Who needs structure, anyway?

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.phpWhen 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]

Who needs structure, anyway?

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