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The Genome of the Sea Urchin Strongylocentrotus purpuratus

Sodergren, Erica and Davidson, Eric H. and Cameron, R. Andrew and Howard-Ashby, Meredith and Materna, Stefan C. and Tu, Qiang and Berney, Kevin and Su, Yi-Hsien and Brown, C. Titus and Chen, Lili and Gray, Rachel F. and Lee, Pei Yun and Nam, Jongmin and Oliveri, Paola and Smith, Joel and Chow, Elly and Yuan, Qiu Autumn (2006) The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science, 314 (5801). pp. 941-952. ISSN 0036-8075. PMCID PMC3159423. https://resolver.caltech.edu/CaltechAUTHORS:20130130-130039894

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Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1126/science.1133609DOIArticle
http://www.sciencemag.org/content/314/5801/941.abstractPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/PubMed CentralArticle
ORCID:
AuthorORCID
Cameron, R. Andrew0000-0003-3947-6041
Brown, C. Titus0000-0001-6001-2677
Additional Information:© 2006 American Association for the Advancement of Science. Received for publication 8 August 2006; accepted for publication 17 October 2006. We gratefully acknowledge the following support: BCM-HGSC, National Human Genome Research Institute (NIH) grant 5 U54 HG003273; Naples Workshop, Stazione Zoologica Naples and the Network of Excellence “Marine Genomics Europe” (GOCE-04-505403); M. Elphick, Biotechnology and Biological Sciences Research Council (BBSRC), UK, grant S19916; J. Rast laboratory, Natural Sciences and Engineering Research Council (NSERC) of Canada, Canadian Institutes of Health Research (CIHR), and the Uehara Memorial Foundation; J. A. Coffman, Mount Desert Island Biological Laboratory (MDIBL), NIH grant GM070840; M. C. Thorndyke, K. H. Wilson, F. Hallböök, R. P. Olinski, Swedish Science Research Council, Network of Excellence Marine Genomics Europe (GOCE-04-505403), European Union Research Training Networks FP5 Trophic Neurogenome HPRN-ct-2002-00263, and the Royal Swedish Academy of Sciences, STINT; E. H. Davidson, R. A. Cameron, the Center for Computational Regulatory Genomics (E. H. Davidson, principal investigator) was supported by the NIH grant RR-15044, NSF IOB- 0212869, and the Beckman Institute; also, support for the E. H. Davidson laboratory is from NIH grants HD-37105 and GM61005 and U.S. Department of Energy (DOE) grant DE-FG02-03ER63584; P. Oliveri, Camilla Chandler Frost Fellowship; G. M. Wessel laboratory supported by NSF IOB-0620607 and NIH grant R01 HD028152; B. Brandhorst, K. Bergeron, and N. Chen, NSERC; K. R. Foltz, NSF, IBN-0415581; M. Hahn, NIH grant R01ES006272; D. Burgess, NIH grant GM058231; L. C. Smith, NSF (MCB-0424235); R. O. Hynes, Howard Hughes Medical Institute and National Cancer Institute (NCI) (MIT Cancer Center core grant P30-CA14051); D. McClay, NIH grants GM61464, HD039948, and HD14483; V. D. Vacquier (group leader), G. W. Moy, H. J. Gunaratne, M. Kinukawa, M. Nomura, A. T. Neill, and Y.