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.
| Species | 454 + Illumina | RNAseq | Assembled Transcripts | Last Common Ancestor to
S. Purpuratus |
|---|---|---|---|---|
| S.franciscanus | SRA | 20 MYA | ||
| A.fragilis | SRA | 20 MYA | ||
| L.variegates | FTP data | SRA | 31,357
After gastrulation Before gastrulation | 50 MYA |
| E.tribuloides | In Progress | SRA | 39,802
Embryo Oocyte | 255 MYA |
| P.miniata | In Progress | SRA | 58,528
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
For information on related large-scale sequencing projects see the International Genome Consortium Database
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]
