About the Project

The genome of the California Purple Sea Urchin (Strongylocentrotus purpuratus) has been sequenced and annotated by the Sea Urchin Genome Sequencing Consortium led by the HGSC.

More recently, this genome has been improved and other echinoderms are being sequenced for comparative analysis.

The sea urchin has been an important model system for studying modern molecular, evolutionary and cell biology particularly in the realm of developmental biology. Echinoderms occupy a key evolutionary position with respect to vertebrates and humans: they, along with their sister phylum hemichordates, are the closest known relatives to chordates.

This project is funded by the National Human Genome Research Institute (NHGRI), National Institutes of Health. The white papers describing this project were developed by Eric Davidson and Andrew Cameron at California Institute of Technology in collaboration with the sea urchin genome advisory group and the HGSC (1, 2).

Access to the Data

Reference Genome Assembly

The S. purpuratus reference genome is available from the links below. The published Sanger version is Spur_2.6. The improved Sanger + Illumina version is Spur_3.1.

The annotations for the Spur 2.1 version including gene predictions and curated gene models are available for browsing and download via the Genboree Sea Urchin site. The annotation database can also be queried directly.

Comparative Echinoderms

The echinoderms that are included in this project are listed in the table below and shown in this figure. Links in the table provide access to the data. S. franciscanus and A. fragilis are sequenced at low coverage.

Species454 + IlluminaRNAseqAssembled TranscriptsLast Common Ancestor to
S. Purpuratus
S.franciscanusSRA20 MYA
A.fragilisSRA20 MYA
L.variegatesFTP dataSRA31,357
After gastrulation
Before gastrulation
50 MYA
E.tribuloidesIn ProgressSRA39,802
Embryo
Oocyte
255 MYA
P.miniataIn ProgressSRA58,528
After gastrulation
Before gastrulation
500 MYA

BLAST Searches

BLAST searches of the Sea Urchin sequence data, including transcript and genome assemblies, are available by using the links in the sidebar.

BAC-based Data Resources

The S. purpuratus genome was sequenced using pools of arrayed BACs from the FPC generated tiling path (BC Genome Sciences Center). The deconvoluted individual BAC sequences as well as assemblies enriched with WGS sequences from the BACs region are available in GenBank.

Other Resources

Conditions for use

For information on related large-scale sequencing projects see the International Genome Consortium Database

Sea Urchin white paper

Additional Echinoderms white paper

SpBase: The Sea Urchin Genome Database

Selected sea urchin companion publications are found in Science, November 10, 2006, and Developmental Biology, December 1, 2006.

Selected PubMed Citations

Sodergren, E, Shen, Y, Song, X, Zhang, L, Gibbs, RA, Weinstock, GM. Shedding genomic light on Aristotle's lantern.  Dev. Biol.  2006 Dec 1; 300(1):2-8. [PubMed]

Sea Urchin Genome Sequencing Consortium, Sodergren, E, Weinstock, GM, Davidson, EH, Cameron, RA, Gibbs, RA, Angerer, RC, Angerer, LM, Arnone, MI et al. The genome of the sea urchin Strongylocentrotus purpuratus.  Science  2006 Nov 10; 314(5801):941-52. [PubMed]

Cai, WW, Chen, R, Gibbs, RA, Bradley, A. A clone-array pooled shotgun strategy for sequencing large genomes.  Genome Res.  2001 Oct; 11(10):1619-23. [PubMed]

Sea Urchin


Featured Publications

Sea Urchin Genome Sequencing Consortium, Sodergren, E, Weinstock, GM, Davidson, EH, Cameron, RA, Gibbs, RA, Angerer, RC, Angerer, LM, Arnone, MI et al. The genome of the sea urchin Strongylocentrotus purpuratus.  Science  2006 Nov 10; 314(5801):941-52. [PubMed]


Sea Urchin Genome Project