-H. Su, NIH grant R37-HD12896; R. D. Burke, NSERC and CIHR; L. M. Angerer, National Institute of Dental and Craniofacial Research (NIDCR), R. C. Angerer (NIDCR), Z. Wei (NIDCR), G. Humphrey, National Institute of Child Health and Human Development (NICHD), M. Landrum, National Center for Biotechnology Information (NCBI), O. Ermolaeva (NCBI), P. Kitts (NCBI), K. Pruitt (NCBI), V. Sapojnikov (NCBI), A. Souvorov (NCBI), W. Hiavina (NCBI), S. Fugmann, National Institute on Aging (NIA), M. Dean, National Cancer Institute–Frederick (NCIFCRF) Intramural Research Program of the NIH; P. Cormier, Association pour la Recherche contre la Cancer (ARC), France, grants 4247 and 3507 to P.C., Ligue Nationale contre le Cancer to P.C., Conseil Régional de Bretagne and Conseil Général du Finistère; W. H. Klein, National Eye Institute, NIH grant EY11930, NICHD HD66219, and the Robert A. Welch Foundation (G-0010); N. Adams, NSF grant IBN 0417003 and the Department of the Navy, Office of Naval Research, under Award N00014-05-1-0855; D. Epel, NSF 0417225; A. Hamdoun, F32-HD47136; C. Byrum, American Heart Association grant 0420074Z; K. Walton, U.S. Army Medical Research and Materiel Command grant W81XWH-04-1-0324; J. Stegeman, NIH 2P42 ESO7381; and J. Goldstone, NIH F32 ESO12794
Errata:Erratum in Science. 2007 Feb 9;315(5813):766.
Funders:
Funding AgencyGrant Number
NIH5 U54 HG003273
Stazione Zoologica Naples and the Network of Excellence GOCE-04-505403
Biotechnology and Biological Sciences Research Council (BBSRC)S19916
Canadian Institutes of Health Research (CIHR)UNSPECIFIED
Uehara Memorial FoundationUNSPECIFIED
Mount Desert Island Biological Laboratory (MDIBL)UNSPECIFIED
NIHGM070840
Swedish Science Research CouncilUNSPECIFIED
Network of Excellence Marine Genomics EuropeGOCE-04-505403
European Union Research Training Networks FP5 Trophic NeurogenomeHPRN-ct-2002-00263
Royal Swedish Academy of SciencesUNSPECIFIED
NIHRR-15044
NSFIOB-0212869
Caltech Beckman InstituteUNSPECIFIED
NIHHD-37105
NIHGM61005
Department of Energy (DOE)DE-FG02-03ER63584
Camilla Chandler Frost FellowshipUNSPECIFIED
NSFIOB-0620607
NIHR01 HD028152
Natural Sciences and Engineering Research Council of Canada (NSERC)UNSPECIFIED
NSFIBN-0415581
NIHR01ES006272
NIHGM058231
NSFMCB-0424235
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
National Cancer Institute (NCI)UNSPECIFIED
MIT Cancer CenterP30-CA14051
NIHGM61464
NIHHD039948
NIHHD14483
NIHR37-HD12896
National Institute of Dental and Craniofacial Research (NIDCR)UNSPECIFIED
National Center for Biotechnology Information (NCBI)UNSPECIFIED
National Institute on Aging (NIA)UNSPECIFIED
Association pour la Recherche contre la Cancer (ARC)4247
Association pour la Recherche contre la Cancer (ARC)3507
Ligue Nationale contre le CancerUNSPECIFIED
Conseil Régional de Bretagne and Conseil Général du FinistèreUNSPECIFIED
National Eye InstituteEY11930
National Institute of Child Health and Human Development (NICHD)HD66219
Robert A. Welch Foundation G-0010
NSFIBN0417003
Office of Naval Research (ONR)N00014-05-1-0855
NSF0417225
NIHF32-HD47136
American Heart Association0420074Z
Army Research Office (ARO)W81XWH-04-1-0324
NIH2P42 ESO7381
NIHF32 ESO12794
Issue or Number:5801
PubMed Central ID:PMC3159423
Record Number:CaltechAUTHORS:20130130-130039894
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20130130-130039894
Official Citation:The Genome of the Sea Urchin Strongylocentrotus purpuratus 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 Science 10 November 2006: 314 (5801), 941-952. [DOI:10.1126/science.1133609]
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36689
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:30 Jan 2013 22:43
Last Modified:03 Oct 2019 04:40

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