About the project

The HGSC is sequencing the genome of the California Purple Sea Urchin (Strongylocentrotus purpuratus) and portions of the genome of the Green Sea Urchin (Lytechinus variegatus) for comparative analysis. The version Spur_2.1 assembly was released in September, 2006 and published in November, 2006 [1].

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.

The sea urchin has been an important model system for many years in the study of basic biology, particularly in developmental biology. The sea urchin occupies an important evolutionary position with respect to vertebrates and humans. There is a large body of information about gene expression in the sea urchin and there are a number of genomic resources available, making the sea urchin an ideal organism for learning how pathways of genes and proteins regulate growth and development, with potentially profound implications for understanding human biology.

The Sea Urchin was sequenced using the Clone-Array Pooled Shotgun Sequencing (CAPSS)[2][3] where shotgun libraries are made from row and column pools of arrayed BACs. The sequence data are assembled by iterative comparison of row and column data. CAPSS reduces the number of sequencing libraries, increases the genome coverage provided by BACs and reduces the need for BAC fingerprinting and mapping.

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 Genboree. The annotation database can also be queried directly.

BLAST searches

The HGSC provides BLAST searches of the current assembly (listed below) as well as previous assemblies.

• Assembled scaffolds, either as a full set or as multiple-contig scaffolds and single-contig scaffolds
• Assembled contigs
• Unplaced contigs
• Unassembled reads
• Gene predictions as protein or DNA sequences

Traces are available from the NCBI Trace Archive, which can be searched 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.

Use the BAC Fisher to find Whole Genome Shotgun reads that overlap sequencing reads from a clone. This program finds similar sequences where the matches extend to the end of the query sequences. BAC-Fisher is tuned to reject repeat matches without masking repeats in the query.

Other Resources

Sea urchin whitepaper

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

Conditions for use

Citations

[1] The Sea Urchin Genome Sequencing Consortium. The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science, November 10, 2006.

[2] 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.

[3] Erica Sodergren, Yufeng Shen, Yingzhi Song, Lan Zhang, Richard A. Gibbs, and George Weinstock. Shedding genomic light on Aristotle's lantern. Dev Biol YDBIO-02882, in press, 2006

Sea urchin companion publications are found in Science, November 10, 2006, and Developmental Biology