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Please sequence my eel

February 8, 2008 By Daniel Cressey This article courtesy of Nature News.

Researchers campaign to get the electric fish genome sequenced.

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A group of researchers have issued an impassioned plea for the genome of the electric eel to be sequenced.

In a paper in the Journal of Fish Biology, the group highlights all the benefits, to areas ranging from human health to nanotechnology, that would result from a full genome of this species1 (Electrophorus electricus), which isn’t actually a true eel but a fish.

This is not the first time scientists have issued a public request for sequencers to look at their research animals: previous examples have included the tammar wallaby and the pacific oyster, sequencing of the first of which is currently under way.

The researchers are asking for a full sequencing effort, where the entire genome is sequenced between seven and ten times to build up a thorough picture. This could cost up to US$10 million using today's technologies. There are plans afoot already to produce a library of what are called expressed sequence tags (small pieces DNA found at the ends of expressed genes), which should be much cheaper at a few tens of thousands of dollars.

But the team maintains that a full-scale genome is needed to capture genes that control development, which may not be active in adults. “The only way to get at those genes is to sequence every last base pair of the genome,” says James Albert, one of the paper’s authors and a fish biologist at the University of Louisiana at Lafayette.

Many applications

In 2005, biologists put a proposal for the electric eel to the Joint Genome Institute in Walnut Creek, California, which oversees sequencing at Department of Energy centres in the United States and is one of the major players in the sequencing arena. This was well reviewed, they say, but eventually declined. Now they're throwing their case out to the community in the hope that as costs go down, the project will be taken up.

One of the things that sequencing the E. electricus genome could lead to, is advances in treatments for spinal injuries, the researchers say. The fish have developed an amazing ability to regenerate, possibly as a result of often having their tails bitten off by electro-sensing predatory catfish, says Albert.

“You can cut off the back third of the body and they will regenerate everything, including the spinal cord,” says Albert.

Finding all the genes linked to the ability to generate electricity could also lead to a whole host of applications. In the paper the authors suggest that cells could be modified to convert sunlight directly into electrical currents, creating bio-batteries; these could spontaneously grow, repair and replace themselves. Medical conditions that involve electrically-excitable membranes, such as Parkinson’s disease, epilepsy and muscular dystrophy, could perhaps be controlled by cells modified to produce current. “It’s kind of science fiction-like because you have to speculate on future technologies,” Albert admits.

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The animals sequenced thus far — including the chimp, mouse and opossum — have largely been chosen because the animals are used as models for human health or because they shed light on human evolution. "Traditionally these organisms have been proposed because they somehow inform human biology," says Jeff Touchman, a researcher at Arizona State University in Tempe and head of the Comparative Sequencing Lab at the non-profit Translational Genomics Research Institute in Phoenix, who was not involved in the request. "An example of that would be the pufferfish. That enabled us to understand where all the coding parts of our genome actually are," he says.

"New organisms that are sequenced need to have a different thrust for their appeal," Touchman says. "The eel is interesting," he agrees, for its unusual abilities and possible insights on human health.

Researchers note that it will become ever easier for smallish projects to get done as the price of sequencing falls, making the current system unnecessary. “Small projects will, more and more, be feasible to do outside a large-scale sequencing context,” says Adam Felsenfeld, a director at the National Human Genome Research Institute in Bethesda, Maryland. “When an individual organism genome can be sequenced de novo and assembled for a few hundred thousand dollars or less — we are not quite there yet, but could be in a year or two — it makes less and less sense to do this via a centralized mechanism.”

Just today, a separate group announced that they had sequenced a person for $100,000, although this has yet to be confirmed (see Company claims to have sequenced man's genome cheaply).

“I think we’re turning a corner with the technology,” Touchman says. “Within five years these debates will start to fall apart as sequencing becomes so cheap.”

Meanwhile, the electric eel researchers await the genome that they say will "bring the study of bioelectrogenesis into the genomic era".

References

  1. Albert, J. et al. Journal of Fish Biology 72, 331-354 (2008).

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