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.
Bibliography
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., Coffman, J. A., Dean, M., Elphick, M. R., Ettensohn, C. A., Foltz, K. R., Hamdoun, A., Hynes, R. O., Klein, W. H., Marzluff, W., ⦠Wright, R. (2006). The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science, 314(5801), 941â952.
Authors
228
- Erica Sodergren (first)
- George M. Weinstock (additional)
- Eric H Davidson (additional)
- R. Andrew Cameron (additional)
- Richard A. Gibbs (additional)
- Robert C. Angerer (additional)
- Lynne M. Angerer (additional)
- Maria Ina Arnone (additional)
- David R. Burgess (additional)
- Robert D. Burke (additional)
- James A. Coffman (additional)
- Michael Dean (additional)
- Maurice R. Elphick (additional)
- Charles A. Ettensohn (additional)
- Kathy R. Foltz (additional)
- Amro Hamdoun (additional)
- Richard O. Hynes (additional)
- William H. Klein (additional)
- William Marzluff (additional)
- David R. McClay (additional)
- Robert L. Morris (additional)
- Arcady Mushegian (additional)
- Jonathan P. Rast (additional)
- L. Courtney Smith (additional)
- Michael C. Thorndyke (additional)
- Victor D. Vacquier (additional)
- Gary M. Wessel (additional)
- Greg Wray (additional)
- Lan Zhang (additional)
- Christine G. Elsik (additional)
- Olga Ermolaeva (additional)
- Wratko Hlavina (additional)
- Gretchen Hofmann (additional)
- Paul Kitts (additional)
- Melissa J. Landrum (additional)
- Aaron J. Mackey (additional)
- Donna Maglott (additional)
- Georgia Panopoulou (additional)
- Albert J. Poustka (additional)
- Kim Pruitt (additional)
- Victor Sapojnikov (additional)
- Xingzhi Song (additional)
- Alexandre Souvorov (additional)
- Victor Solovyev (additional)
- Zheng Wei (additional)
- Charles A. Whittaker (additional)
- Kim Worley (additional)
- K. James Durbin (additional)
- Yufeng Shen (additional)
- Olivier Fedrigo (additional)
- David Garfield (additional)
- Ralph Haygood (additional)
- Alexander Primus (additional)
- Rahul Satija (additional)
- Tonya Severson (additional)
- Manuel L. Gonzalez-Garay (additional)
- Andrew R. Jackson (additional)
- Aleksandar Milosavljevic (additional)
- Mark Tong (additional)
- Christopher E. Killian (additional)
- Brian T. Livingston (additional)
- Fred H. Wilt (additional)
- Nikki Adams (additional)
- Robert BelleÌ (additional)
- Seth Carbonneau (additional)
- Rocky Cheung (additional)
- Patrick Cormier (additional)
- Bertrand Cosson (additional)
- Jenifer Croce (additional)
- Antonio Fernandez-Guerra (additional)
- Anne-Marie GenevieÌre (additional)
- Manisha Goel (additional)
- Hemant Kelkar (additional)
- Julia Morales (additional)
- Odile Mulner-Lorillon (additional)
- Anthony J. Robertson (additional)
- Jared V. Goldstone (additional)
- Bryan Cole (additional)
- David Epel (additional)
- Bert Gold (additional)
- Mark E. Hahn (additional)
- Meredith Howard-Ashby (additional)
- Mark Scally (additional)
- John J. Stegeman (additional)
- Erin L. Allgood (additional)
- Jonah Cool (additional)
- Kyle M. Judkins (additional)
- Shawn S. McCafferty (additional)
- Ashlan M. Musante (additional)
- Robert A. Obar (additional)
- Amanda P. Rawson (additional)
- Blair J. Rossetti (additional)
- Ian R. Gibbons (additional)
- Matthew P. Hoffman (additional)
- Andrew Leone (additional)
- Sorin Istrail (additional)
- Stefan C. Materna (additional)
- Manoj P. Samanta (additional)
- Viktor Stolc (additional)
- Waraporn Tongprasit (additional)
- Qiang Tu (additional)
- Karl-Frederik Bergeron (additional)
- Bruce P. Brandhorst (additional)
- James Whittle (additional)
- Kevin Berney (additional)
- David J. Bottjer (additional)
- Cristina Calestani (additional)
- Kevin Peterson (additional)
- Elly Chow (additional)
- Qiu Autumn Yuan (additional)
- Eran Elhaik (additional)
- Dan Graur (additional)
