The genome of the sea urchin Strongylocentrotus purpuratus - PubMed (original) (raw)

. 2006 Nov 10;314(5801):941-52.

doi: 10.1126/science.1133609.

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, Rita Wright

The genome of the sea urchin Strongylocentrotus purpuratus

Sea Urchin Genome Sequencing Consortium et al. Science. 2006.

Erratum in

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.

PubMed Disclaimer

Figures

Fig. 1

Fig. 1

The phylogenetic position of the sea urchin relative to other model systems and humans. The chordates are shown on the darker blue background overlapping the deuterostomes as a whole on a lighter blue background. Organisms for which genome projects have been initiated or finished are shown across the top.

Fig. 2

Fig. 2

Orthologs among the Bilateria. The number of 1:1 orthologs captured by BLAST alignments at a match value of e = 1 × 10−6 in comparisons of sequenced genomes among the Bilateria. The number of orthologs is indicated in the boxes along the arrows, and the total number of International Protein Index database sequences is shown under the species symbol. Hs, Homo sapiens; Mm, Mus musculus; Ci, Ciona intestinalis; Sp, S. purpuratus; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans.

Fig. 3

Fig. 3

Protein kinase evolution: Invention and loss of protein kinase subfamilies in metazoan lineages. Deuterostomes share 9 protein kinase subfamilies absent from C. elegans and Drosophila, and the sea urchin has not lost any of the 158 metazoan primordial kinase classes, unlike insects or nematodes. [From (23)]

Fig. 4

Fig. 4

Partial phylogenies of the Rho (A) and the Rab families (B)ofsmallGTPases. The pink boxes highlight gene-specific duplications that increased sea urchin GTPase numbers, resulting in a complexity comparable to vertebrates. Numbers at each junction represent confidence values obtained via three independent phylogenetic methods [neighbor-joining (green), maximum parsimony (blue), and Bayesian (black)]; red stars indicate nodes retained by maximum likelihood. [From (28)]

Fig. 5

Fig. 5

Survey of the Wnt family of secreted signaling molecules in selected metazoans. Each square indicates a single Wnt gene identified either through genome analyses or independent studies, and squares with a question mark indicate uncertainty of the orthology. Letter X’s represent absence of members of that subfamily in the corresponding annotated genome; empty spaces have been left for species for which genomic databases are not yet available. [From (30)]

Fig. 6

Fig. 6

Presence of Wnt signaling machinery components (A) and target genes (B) in the S. purpuratus genome. (A) The 126 genes involved in the transduction of the Wnt signals have been separated into four categories from the extracellular compartment to the nucleus. Sea urchin homologs are identified by the lighter shade (indicated by both the number and the percentage of homologs that were identified within the chart); the total number of known genes is indicated in the chart legend. (B) The 93 reported Wnt targets have been divided into three categories: signaling molecules, transcription factors, and cell adhesion molecules. Colors and numbers are as in (A).

Fig. 7

Fig. 7

Gene families encoding important innate immune receptors and complement factors in animals with sequenced genomes. For some key receptor classes, gene numbers in the sea urchin exceeds other animals by more than an order of magnitude. Representative animals include H.s., Homo sapiens; C.i., Ciona intestinalis; S.p. Strongylocentrotus purpuratus; D.m. Drosophila melanogaster; and C.e. Caenorhabditis elegans. Indicated gene families include TLR, toll-like receptors; NLR, NACHT and leucine-rich repeat (LRR) domain–containing proteins similar to the vertebrate Nod/NALP genes; SRCR, Scavenger receptor cysteine-rich domain genes; PGRP, peptidoglycan recognition protein domain genes; and GNBP, Gram-negative binding proteins. C3/4/5, thioester proteins homologous to vertebrate C3, C4, and C5; Bf/C2, complement factors homologous to vertebrate C2 and factor B; C1q/MBP, homologs of vertebrate lectin pathway receptors; and Terminal pathway, homologs of vertebrate C6, C7, C8, and C9. SRCR gene statistics are given as domain number/gene number for multiple SRCR-containing proteins (numbers for C. intestinalis includes all SRCR proteins). Asterisk in the D. melanogaster C3/4/5 column is meant to denote the presence of related thioester genes (TEPs) and a true C3/4/5 homolog from another arthropod. +/− for C. intestinalis Terminal pathway column indicates the presence of genes with similarity to C6 only (Nonaka and Yoshizaki 2004). Phylogenetic relations among species are indicated by a cladogram at the left.

Similar articles

Cited by

References

    1. Gibbs RA, et al. Nature. 2004;428:493. - PubMed
    1. Cai WW, Chen R, Gibbs RA, Bradley A. Genome Res. 2001;11:1619. - PubMed
    1. Britten RJ, Cetta A, Davidson EH. Cell. 1978;15:1175. - PubMed
    1. Dehal P, et al. Science. 2002;298:2157. - PubMed
    1. Vinson JP, et al. Genome Res. 2005;15:1127. - PMC - PubMed

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources