursued in the lab: 1) identifying the role of chromosomal rearrangements in facilitating adaptive evolution, 2) determining the consequences of sex-linked transmission, and 3) defining common pathways of sex-chromosome evolution.
JVK
1 / 5 (5) Sep 15, 2014
Will someone comment on the role of amino acid substitutions and retrotransposons that link ecological variation and nutrient-uptake to the metabolism of nutrients and species-specific pheromones that control the physiology of reproduction and ecological adaptations in species from microbes to man?

The anonymous fool is citing experts who can't think in terms of 'RNA-mediated events' or 'indirect genetic events' or 'genome dynamics events' or anything else that doesn't portray their ignorance of biologically-based cause and effect. They've been taught to believe in pseudoscientific nonsense about mutations and natural selection and other believers continue to cite them while ignoring anything that does not echo ridiculous theories.

Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats http://mbe.oxford...abstract

Did the bats eat, or simply mutate & radiate?
anonymous_9001
5 / 5 (5) Sep 16, 2014
As usual, Kohl dismissed my 11 examples of experimental support without being able to point out flaws in their assumptions, methodology, or interpretation of their data, merely stating they were taught pseudoscience.

Did the bats eat, or simply mutate & radiate?


Do you know what a false dichotomy is? Where did you get the ridiculous idea that evolution supporters don't think organisms need to eat? Also, why are you under the impression eating is at odds with mutation and natural selection?
JVK
1 / 5 (5) Sep 16, 2014
Andrew Jones (aka anonymous_9001) has dismissed everything I've written about RNA-mediated cell type differentiation via nutrient-dependent amino acid substitutions. If he sees the word mutation mentioned in an article, he thinks it means the mutation caused something via natural selection that somehow leads to the evolution of biodiversity.

For comparison, see any of my published works or links in 37 blog posts about RNA-mediated events:
http://perfumingt...bmit.y=0

See also: http://jonlieffmd...volution
"It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures."
JVK
1 / 5 (5) Sep 16, 2014
Re: Combating Evolution to Fight Disease http://www.scienc...88.short

"Widespread occurrence of phage sequences in almost all studied M. abscessus complex isolates suggests that the rate of prophage invasion is faster than the rate of mutation, implying rapid evolution of M. abscessus." http://www.biolog...abstract

The information on chromosomal rearrangements in gibbons and everything known about species diversification in microbes attests to the likelihood that biodiversity is nutrient-dependent and pheromone-controlled via RNA-mediated events that are consistently reported as if they were evolutionary events.

No evolutionary events have been described in the context of biologically-based cause and effect. Which will be more important to scientific progress:

1) The pseudoscientific nonsense about mutations, natural selection and the evolution of biodiversity?

or

2) Facts about RNA-mediated events?

Help stop death by theory!
Uncle Ira
4.2 / 5 (5) Sep 16, 2014
Will someone comment on the role of amino acid substitutions and retrotransposons that link ecological variation and nutrient-uptake to the metabolism of nutrients and species-specific pheromones that control the physiology of reproduction and ecological adaptations in species from microbes to man?


Well, I'll comment if that is what you want Cher. I don't think those stinky love potions are going to increase your uptake in your finances. Matter the fact, it will probably get you landed in jail when the police hear about it.
JVK
1 / 5 (5) Sep 16, 2014
"Much of his group's current work involves extending discoveries about translation in E. coli to the process in eukaryotes, with an eye toward human health and disease."
http://www.the-sc...ualizer/

This sums up the frustration that serious scientists share when others tout their pseudoscientific nonsense about mutations, natural selection and the evolution of biodiversity, which is obviously nutrient-dependent and pheromone-controlled.

RNA-mediated events link ecological variation to nutrient-dependent amino acid substitutions that differentiate cell types. Cell type differentiation in species is controlled by the metabolism of nutrients to species-specific pheromones. The pheromones control the species-specific physiology of reproduction, which leads to ecological adaptations.

Those with no understanding of biologically-based cause and effect comment on mutations and stinky love potions.
Uncle Ira
4.3 / 5 (6) Sep 16, 2014
Those with no understanding of biologically-based cause and effect comment on mutations and stinky love potions.


Look Skippy, you the one who asked for me to comment. Next time don't ask. Now put that silly looking pointy cap back on and get back in the corner you.
JVK
1 / 5 (4) Sep 16, 2014
Will someone comment on the role of amino acid substitutions and retrotransposons...


...was an invitation for someone intelligent to comment, not an invitation to an anonymous fool to comment on something he knows nothing about.

"Pseudogene-derived transcripts can regulate gene expression by generating small RNAs, regulating mRNA stability via direct binding or sequestration of trans-acting RNA decay proteins, sponging of endogenous miRNAs and promoter recruitment of epigenetic remodeling complexes. The extent to which pseudogenes are important in gene regulation and the pathogenesis of disease has so far been underappreciated for a number of reasons." http://dx.doi.org...s.13.172

The primary reason the importance of pre-mRNAs and alternative splicings have been under appreciated in the context of health and pathology is idiots who comment in discussions that might otherwise inform others who are not idiots.

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