One Genome, One Piece of the Puzzle

Abstract

The publication of species genomes is becoming almost commonplace--almost. In the last few months, the genomes of the honeybee (Wilson, 2006), the black cottonwood tree, a poplar (Stokstad, 2006), and the bacteria living in the gut of a parasitic worm (Stahl & Davidson, 2006) have been published. I must admit that I don't attend to this deluge of information too carefully. I do read summary essays that often accompany these publications, but that's about it. With so many other areas of biology to explore, I can't spend too much time on genomics. However when the genome of the purple sea urchin, Stronglyocentrotus purpuratus, was published in November (Sea Urchin Genome Sequencing Consortium et al., 2006), I did pay a little more attention to the results for a number of reasons. First, my interest was whetted by the Science cover photo of sea urchin larvae which caught my eye with their colors and delicacy. Also, when I was in high school I had a teacher who was involved in research on an anti-cancer drug derived from sea urchins. I don't think anything came of this work, but she woke me up to the beauty and mystery of these creatures. Finally, the summary of the findings on this genome made me want further information; this publication was more than just another run-of-the-mill genome-if such a thing exists. It is only a half dozen years since the publication of the human genome, and the number of species that have sequenced genomes is still minuscule relative to the diversity of life. The black cottonwood, Populus trichocarpa, was only the third plant to be sequenced, after Arabidopsis and rice. And though there are hundreds of thousands of named insect species, the honeybee is only the third insect to have its genome sequenced, along with fruit flies and mosquitoes: With such rarity, genome sequencing is still news, and as in any field where there is a scarcity of information, there is a wealth of surprises. Every article describing a new genome sequence highlights the unexpected in the findings: Honeybees have fewer genes for immunity than do other insects, even though bees live in close quarters, and the cottonwood sequence has been duplicated at least three times. This element of surprise is what makes genome exploration fun: there are wonders lurking around every genetic corner. Humans love to make generalizations from limited data, for example extrapolating all insects' genetic characteristics based on a couple of genomes. The only good thing about this dangerous habit is that it makes for a lot of wonderful surprises as assumptions are ripped to shreds by each new genome publication. The sea urchin genome is no exception, but it also has special importance for other reasons. Though u might seem surprising, this work provides crucial insights into the human genome. This is because, like the chordates--the taxon that humans belong to--the sea urchin is a deuterosome. And as its genome sequence verifies, this makes the sea urchin and other echinoderms more closely related to humans and other chordates than to other invertebrates such as insects, mollusks, and crustaceans (Pennisi, 2006). Finding out about sea urchin genes is another step in making sense of the human genome because it provides information about the genetic makeup of early chordates. and about where these genes might have originated. The sea urchin serves as a valuable outgroup for evolutionary comparisons. While the publication of the chimpanzee genome shed great light on the human genetic sequence, it is also important to have information about more distantly related species as points of comparison (Bottjer, Davidson, Peterson & Cameron. 2006? This made the mouse genome particularly useful, relative to that of the primates, but still more distant relatives, like the sea urchin, are also crucial for filling in the picture. History Yet another reason why the sea urchin genome merited a special section in the November 10. …