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Anyone who has spent any time taking courses in developmental biology has heard about the sea urchin. It has been a major experimental model for over a century, and the elucidation of its genomic sequence described here will be of interest to communities studying everything from economics and ecology in marine ecosystems to fundamental questions in evolution and development.
Davidson (p. 939) introduces us to this organism and to the reasons for its importance. Vertebrates share specific features of embryonic development with the sea urchin (which is the basis for their classification as deuterostomes). The sea urchin genome represents the first full sequence of a nonchordate deuterostome, and as such, makes it possible to identify genes that are truly vertebrate innovations and others that have been lost during evolution. Although much is known about developmental gene regulatory modules, a more detailed picture of these genetic elements and underlying principles of gene regulation that may apply across phyla is now possible. [For further discussion, see Science's Signal Transduction Knowledge Environment site (STKE; www.stke.sciencemag.org)].
To help you visualize the history of sea urchin research and this latest achievement, the section contains a poster, done with the scientific input of A. Cameron and E. Davidson and sure to enrich many walls. An interactive version of the poster, including additional images, video, and Web resources, was created by T. Marathe and S. Wills with images assembled by A. Ransick (www.sciencemag.org/sciext/seaurchin/).
Initial analyses of the 814-megabase genome led to an outpouring of insights, which can be found here in Science (Sea Urchin Genome Sequencing Consortium, p. 941), with additional details appearing in a special issue of Developmental Biology on 1 December. See also the News article by Elizabeth Pennisi (p. 908). Some of the most striking findings from the sea urchin genome sequence relate to immunity, as described by Rast et al. (p. 952). These include an expansion of some innate immune receptors by more than an order of magnitude relative to vertebrates. To complement the genomic sequencing effort, Samanta et al. (p. 960) used high-resolution custom tiling arrays to generate a picture of the repertoire of genes expressed during embryogenesis. Having this picture proved to be very valuable to the community in the annotation process.
One fascinating trend is the creative ways in which genomic data can be combined with data from very different disciplines to yield new insights. By examining sequence data for extant sea urchins and combining this information with what is known from the fossil record, it is possible to speculate about the genes that underlie the structural composition of the earliest echinoderms that appeared during the early Cambrian Period. As described by Bottjer (p. 956), paleogenomic analyses of the sea urchin provide insight into genes participating in the generation of fossil-recorded structures. Pearse (p. 940) describes the cause and effect of population fluctuations in this animal, which has economic value as a fishery resource and is a vital component of marine benthic ecosystems. The sequence of the purple sea urchin (and sequences we hope are to come of related species) will help in understanding the basis for variations that affect the cycle between rich kelp forests (on which the urchin grazes) and sea urchin-filled "barrens." The sequencing of the sea urchin moves us a further step away from the past, when the analysis of an individual gene was a breathtaking achievement, toward a future where we will be following multidimensional changes in gene networks and relating them to the world around us.
The editors suggest the following Related Resources on Science sites:
In Science Magazine
