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Sea squirt spouts its genome
By Kate Dalke

Sea squirts are oddballs. They spend their first days of life in the ocean as swimming tadpoles. Then something weird happens: the tadpoles attach to rocks and undergo a drastic metamorphosis, transforming themselves into tubular creatures fixed to the ocean floor.

Embryonic Ciona with blue stained muscle tissue.

Now scientists have sequenced the genome of this ocean oddity. The announcement comes with little of the fanfare afforded the sequencing of humans, mice, or even pufferfish. Instead, sea squirts seem to occupy a more serene and scholarly place in the hearts and minds of biologists.

Nevertheless, the sea squirt genome could help answer key evolutionary questions about humans' oldest ancestors, as well as providing a benchmark for understanding the development of complex systems like the human heart or immune system. An international team of researchers collaborated on the project, led by the Department of Energy Joint Genome Institute in Walnut Creek, California.

Scientists' fascination with sea squirts is nothing new. Aristotle noticed the squishy adult ocean-dwellers and classified them as mollusks. Then, in the late 19th century, a Russian biologist noticed that tadpole sea squirts closely resemble vertebrates—animals with backbones.

Today, most researchers agree that sea squirts and vertebrates share a common ancestor that lived about 550 million years ago. How these two groups diverged over hundreds of millions of years is what keeps sea squirt aficionados up at night.

"The animal occupies a blessed position on the evolutionary tree of life," says Michael Levine of the University of California at Berkeley, who was a member of the genome project. The sea squirt tadpole may resemble our original ancestors, the earliest vertebrates.

An adult C. intestinalis.

An evolutionary comparison of the human and sea squirt genomes may reveal when specific genes appeared in the human genome, says Daniel Rokhsar of JGI, noting that the goal of the project is to better understand human biology.

The sea squirt genome contains roughly 16,000 genes—half the number found in mice and humans, but in line with other invertebrates like the fruit fly. It was sequenced using the whole-shotgun sequencing method. The genome is extremely compact, nearly 20 times smaller than the human genome.

Ciona intestinalis has many of the same genes as humans, but has single gene copies instead of the multiple copies found in higher organisms. Gene duplication is thought to lead to an increased number of genes and the evolution of more specialized and complex traits.

"Despite how simple and humble it looks, the sea squirt has rudiments of vertebrate organs," says Levine.

Researchers found sea squirt genes that match human thyroid hormone genes, yet much of the genome seems tailored to the life of a sea squirt. Indeed, it appears that sea squirts and vertebrates have used the same "raw materials" of an ancestral genome to "their unique purposes and needs," the scientists write Science.

The team found genes involved in producing the tough sheath—made of cellulose—that encompasses the sea squirt. This was unexpected because only plant and bacteria are known to produce cellulose.

DNA for the genome was taken from two sea squirts captured at a marina in Half Moon Bay, California. Researchers isolated their sperm, extracted DNA and then the bulk of the genome sequence came from one of the two lucky squirts.

Rokhsar says that the using sea squirts in the lab to study regulatory regions could be the most exciting aspect of the newly sequenced genome. They are hoping to find parts of the genome that turn certain genes on and off. Sea squirts are easy to work with because researchers can insert DNA into developing eggs and create thousands of individuals rapidly.

"The genome catapults sea squirt into the elite group of model organisms," says Rokhsar.

Levine agrees. "In the early 1900s, sea squirt was one of the major model organisms," he says. Then it hit hard times in the 30s, 40s and 50s when fruit flies, fish and mice became more fashionable. "But I think the sea squirt is going to make a comeback," he adds.

The side of a dock at Pillar Point Harbor in Half Moon Bay, Ca., where JGI scientists collect Ciona.

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Dehal et al. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298, 2157-2167 (December 13, 2002).

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