- Justin T. Reese (additional)
- Ian Bosdet (additional)
- Shin Heesun (additional)
- Marco A. Marra (additional)
- Jacqueline Schein (additional)
- Michele K. Anderson (additional)
- Virginia Brockton (additional)
- Katherine M. Buckley (additional)
- Avis H. Cohen (additional)
- Sebastian D. Fugmann (additional)
- Taku Hibino (additional)
- Mariano Loza-Coll (additional)
- Audrey J. Majeske (additional)
- Cynthia Messier (additional)
- Sham V. Nair (additional)
- Zeev Pancer (additional)
- David P. Terwilliger (additional)
- Cavit Agca (additional)
- Enrique Arboleda (additional)
- Nansheng Chen (additional)
- Allison M. Churcher (additional)
- F. HallboÌoÌk (additional)
- Glen W. Humphrey (additional)
- Mohammed M. Idris (additional)
- Takae Kiyama (additional)
- Shuguang Liang (additional)
- Dan Mellott (additional)
- Xiuqian Mu (additional)
- Greg Murray (additional)
- Robert P. Olinski (additional)
- Florian Raible (additional)
- Matthew Rowe (additional)
- John S. Taylor (additional)
- Kristin Tessmar-Raible (additional)
- D. Wang (additional)
- Karen H. Wilson (additional)
- Shunsuke Yaguchi (additional)
- Terry Gaasterland (additional)
- Blanca E. Galindo (additional)
- Herath J. Gunaratne (additional)
- Celina Juliano (additional)
- Masashi Kinukawa (additional)
- Gary W. Moy (additional)
- Anna T. Neill (additional)
- Mamoru Nomura (additional)
- Michael Raisch (additional)
- Anna Reade (additional)
- Michelle M. Roux (additional)
- Jia L. Song (additional)
- Yi-Hsien Su (additional)
- Ian K. Townley (additional)
- Ekaterina Voronina (additional)
- Julian L. Wong (additional)
- Gabriele Amore (additional)
- Margherita Branno (additional)
- Euan R. Brown (additional)
- Vincenzo Cavalieri (additional)
- VeÌronique Duboc (additional)
- Louise Duloquin (additional)
- Constantin Flytzanis (additional)
- Christian Gache (additional)
- François Lapraz (additional)
- Thierry Lepage (additional)
- Annamaria Locascio (additional)
- Pedro Martinez (additional)
- Giorgio Matassi (additional)
- Valeria Matranga (additional)
- Ryan Range (additional)
- Francesca Rizzo (additional)
- Eric RoÌttinger (additional)
- Wendy Beane (additional)
- Cynthia Bradham (additional)
- Christine Byrum (additional)
- Tom Glenn (additional)
- Sofia Hussain (additional)
- Gerard Manning (additional)
- Esther Miranda (additional)
- Rebecca Thomason (additional)
- Katherine Walton (additional)
- Athula Wikramanayke (additional)
- Shu-Yu Wu (additional)
- Ronghui Xu (additional)
- C. Titus Brown (additional)
- Lili Chen (additional)
- Rachel F. Gray (additional)
- Pei Yun Lee (additional)
- Jongmin Nam (additional)
- Paola Oliveri (additional)
- Joel Smith (additional)
- Donna Muzny (additional)
- Stephanie Bell (additional)
- Joseph Chacko (additional)
- Andrew Cree (additional)
- Stacey Curry (additional)
- Clay Davis (additional)
- Huyen Dinh (additional)
- Shannon Dugan-Rocha (additional)
- Jerry Fowler (additional)
- Rachel Gill (additional)
- Cerrissa Hamilton (additional)
- Judith Hernandez (additional)
- Sandra Hines (additional)
- Jennifer Hume (additional)
- LaRonda Jackson (additional)
- Angela Jolivet (additional)
- Christie Kovar (additional)
- Sandra Lee (additional)
- Lora Lewis (additional)
- George Miner (additional)
- Margaret Morgan (additional)
- Lynne V. Nazareth (additional)
- Geoffrey Okwuonu (additional)
- David Parker (additional)
- Ling-Ling Pu (additional)
- Rachel Thorn (additional)
- Rita Wright (additional)
References
54
Referenced
910
10.1038/nature02426
10.1101/gr.198101
10.1016/0092-8674(78)90044-2
10.1126/science.1080049
10.1101/gr.3722605
10.1016/0003-2697(71)90476-3
- C. G. Elsik A. J. Mackey J. T. Reese N. V. Milshina D. S. Roos G. M. Weinstock Genome Biol . in press.
- Sea Urchin Genome Project (http://sugp.caltech.edu/resources/annotation.php).
- Genboree (www.genboree.org).
