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Who needs structure, anyway?

A tiny, mucus-covered animal shatters assumptions about genome architecture

By | November 18, 2010

The architecture features of the animal genome may not be as valuable as scientists once thought. The newly described genome of a tiny, transparent marine animal breaks all the structural rules previously thought to be important for animal genomes -- overturning the belief that common architectural features of genomes, observed across all animal kingdoms, are maintained by natural selection.
Oikopleura dioica
Image by Jean-Marie Bouquet and Jiri Slama, copyright Science/AAAS
The finding, published online today at linkurl:Science,;http://www.sciencemag.org/content/early/recent shows that an animal genome can be highly flexible and still maintain its function. "Given the large number of genomes that have been nearly completely sequenced over the past ten years, one would expect us to have reached near saturation with respect to new findings, but surprises still emerge," linkurl:Michael Lynch,;http://www.bio.indiana.edu/faculty/directory/profile.php?person=milynch a researcher studying evolution and genomics at Indiana University who was not involved in the research, said in an email to The Scientist. Scientists have observed remarkable similarities in genome organization between species as distant as humans and sea sponges. These common genome elements -- including the order of genes, the organization of introns and exons, and the repertoire of developmental genes -- has led many to infer that animal genome architecture is essential to preserve function and is actively maintained by natural selection. The genome of a tunicate, Oikopleura dioica -- a small, rapidly evolving underwater filter feeder abundant in plankton -- shatters those preconceptions. "The paper is outstanding in the sense that it revealed several peculiarities that will certainly shed light on the evolution of life in this planet," said linkurl:Sandro Jose de Souza,;http://www.compbio.ludwig.org.br/home a biologist at the Ludwig Institute for Cancer Research in Brazil who was not involved in the research, in an email. Researchers at the Sars International Centre for Marine Molecular Biology at the University of Bergen in Norway, together with colleagues at Genoscope, a national sequencing center in France, sequenced and analyzed the Oikopleura genome, the smallest known animal genome at only 70 million base pairs (Mb). Oikopleura, closely related to sea squirts on the ocean floor, is a rapidly evolving animal, with constant mutations in its nuclear and mitochondrial genomes. This speedy evolution is likely due to the fact that the animal spends most its life just below the ocean surface, bombarded by UV rays and other mutagens. "When evolution is rapid, there are things you can apprehend that you cannot detect in slow moving genomes, including human," said senior author linkurl:Daniel Chourrout.;http://www.sars.no/research/ChourroutGrp.php When the team compared the Oikopleura genome to those from animals across all main branches of the animal kingdom, it was unrecognizable. First, the genome was extremely compact, with roughly the same number of genes as the human genome (approximately 18,000) but tucked into a DNA sequence 40 times shorter. Additionally, while animals from sea anemones to primates have conserved the physical location of certain genes near each other, Oikopleura's genes appeared to have been shuffled like a deck of cards. "The order you find in Oikopleura is no different than random," said Chourrout. Yet Oikopleura has many of the same essential phenotypic features as other tunicates with traditional genome architecture. Another significant peculiarity was the locations of introns, non-coding segments of DNA that interrupt coding sequences of most genes. Most intron locations -- another structural feature conserved across other animal phylums -- were gone, yet new introns had popped up all over. Approximately five out of six are new, said Chourrout. Of those, some were very similar in sequence to their neighboring introns, adding new evidence to an old scientific debate -- where do introns originate?
Oikopleura dioica
Image by Jean-Marie Bouquet and Jiri Slama, copyright Science/AAAS
Introns in most animals are so ancient that they look nothing like their precursors, so it has been difficult to determine their origins. But some of the new introns in Oikopleura look very similar to each other, including four pairs of identical introns, lending weight to scenarios in which introns can be multiplied in the genome. Overall, the "alien-like" genome, as the authors refer to it in a press release, defies the idea that the "normal" genome architecture observed in many animals is preserved as a necessity by natural selection. "In this case, we have to consider an alternative hypothesis, that these things can happen by chance," said Chourrout. The research "provides abundant evidence that there is little connection between the evolution of morphological/developmental complexity and structural aspects of genome evolution," added Lynch. Denoeud, F. et al., "Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate," Science, published online 18 November 2010, doi:10.1126/science.1194167.
**__Related stories:__***linkurl:DNA repeats hold RNA starts;http://www.the-scientist.com/blog/display/55625/
[20th April 2009] *linkurl: Tunicate classification;http://www.the-scientist.com/2008/01/1/55/1/
[1st January 2008] *linkurl:Ascidian genome;http://www.the-scientist.com/news/20021213/01/
[13th December 2002]
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Comments

