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. Currently, the echinoderms Strongylocentrotus franciscanus and Allocentrotus fragilis (fragile urchin) 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 an important evolutionary position with respect to vertebrates and humans: they, along with their sister phylum hemichordates, are the closest known relatives to chordates.

The S. purpuratus genome was analyzed and published in 2006 in Science [PubMed] and Developmental Biology [PubMed]. A series of assemblies were produced:

Assembly	Description
Spur_0.3	preliminary assembly of Whole Genome Shotgun (WGS) sequence (Spur20041123)
Spur_0.4	preliminary assembly of WGS sequence (Spur20050323)
Spur_v0.5	[NCBI build 1.1] - assembly of WGS sequence (Spur20050415) used for initial annotation and analysis of the genome
Spur_v2.0	interim assembly of BAC plus WGS sequence
Spur_v2.1	[NCBI build 2.1] - assembly of BAC plus WGS sequence

The Spur_v0.5 assembly covers 84-97% (EST representation) of the ~800Mbase genome while including a 13% redundancy level. The Spur_v2.1 assembly covers 90-94% of the genome with 5% redundancy. All the above assemblies are available for download using the FTP Data link in the sidebar to the right. Genome browsers for this data are listed in the resource section below.

The sea urchin was sequenced using the Clone-Array Pooled Shotgun Sequencing (CAPSS) method where shotgun libraries are made from row and column pools of arrayed BACs from an FPC generated tiling path (BC Genome Sciences Center). The deconvoluted individual BAC sequences as well as assemblies enriched with WGS sequences from the BAC region are available in GenBank.

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

Access to the Data

Genome Assembly

The genome assembly, Spur_2.1 is available for download as linearized scaffolds and as individual contigs files. The scaffolds are not placed on chromosomes. The assembly is described in more detail in the README file.

Genome Browser

The genome assembly, Spur 2.1 and annotated features including gene predictions and curated gene models are available for browsing and download via the Genboree Sea Urchin site by using the link in the sidebar. The annotation database can also be queried directly.

BLAST Searches

A BLAST search of the Sea Urchin preliminary assembly is now available by using the link in the sidebar. Contig sequences are now available from the BLAST output and the FTP site, as of November 23, 2004.

Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query.

BAC-based Data Resources

Individual BAC assemblies are available in GenBank as enriched BAC assemblies.

Other Resources

Sea urchin whitepaper

Sea Urchin Genome Project at California Institute of Technology

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

Conditions for use

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]