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Saturday, November 11, 2006

Sea Urchin Genome Sequenced

The sequence of the genome of the California purple urchin, Strongylocentrotus purpuratus was reported in the November 10 issue of Science magazine. The Science webpage contains a number of links to important articles and, more importantly, a link to a special interactive poster.

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team. We can expect the number to drop as annotation proceeds because most of the gene prediction programs tend to over-estimate the number of genes. I've looked at the current draft of the sequence to see how many HSP70 genes are in the genome and discovered that there are more pseudogenes and gene fragments than real genes. This is not unusual in a first draft.

There are two important links to the Sea Urchin genome project. The first is at CalTech, the home of Eric Davidson who is one of the key movers and shakers in the study of sea urchins. The second site is at the Human Genome Sequencing Center at Baylor College of Medicine. This is one of the large sequencing centers that sprung up during the rush to finish the human genome sequence.

The first assembly has been deposited in GenBank and the National Center for Biotechnology Information (NCBI) has set up a website for Sea Urchin Genome Resources.

According to the original proposal [White Paper] the cost of sequencing the sea urchin genome would be about $30 million. The proposal gives several different reasons for funding the project but one of the key motives is to fill in a gap in the phylogeny of sequenced animal genomes. The figure above shows the position of sea urchins relative to chordates (including mammals) and most invertebrates. The phylum Echinoderma clusters with the phylum Chordata (shaded area on the right) in a group known as Deuterostomes. Thus, sea urchin genes are more closely related to chordate/vertebrate genes than to mussel or arthropod genes. In other words sea urchins are more like humans than octopus or squid.

From .....

Scientists have sequenced the genome of the sea urchin, an invertebrate surprisingly similar to man, a step that could help develop new treatment for human disease such as cancer, said a study released Thursday. [more ...]

From the National Center for Research Resources (by Aaron Levin) ...
For more than 30 years, Dr. Eric Davidson and his research team at the California Institute of Technology in Pasadena have steadily teased apart the molecular genetics of a common ocean-dwelling creature, the purple sea urchin (Strongylocentrotus purpuratus), searching for the regulatory mechanisms that underlie its development from fertilized egg to free-swimming larva. The Caltech scientists have long recognized what a growing segment of the biomedical community is beginning to appreciate—that the sea urchin is a unique and tractable organism with enormous potential for shedding light on the most basic biological processes, including many that are relevant to human health. Indeed, the National Human Genome Research Institute recently selected the sea urchin as a top priority for genome sequencing, along with the genomes of the chimpanzee, dog, cow, and other animals of scientific interest. [more ...]

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