The sea squirt, Ciona intestinalis, is a barrel-shaped tunicate or ascidian found worldwide and considered by marinas and marine farmers to be a pest because it forms colonies on piers and anything submerged. Though as an adult it spends its life attached to one spot, sucking in water through one hole, filtering out small animals and squirting the water back out another hole, it looks more like a vertebrate in its immature, tadpole form.
"A Russian biologist noted in 1870 that the sea squirt tadpole is just a very simplified version of the frog tadpole," said coauthor Michael S. Levine, professor of molecular and cell biology and director of UC Berkeley's Center for Integrative Genomics. "This prompted Darwin to propose that these are progenitors of the vertebrates - our relatives."
Since then, the sea squirt tadpole, about a millimeter long, has become a popular focus of study at marine labs around the world and is an animal whose genome is as important for understanding evolution as that of the fruit fly or the mouse. The genome sequence of the latter was reported last week.
Ascidians, as scientists refer to them, are members of a phylum called chordates - animals that, at some point in their lives, have a nerve cord and a cartilaginous rod, a notochord, supporting it, plus some kind of tail. The chordates, which first appeared 550 million years ago during the Cambrian explosion, eventually split into several lineages, one of them leading to backboned animals, the vertebrates, and another leading to animals like the sea squirt, which is a member of a group called the urochordates.
Scientists think the sea squirt tadpole is a good candidate for what the ancestral chordate, the last shared ancestor of vertebrates, sea squirts and other chordates, looked like half a billion years ago.
In fact, the animal's genome shows many similarities with the human and mouse genomes. Though containing only 15,000-16,000 protein-coding genes - half the size of the human genome - the Ciona genome contains genes similar to human genes that code for hormones and for components of the human immune system and nervous system. About 80 percent of Ciona's genes are also found in humans and other vertebrates. Comparison of the Ciona genome with the genomes of other animals also provides clues to the evolutionary origins of the human brain, spine, heart, eye and thyroid gland.
According to Daniel S. Rokhsar, head of JGI's computational genomics department and a professor of physics at UC Berkeley, the sea squirt has a slimmed-down genome because it hasn't developed multiple copies of many genes, as have humans and other vertebrates.
"One of two things can happen to these redundant copies," said Rokhsar, who will soon join both the Department of Molecular and Cell Biology and the Center for Integrative Genomics at UC Berkeley. "Either they mutate away and disappear, or they evolve to perform other functions. By looking at Ciona's genome, we can see what innovations occurred in the human lineage that enabled us to advance in complexity."
For example, the Ciona analysis revealed a number of vertebrate-like genes, including genes for complement, lectin, and Toll-like receptors, that researchers said may play a role in Ciona's primitive "innate" immune system. The scientists found no evidence of the hundreds of genes, coding for proteins such as immunoglobulin or T-cell receptors, involved in the adaptive immune systems found in higher vertebrates.
"In a sense, in Ciona we are seeing our ancestral genes," Levine said. "We are seeing, at the genomic level, the evolutionary biology we have been talking about for 130 years."
Interestingly, Ciona has acquired at least one trait found in no other vertebrate - the ability to make cellulose, the woody substance of plants. The tough tunic that encases the adult tunicate and gives it its name is composed of cellulose fibers. Levine and his associates took advantage of the new genome sequence to get to the bottom of the mystery of where this ability came from.
The genome sequence shows that Ciona has seven genes that degrade cellulose and one gene that synthesizes cellulose. Surprisingly, the degradation enzymes are more closely related to enzymes found in termites and wood-eating cockroaches than to enzymes in plants, such as Arabadopsis thaliana, a mustard-like plant whose genome was sequenced two years ago.
"Ciona probably picked up these genes by horizontal gene transfer from microbes that digest cellulose, like those living in the guts of termites," he said. "This is one example of many funny genes that have gotten into animal genomes, and shows that horizontal gene transfer between very distant organisms has taken place throughout evolution."
Levine has been a self-described "fruit fly guy" for decades, but began studying the sea squirt in 1995 because of its unique attributes. The creature is about as easy to manipulate as the nematode C. elegans but more closely related to humans. It has a small number of cells - about 2,500 - whose lineages can be followed from egg fertilization to tadpole stage.
"The entire nervous system is just 300 cells, and the notochord is composed of only 40," Levine said. "We hope that studying it will allow us to understand the process of how to build a vertebrate nervous system."
In addition, genetic manipulation is easier with the sea squirt than with most lab animals, including fruit flies, frogs and nematodes. While Levine was at UC San Diego, before moving to UC Berkeley in 1996, post-doctoral fellow Bob Zeller and MD-PhD student Joe Corbo developed a way to shock fertilized sea squirt eggs and get nearly 100 percent to take up new genes and parcel them out to all cells as the organism develops.
"This is the only organism where you can get DNA into all cells of the developing embryo," Levine said.
This made genetic manipulation easy, and allowed Levine to map some 40 genes involved in notochord development in the tadpole. The Science cover photo depicts Ciona tadpoles labeled with green fluorescent protein that shows where certain regulatory genes are turned on along the notochord.
As director of the new Center for Integrative Genomics, Levine's primary interest is identifying the many regulatory genes in the genomes emerging from sequencing labs around the world. Most scientists have concentrated on the protein-coding genes, he said, but there may be nearly as much DNA in the genome controlling when and where these genes are expressed. Ciona's 15,000-plus genes may be controlled by some 10,000 regulatory DNAs, including enhancers and silencers.
"Regulatory DNA is the software in the system, but it is all but invisible now," Levine said. "One important goal for the center is to identify all the regulatory DNA in Ciona, and develop a way to decode regulatory DNA in any organism."
The leaders of the major teams reporting the Ciona genome are Levine, Rokhsar, Nori Satoh of the Department of Zoology at Kyoto University and Yuji Kohara of the National Institute of Genetics in Japan.
The work was supported by the Department of Energy, the National Institutes of Health and various U.S. and Japanese organizations.