Our fellow deuterostome. Photograph: Jeffrey L. Rotman/CORBIS

The sea urchin, that spiny round creature hiding in coral reefs and rocks, is like an uncle you wish wouldn’t visit. It’s homely, not bright or social, and it sits around doing just about nothing. Yet there’s no denying the familial tie: The recent sequencing of the genome of a 20-year-old California male purple sea urchin has revealed that 70 percent of the species’ genes share common ancestry with human genes.

The massive effort to delineate the urchin genome was the joint work of 240 molecular and developmental biologists, zoologists, geneticists, bioinformaticists, and other scientists at more than 70 institutions, including the laboratory team of biology professor David Burgess at Boston College. The project results were made public late last year with publication of 42 papers in special issues of Science and Developmental Biology. The sea urchin code amounts to 23,300 genes, including quite a few that scientists never expected to find.

The work at Boston College was done over 18 months and drew in graduate and undergraduate students. Researchers were provided with a computer-generated rough draft of the genome, produced from laboratory analysis conducted by the project’s organizers at Cal Tech. Their job, carried out entirely in front of computer screens, was twofold: to comb through the raw data and neaten it up (“kind of like putting pieces of a puzzle back together,” says doctoral student Matthew Hoffman); and, cued by a computer program, to follow up in detail on near-matches with other known genomes, including the human genome.

Humans and urchins alike fall into a class of creatures known as deuterostomes—the word means “mouth second,” a reference to the sequence in which the digestive system’s orifices take shape after conception. Some 540 million years ago, according to the fossil record, deuterostomes split, diverging into two principal groups—echinoderms (urchins, starfish, sea cucumbers, etc.) and chordates (humans and other vertebrates). Comparing the sea urchin’s genome to our own (made public in 2003), will help scientists determine which human genes predate the split, filling in details of the genetic road map of life. As lead scientist Eric Davidson of Cal Tech wrote in Science, the sea urchin offers “an extremely useful outgroup for the understanding of our own genomes—an intellectual version of Archimedes’s idea that with a leverage point removed from Earth he could move the globe.”

Interesting findings have emerged already. For instance, Jonathan Rast, a comparative immunologist at the University of Toronto, and colleagues found a number of the urchin’s genes that produce immune system proteins previously believed to exist only in vertebrates. Another group reported that the urchin genome includes nearly a thousand genes associated with sight and smell—despite the fact that the urchin has neither eyes nor nose. Genes that code for light-sensing proteins called opsins were among those discovered. Apparently, the urchins express these proteins in their spines and in the tubules they use as feet.

At Boston College, Burgess’s lab group studied genes governing the sea urchin’s cytoskeleton, the protein-based, internal scaffolding that organizes and gives cells their shape. Along with scientists at Wheaton College, Massachusetts, and the University of California, Berkeley, they focused on the portion of the genome that encodes the cytoskeleton’s building instructions. One of their more surprising findings, reported in the November 10, 2006, issue of Science, involves genes associated in humans with Usher syndrome, a congenital disease that leads to hearing loss. In the sea urchin’s genetic material, the Boston College researchers and others discovered homologs (genes having shared ancestry) of the Usher genes found in humans. The function of the homologs in urchins is still to be determined.

Gregory Mone is a contributing editor at Popular Science and the author of The Wages of Genius (2003).

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