Sea Urchin Genome Sequencing Consortium, Erica Sodergren, George M. Weinstock, Eric H Davidson, R. Andrew Cameron, Richard A. Gibbs, Robert C. Angerer, Lynne M. Angerer, Maria Ina Arnone, David R. Burgess, Robert D. Burke, James A. Coffman, Michael Dean, Maurice R. Elphick, Charles A. Ettensohn, Kathy R. Foltz, Amro Hamdoun, Richard O. Hynes, William H. Klein, William Marzluff, David R. McClay, Robert L. Morris, Arcady Mushegian, Jonathan P. Rast, L. Courtney Smith, Michael C. Thorndyke, Victor D. Vacquier, Gary M. Wessel, Greg Wray, Lan Zhang, Christine G. Elsik, Olga Ermolaeva, Wratko Hlavina, Gretchen Hofmann, Paul Kitts, Melissa J. Landrum, Aaron J. Mackey, Donna Maglott, Georgia Panopoulou, Albert J. Poustka, Kim Pruitt, Victor Sapojnikov, Xingzhi Song, Alexandre Souvorov, Victor Solovyev, Zheng Wei, Charles A. Whittaker, Kim Worley, K. James Durbin, Yufeng Shen, Olivier Fedrigo, David Garfield, Ralph Haygood, Alexander Primus, Rahul Satija, Tonya Severson, Manuel L. Gonzalez-Garay, Andrew R. Jackson, Aleksandar Milosavljevic, Mark Tong, Christopher E. Killian, Brian T. Livingston, Fred H. Wilt, Nikki Adams, Robert Bellé, Seth Carbonneau, Rocky Cheung, Patrick Cormier, Bertrand Cosson, Jenifer Croce, Antonio Fernandez-Guerra, Anne-Marie Genevière, Manisha Goel, Hemant Kelkar, Julia Morales, Odile Mulner-Lorillon, Anthony J. Robertson, Jared V. Goldstone, Bryan Cole, David Epel, Bert Gold, Mark E. Hahn, Meredith Howard-Ashby, Mark Scally, John J. Stegeman, Erin L. Allgood, Jonah Cool, Kyle M. Judkins, Shawn S. McCafferty, Ashlan M. Musante, Robert A. Obar, Amanda P. Rawson, Blair J. Rossetti, Ian R. Gibbons, Matthew P. Hoffman, Andrew Leone, Sorin Istrail, Stefan C. Materna, Manoj P. Samanta, Viktor Stolc, Waraporn Tongprasit, Qiang Tu, Karl-Frederik Bergeron, Bruce P. Brandhorst, James Whittle, Kevin Berney, David J. Bottjer, Cristina Calestani, Kevin Peterson, Elly Chow, Qiu Autumn Yuan, Eran Elhaik, Dan Graur, Justin T. Reese, Ian Bosdet, Shin Heesun, Marco A. Marra, Jacqueline Schein, Michele K. Anderson, Virginia Brockton, Katherine M. Buckley, Avis H. Cohen, Sebastian D. Fugmann, Taku Hibino, Mariano Loza-Coll, Audrey J. Majeske, Cynthia Messier, Sham V. Nair, Zeev Pancer, David P. Terwilliger, Cavit Agca, Enrique Arboleda, Nansheng Chen, Allison M. Churcher, F. Hallböök, Glen W. Humphrey, Mohammed M. Idris, Takae Kiyama, Shuguang Liang, Dan Mellott, Xiuqian Mu, Greg Murray, Robert P. Olinski, Florian Raible, Matthew Rowe, John S. Taylor, Kristin Tessmar-Raible, D. Wang, Karen H. Wilson, Shunsuke Yaguchi, Terry Gaasterland, Blanca E. Galindo, Herath J. Gunaratne, Celina Juliano, Masashi Kinukawa, Gary W. Moy, Anna T. Neill, Mamoru Nomura, Michael Raisch, Anna Reade, Michelle M. Roux, Jia L. Song, Yi-Hsien Su, Ian K. Townley, Ekaterina Voronina, Julian L. Wong, Gabriele Amore, Margherita Branno, Euan R. Brown, Vincenzo Cavalieri, Véronique Duboc, Louise Duloquin, Constantin Flytzanis, Christian Gache, François Lapraz, Thierry Lepage, Annamaria Locascio, Pedro Martinez, Giorgio Matassi, Valeria Matranga, Ryan Range, Francesca Rizzo, Eric Röttinger, Wendy Beane, Cynthia Bradham, Christine Byrum, Tom Glenn, Sofia Hussain, Gerard Manning, Esther Miranda, Rebecca Thomason, Katherine Walton, Athula Wikramanayke, Shu-Yu Wu, Ronghui Xu, C. Titus Brown, Lili Chen, Rachel F. Gray, Pei Yun Lee, Jongmin Nam, Paola Oliveri, Joel Smith, Donna Muzny, Stephanie Bell, Joseph Chacko, Andrew Cree, Stacey Curry, Clay Davis, Huyen Dinh, Shannon Dugan-Rocha, Jerry Fowler, Rachel Gill, Cerrissa Hamilton, Judith Hernandez, Sandra Hines, Jennifer Hume, LaRonda Jackson, Angela Jolivet, Christie Kovar, Sandra Lee, Lora Lewis, George Miner, Margaret Morgan, Lynne V. Nazareth, Geoffrey Okwuonu, David Parker, Ling-Ling Pu, Rachel Thorn, and Rita Wright (10 November 2006) Science314 (5801), 941.
[DOI: 10.1126/science.1133609] |Abstract »|Full Text »|PDF »|Supporting Online Material »