Avatar of: donald robison

donald robison

Posts: 8

November 19, 2010

The article raises some really interesting questions,such as why do bigger organisms like people need more DNA between there genes. In discussing the genome of this tiny creature the author of the article states: "First, the genome was extremely compact, with roughly the same number of genes as the human genome (approximately 18,000) but tucked into a DNA sequence 40 times shorter." \nThe author goes on to point out that these creatures are prone to mutate from UV rays \n"This speedy evolution is likely due to the fact that the animal spends most its life just below the ocean surface, bombarded by UV rays and other mutagens." (the other mutagens probably referring to our friends at BP). \nLooking at the statistics, because there is less intragenic DNA, there is higher probability in the Oikopluera that a UV blast will hit a nucletide in functioning gene rather than in the non-functioning filler dna.\nIf people have 40% more filler, would that mean a uv blast into a nucletide would be 40X more likely (the the Oikupluera) to hit a filler nucleotide than a nucleotide in a functionin gene? If the majority of mutations to filler would have no net effect on evolution or mutation; then would could say that the advantage of filler is gene "body armor" or a decoy, absorbing the blows of uv rays. Our environment, and the chances of very rapid changes in it are not that great, so maybe we should not be mutating too fast - perhaps then the filler keeps our mutation rate down so our evolution rate keeps constant with rate of change of the environment.\nCan anyone tell that it is Friday and I am at lunch? This is an interesting topic, lets chat about it :)- Don dnldedmnd@hotmail.com\n\n\n\nRead more: Who needs structure, anyway? - The Scientist - Magazine of the Life Sciences http://www.the-scientist.com/news/display/57814/#ixzz15koDaPX2\n\n\n\n\n\nRead more: Who needs structure, anyway? - The Scientist - Magazine of the Life Sciences http://www.the-scientist.com/news/display/57814/#ixzz15knOrFVG
Avatar of: Dov Henis

Dov Henis

Posts: 97

November 19, 2010

Just As EpiDNAetics Is Not EpiGenetics\n\nSome Figments Of Present Science Imagination Cleared\n\n\n- Dark energy and matter YOK. Per E=Total[m(1 + D)] all the energy and matter of the universe are accounted for.\n\n- Higgs Particle YOK. Mass begins to form at some value of the above D.\n\n- Sleep is inherent for life via the RNAs, the primal Earth organisms formed and active only under direct sunlight in pre-metabolism genesis era.\n\n- Natural selection is ubiquitous for ALL mass formats. It derives from the expansion of the universe.\n\n- Epigenetics: Where Life Meets the Genome\nhttp://www.bionews.org.uk/page_66997.asp?dinfo=rWfnKzZO4tkhJf38jsJ5EeJo\n\nEpigenetics = \na) the study of heritable changes in gene function that do not involve changes in DNA sequence\nb) the science of enduring changes in the pattern of gene activity, during embryo development and beyond, that do not involve alteration of the DNA sequence.\n\nThe "heritable or enduring changes" are epiDNAtics, not epigenetics. Alternative splicing is not epigenetics, even if/when not involving alteration of the DNA sequence. Earth life is an RNA world.\n\nIt's the RNAs that evolve proteins. AND IT'S THE RNAs THAT HAVE EVOLVED AND PRODUCE AND EMPLOY THE DNA templates to carry out life processes, for enhancing Earth's biosphere, for enhancing and constraining as long as possible some energy, some of the total energy of the universe, all of which is destined to fuel the ongoing cosmic expansion. \n\nScience should adjust its vision, comprehension and conception. \n\nIT HAS ALWAYS BEEN AND IT STILL IS AN RNA EARTH LIFE. \n\n\nDov Henis \n(Comments From The 22nd Century) \nhttp://www.the-scientist.com/community/user/profile/1655.page\n\nSeed of Human-Chimp Genomes Diversity\nhttp://pulse.yahoo.com/_2SF3CJJM5OU6T27OC4MFQSDYEU/blog/articles/53079 \n03.2010 Updated Life Manifest \nhttp://www.the-scientist.com/community/posts/list/54.page#5065 \nCosmic Evolution Simplified \nhttp://www.the-scientist.com/community/posts/list/240/122.page#4427 \nGravity Is The Monotheism Of The Cosmos \nhttp://www.the-scientist.com/community/posts/list/260/122.page#4887 \nEvolution, Natural Selection, Derive From Cosmic Expansion\nhttp://darwiniana.com/2010/09/05/the-question-reductionists-fear/
Avatar of: PAUL STEIN

