What's the big deal with Purple Sea Urchins?

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Posted by on November 10, 2006 at 17:06:50:

With genomes being completed on a regular basis, the wrapping up of a new one is making less and less of a splash. An exception to this trend occurred yesterday with the completion of the sea urchin genome, specifically the one from the purple species Strongylocentrotus purpuratus. Not only did this rate six separate articles in the latest issue of Science, but a special issue of Developmental Biology will be devoted to it in December. This is far more attention than the dog genome got, and is probably on par with the excitement that greeted the chimp genome.

Those of you familiar with sea urchins from tide pools, aquariums, or Japanese restaurants may be a bit shocked by this level of buzz. After all, what could a prickly sphere tell us about humans, with our asymmetrically placed limbs and sensory organs? At the risk of making two-part posts a habit, I'll spend today's post letting you know why there's so much excitement. A detailed analysis of the six papers will follow over the weekend.

Sea urchins actually have a long history in biology. They're easy to keep, thriving in a combination of sterilized tap water and a collection of salts sold under the trade name "Instant Ocean." They're also long lived—the source of the genome in question was estimated at 20 years old, based on its size— and can produce copious numbers of offspring. Critically, these offspring develop externally, and are transparent for their earliest stages, making them very amenable to development studies. In fact, one of the perspectives cites a century-old paper as using sea urchins to show that embryonic development is a fundamentally genetic process: deleting any of its chromosomes from any of its early cells was enough to bring development to a crashing halt.

Further analysis of urchin development has continued to this day. When I cloned a gene from mice that I was working on a couple of years back, I was surprised to find that an equivalent gene didn't exist in things like Drosophila and most other invertebrate model organisms. The only other organism where it had been described, in fact, was the sea urchin, where the transparent embryos had allowed researchers to visualize cells migrating along tracks composed of the urchin's equivalent of my gene.

The presence of this gene in the urchin genome was no fluke; despite their almost other-worldly appearance, sea urchins are family. They and humans belong to a group called the deuterostomes, identified by common processes we both undertake during early development. Some of the commonalities are a bit surprising. Even though they look like a sphere, sea urchins develop with clear "sides" internally, and these sides express the same genes that we vertebrates use to differentiate our left from our right.

Sea urchins represent the most distant members of the deuterostome family that we're likely to get a genome from any time soon, and the first one sequenced that doesn't form any sort of nerve cord. As such, they will be critical in identifying those genes that all deuterostomes have in common—the raw material that all of the species in this group inherited from a distant ancestor. It appears that that ancestor was more sophisticated than we might think. Despite their lack of an obvious sensory system, urchins have nearly as many genes involved in odorant receptors as we do, and six different light sensing pigments (compared to our four). It's also expected that an analysis of non-coding sequences may reveal the sites where regulatory factors bind to DNA to turn genes on and off, which will identify those regulatory circuits have been present since the first deuterostomes.

Identifying the similarities is also a key step in identifying the differences. Vertebrates have many novelties that aren't present in other deuterostomes, and the genome sequence will help answer one of the basic questions in evo-devo: how much of this novelty is the result of something truly new, and how much comes from using the same material in new ways? A quick skim of the articles reveals that the immune system of urchins appears radically different, which will not only help us understand our own better, but may point towards new directions to take in developing antibiotics.

So, if you were tempted to shrug your shoulders at what may have appeared to be hype, I hope this has convinced you that there are many reasons for the buzz surrounding this genome. If nothing else, I hope I've convinced you to check back when I go through the actual data.

from a ars technica article

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