10.1126/science.1131898
10.1093/nar/gkj020
10.1016/j.ydbio.2006.08.032
- F. Raible et al. Dev. Biol. in press.
- K. Grobben, Verh. Zool. Bot. Ges. Wien58, 491 (1908). / Verh. Zool. Bot. Ges. Wien (1908)
- E. H. Davidson in Gene Regulatory Networks in Development and Evolution (Academic Press/Elsevier San Diego CA 2006).
10.1126/science.1069883
10.1006/dbio.2002.0635
10.1016/j.ydbio.2006.08.034
10.1242/dev.129.13.3021
- M. Howard-Ashby C. T. Brown S. C. Materna L. Chen E. H. Davidson Dev. Biol. in press.
10.1016/S0968-0004(02)02179-5
10.1126/science.1075762
10.1016/j.ydbio.2006.08.074
- C. Byrum et al. Dev. Biol. in press.
10.1371/journal.pbio.0030314
10.1038/ng902
10.1038/ng884
10.1016/j.ydbio.2006.08.046
10.1038/nature03158
- J. Croce et al. Dev. Biol. in press.
- The Wnt homepage (www.stanford.edu/~rnusse/wntwindow.html).
10.1016/j.ydbio.2006.07.044
10.1073/pnas.230096397
10.1007/s002510050551
10.1016/j.cell.2006.02.015
10.1073/pnas.0509720103
10.1371/journal.pbio.0030181
10.1126/science.1134301
10.1016/S0162-3109(99)00009-0
10.1034/j.1600-065X.2001.1800102.x
10.1016/j.ydbio.2006.08.065
10.1016/j.ydbio.2006.08.066
10.1016/j.ydbio.2004.02.004
10.1073/pnas.0504757102
10.1101/gad.12.9.1290
10.1074/jbc.R100033200
10.1016/j.ydbio.2006.08.007
- J. L. S. Cobb, in Nervous Systems of Invertebrates, M. A. Ali, Ed. (Plenum, New York, 1987), pp. 483â525. / Nervous Systems of Invertebrates (1987)
10.1016/0040-8166(77)90054-4
10.1016/j.ydbio.2006.07.047
10.1073/pnas.0404279101
10.1016/j.ydbio.2006.08.052
10.1038/sj.cdd.4400991
- 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 âMarine Genomics Europeâ (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. HallboÌoÌk 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 InstituteâFrederick (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 ReÌgional de Bretagne and Conseil GeÌneÌral du FinisteÌre; 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.
Dates
Type | When |
---|---|
Created | 18 years, 9 months ago (Nov. 9, 2006, 4:53 p.m.) |
Deposited | 1 year, 7 months ago (Jan. 10, 2024, 4:31 a.m.) |
Indexed | 1 day, 17 hours ago (Aug. 27, 2025, 12:36 p.m.) |
Issued | 18 years, 9 months ago (Nov. 10, 2006) |
Published | 18 years, 9 months ago (Nov. 10, 2006) |
Published Print | 18 years, 9 months ago (Nov. 10, 2006) |
@article{Sodergren_2006, title={The Genome of the Sea Urchin Strongylocentrotus purpuratus}, volume={314}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.1133609}, DOI={10.1126/science.1133609}, number={5801}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Sodergren, Erica and Weinstock, George M. and Davidson, Eric H and Cameron, R. Andrew and Gibbs, Richard A. and Angerer, Robert C. and Angerer, Lynne M. and Arnone, Maria Ina and Burgess, David R. and Burke, Robert D. and Coffman, James A. and Dean, Michael and Elphick, Maurice R. and Ettensohn, Charles A. and Foltz, Kathy R. and Hamdoun, Amro and Hynes, Richard O. and Klein, William H. and Marzluff, William and McClay, David R. and Morris, Robert L. and Mushegian, Arcady and Rast, Jonathan P. and Smith, L. Courtney and Thorndyke, Michael C. and Vacquier, Victor D. and Wessel, Gary M. and Wray, Greg and Zhang, Lan and Elsik, Christine G. and Ermolaeva, Olga and Hlavina, Wratko and Hofmann, Gretchen and Kitts, Paul and Landrum, Melissa J. and Mackey, Aaron J. and Maglott, Donna and Panopoulou, Georgia and Poustka, Albert J. and Pruitt, Kim and Sapojnikov, Victor and Song, Xingzhi and Souvorov, Alexandre and Solovyev, Victor and Wei, Zheng and Whittaker, Charles A. and Worley, Kim and Durbin, K. James and Shen, Yufeng and