PAUL STEIN

Posts: 61

November 19, 2010

One-fortieth the size? Then say so. 2.5% of the same size? Forty times shorter is mathematically nonsensical, like Advil's "four times fewer pills" (compared to Tylenol). Why do people have such problems with proportions?! Sorry, it's been a long week.
Avatar of: Mike Waldrep

Mike Waldrep

Posts: 155

November 19, 2010

Interesting! I hope that everyone has a great weekend!
Avatar of: Michael Keating

Michael Keating

Posts: 6

November 19, 2010

There is evidence of different organisms joining together for good or bad reasons; virus and many bacteria show the bad side, whereas the presence mitochondria probably shows an early case of symbiosis. It doesn't take too much imagination to understand that "in the beginning" there was no real organisation.\n10,000 years ago human civilisation was scattered and disorganised, robbers and thieves soon realised that setting up a structure to "milk" (tax) the population served them better - the origin of kings etc.\nIt is more difficult to understand how cells started to organise themselves. It would imply that very early on an "organising" genome moved into a creature very much like Oikopleura dioica and, why not, created "back-ups" within the nucleus/cell - giving a longer DNA sequence.
Avatar of: donald robison

donald robison

Posts: 8

November 19, 2010

Michael,\nAmerican goverment works like this:\n(1) people in congress figure out ways to take money from you;\n(2) you have to get together with other people who have your interest, and pay a lobbyist to get your money back\n(3) the lobbyists pay money to the people in congress who passed laws to take your money,to give your money back to you.\n(4) then you elect those lobyists to congress\n(5) and if your lobbyists can't get your money back, make sure you buy yourself a supreme court, they will rule that the original taking of your money was unconstitutional; it works for Exxon and BP\nThat is how political organizations,including governments, and our governmental corporations evolve. We dont need UV rays, greed causes enough damage, and evolves us from democracy to oligarchy.
Avatar of: anonymous poster

anonymous poster

Posts: 85

November 20, 2010

?????????????????????????\n\nHave we reached the point where comments need to be monitored and/or edited? \n\n
Avatar of: DENNIS HOLLENBERG

DENNIS HOLLENBERG

Posts: 26

November 20, 2010

How else can we explain the origin of the, ahem, exceptionally 'bottom-up' comments in this otherwise cogent field of observations?
Avatar of: Alison McCook

Alison McCook

Posts: 2

November 21, 2010

We do moderate the comment board, and delete comments that are advertisements or offensive. There was an advertisement posted here, which we have deleted.\n\nThanks again,\nAlison McCook\nNews Editor
Avatar of: JOHN COLLINS

JOHN COLLINS

Posts: 37

November 22, 2010

This is a fascinating finding! Maybe Oikopleura has a unique method of dealing with DNA recombination compared to other eukaryotes. Many Rotifera also survive massive radiation doses by basically having degenerate copies of each chromosome present and available for mismatch repair, as well as allowing fusion and repair of double-strand DNA breaks. It would be interesting to hear more about what is known about DNA repair in this organism.\n\nThose familiar with karyotyping cell cultures know that chromosome structure degenerates rapidly when cells are cultivated for months outside of their normal environment in the animal body. There are therefore either some local (environmental)factors reducing such degeneration in the normal body environment ( or maybe just lack of growth or slow growth; or fast growth and short half-life ) or a strong selection pressure to remove cells that have degenerated. The fact that only a hand full of chromosome rearrangements have taken place over 7 million years (e.g. comparing the divergence of Gorilla and Homo sapiens from some common ancestor) does strongly imply that very different selection mechanisms are at work here. It will be very interesting to try to establish why this is.
Avatar of: Maggie Zhou

Maggie Zhou

Posts: 1

December 22, 2010

This is a reply to the first commenter, donald robison. Mutation is generally understood as happening at a certain rate per kilobases, which means that having 40 times more genome made up of filler DNA doesn't help reduce the number of mutations in our coding DNA - we just get 40 times more mutations.\n\nThe mutation rate is actually not necessarily stable throughout evolution. A couple years ago I corresponded with some experts in this field, and found that there is just not enough evidence to know whether the rate has actually remained the same through evolution, especially now. My fear is that the environmental destruction we have caused (both chemical and electromagnetic) can lead to higher general mutation rates, in humans and in wildlife.

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