The Sea Urchin Genome and its Regulatory Gene Networking

The Science

The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. Researchers examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.

Comparative analysis of the sea urchin genome has broad implications for the primitive state of deuterostome host defense and the genetic underpinnings of immunity in vertebrates. The sea urchin has an unprecedented complexity of innate immune recognition receptors relative to other animal species yet characterized. These receptor genes include a vast repertoire of 222 Toll-like receptors, a superfamily of more than 200 NACHT domain–leucine-rich repeat proteins (similar to nucleotide-binding and oligomerization domain (NOD) and NALP proteins of vertebrates), and a large family of scavenger receptor cysteine-rich proteins. More typical numbers of genes encode other immune recognition factors. Homologs of important immune and hematopoietic regulators, many of which have previously been identified only from chordates, as well as genes that are critical in adaptive immunity of jawed vertebrates, also are present. The findings serve to underscore the dynamic utilization of receptors and the complexity of immune recognition that may be basal for deuterostomes and predicts features of the ancestral bilaterian form.


The DNA sequence of the purple sea urchin genome, with interpretations of gene function and their networking during embryogenesis, is published in a special section of the November 10 Science magazine. The sea urchin is an ideal model system because it readily accepts DNA injected into the egg, and the effects can be observed using a simple light microscope. The overall genome analysis reveals a rich lode of information on gene function, evolution, and embryonic development. Among the more striking findings is that despite a much simpler body plan, the 23,000 genes sea urchin are only slightly fewer than the 26,000 genes of humans. Many of the sea urchin genes have representatives in humans, while there are many others evidently lost during the long evolutionary tract to the primates. With a capacity to digest tough sea kelp vegetation, some of the sea urchin digestive enzymes may also be of interest in broader biomass processing. This study was done in the Cal Tech laboratory of Eric Davidson, with a sucontract to David McClay at Duke University.


Davidson, E. H. 2006. “The Sea Urchin Genome: Where Will It Lead Us?,” Science 314. DOI:10.1126/science.1136252.

Sea Urchin Genome Sequencing Consortium. 2006.”The Genome of the Sea Urchin Strongylocentrotus purpuratus,” Science 314. DOI:10.1126/science.1133609.

Samanta, M. P., W. Tongprasit, S. Istrail, R. A. Cameron, Q. Tu, E. H. Davidson, and V. Stolc. 2006. “The Transcriptome of the Sea Urchin Embryo,” Science 314. DOI:10.1126/science.1131898.

Rast, J. P., L. C. Smith, M. Loza-Coll, T. Hibino, and G. W. Litman. 2006. “Genomic Insights in the Immune System of the Sea Urchin,” Science 314. DOI:10.1126/science.1134301.