Fedrigo, Olivier and Garfield, David and Haygood, Ralph and Primus, Alexander and Satija, Rahul and Severson, Tonya and Gonzalez-Garay, Manuel L. and Jackson, Andrew R. and Milosavljevic, Aleksandar and Tong, Mark and Killian, Christopher E. and Livingston, Brian T. and Wilt, Fred H. and Adams, Nikki and BelleÌ, Robert and Carbonneau, Seth and Cheung, Rocky and Cormier, Patrick and Cosson, Bertrand and Croce, Jenifer and Fernandez-Guerra, Antonio and GenevieÌre, Anne-Marie and Goel, Manisha and Kelkar, Hemant and Morales, Julia and Mulner-Lorillon, Odile and Robertson, Anthony J. and Goldstone, Jared V. and Cole, Bryan and Epel, David and Gold, Bert and Hahn, Mark E. and Howard-Ashby, Meredith and Scally, Mark and Stegeman, John J. and Allgood, Erin L. and Cool, Jonah and Judkins, Kyle M. and McCafferty, Shawn S. and Musante, Ashlan M. and Obar, Robert A. and Rawson, Amanda P. and Rossetti, Blair J. and Gibbons, Ian R. and Hoffman, Matthew P. and Leone, Andrew and Istrail, Sorin and Materna, Stefan C. and Samanta, Manoj P. and Stolc, Viktor and Tongprasit, Waraporn and Tu, Qiang and Bergeron, Karl-Frederik and Brandhorst, Bruce P. and Whittle, James and Berney, Kevin and Bottjer, David J. and Calestani, Cristina and Peterson, Kevin and Chow, Elly and Yuan, Qiu Autumn and Elhaik, Eran and Graur, Dan and Reese, Justin T. and Bosdet, Ian and Heesun, Shin and Marra, Marco A. and Schein, Jacqueline and Anderson, Michele K. and Brockton, Virginia and Buckley, Katherine M. and Cohen, Avis H. and Fugmann, Sebastian D. and Hibino, Taku and Loza-Coll, Mariano and Majeske, Audrey J. and Messier, Cynthia and Nair, Sham V. and Pancer, Zeev and Terwilliger, David P. and Agca, Cavit and Arboleda, Enrique and Chen, Nansheng and Churcher, Allison M. and HallboÌoÌk, F. and Humphrey, Glen W. and Idris, Mohammed M. and Kiyama, Takae and Liang, Shuguang and Mellott, Dan and Mu, Xiuqian and Murray, Greg and Olinski, Robert P. and Raible, Florian and Rowe, Matthew and Taylor, John S. and Tessmar-Raible, Kristin and Wang, D. and Wilson, Karen H. and Yaguchi, Shunsuke and Gaasterland, Terry and Galindo, Blanca E. and Gunaratne, Herath J. and Juliano, Celina and Kinukawa, Masashi and Moy, Gary W. and Neill, Anna T. and Nomura, Mamoru and Raisch, Michael and Reade, Anna and Roux, Michelle M. and Song, Jia L. and Su, Yi-Hsien and Townley, Ian K. and Voronina, Ekaterina and Wong, Julian L. and Amore, Gabriele and Branno, Margherita and Brown, Euan R. and Cavalieri, Vincenzo and Duboc, VeÌronique and Duloquin, Louise and Flytzanis, Constantin and Gache, Christian and Lapraz, François and Lepage, Thierry and Locascio, Annamaria and Martinez, Pedro and Matassi, Giorgio and Matranga, Valeria and Range, Ryan and Rizzo, Francesca and RoÌttinger, Eric and Beane, Wendy and Bradham, Cynthia and Byrum, Christine and Glenn, Tom and Hussain, Sofia and Manning, Gerard and Miranda, Esther and Thomason, Rebecca and Walton, Katherine and Wikramanayke, Athula and Wu, Shu-Yu and Xu, Ronghui 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 Muzny, Donna and Bell, Stephanie and Chacko, Joseph and Cree, Andrew and Curry, Stacey and Davis, Clay and Dinh, Huyen and Dugan-Rocha, Shannon and Fowler, Jerry and Gill, Rachel and Hamilton, Cerrissa and Hernandez, Judith and Hines, Sandra and Hume, Jennifer and Jackson, LaRonda and Jolivet, Angela and Kovar, Christie and Lee, Sandra and Lewis, Lora and Miner, George and Morgan, Margaret and Nazareth, Lynne V. and Okwuonu, Geoffrey and Parker, David and Pu, Ling-Ling and Thorn, Rachel and Wright, Rita}, year={2006}, month=nov, pages={941–952} }