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Sea Urchin Genome Project

About the Project

image: purple sea urchin
Image source: Wikimedia Commons

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 draft quality genome for the California Purple Sea Urchin (Strongylocentrotus purpuratus) has been sequenced and annotated by the Sea Urchin Genome Sequencing Consortium led by the HGSC (published in Science [PubMed] and Developmental Biology [PubMed].

Currently, several echinoderms are being sequenced for comparative analysis including Strongylcentrotus franciscanus, Allocentrotus fragilis, Patiria miniata, Lytechinus variegates, P. flava, A. punctulata.

This series of evolutionary distances within one clade is not available elsewhere. The comparisons will highlight the cis-regulatory networks and their evolution in these well studied developmental models.

The green urchin (L. variegates) is of an appropriate distance such that putative exons and cis-regulatory sequence regions are identifiable by sequence conservation while most sequence is too divergent to align to S. purpuratus. The goal is to define the genome sequence so that the intergenic sequence on either side of a gene of interest is included in the contig with the gene itself.

The sea star (P. miniata) is more distant to S. purpuratus and will provide evidence for assessing the difference between flexible and inflexible gene regulatory networks in evolution.  Other related species included in this project are the “modern” sea urchin (A. punctulata), “primitive” sea urchin (E. tribuloides), the sea star (D. imbricata), and the hemichordate (P. flava).

A. punctulata is the most distantly related euechinoid to S. purpuratus in frequent use as an experimental laboratory organism.  D. imbricata would be useful to identify cis-regulatory sequences in P. miniata (similar to the S. purpuratus – L. variegates comparision). 

Assembly Description
Spur_v0.3 preliminary assembly of Whole Genome Shotgun (WGS) sequence (Spur20041123)
Spur_v0.4 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.


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 BCM-HGSC.

S. purpuratus

The S. purpuratus 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.

Preliminary genome assemblies, as well as published version Spur_v2.1 [NCBI build 2.1], and the later version Spur_v2.6 with additional scaffolding, are available from the NCBI and the HGSC ftp site.

Distance to S. purpuratus cDNA Genome Assembly
Strongylocentrotus purpuratus
    Spur_v2.1 - WGS + BAC draft assembly Spur_v2.5 – with SOLiD scaffolding data
Planned improvement
Strongylocentrotus fransciscanus
20 mya    
Allocentrotus fragilis     Planned comparative Illumina for indels
Lytechinus variegates 50 mya
  Planned assembly
Arbacia punctulata
160 mya    
Eucidaris tribuloides 250 mya   Planned comparative Illumina for indels
Pateria miniata
500 mya    
Dermasterias inbricata Near P. miniata    
Ptychodera flava Hemichordate

Sequence reads are available in the NCBI Trace and Sequence Read archives.  Species names in the table are linked to the NCBI Taxonomy pages where there are links to the read data

and assembled genome and transcript sequences when available.

Genomic Resources

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.

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.


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.

Additional Resources

Learn more about the purple sea urchin

Related Publications

Analysis of prostate-specific antigen transcripts in chimpanzees, cynomolgus monkeys, baboons, and african green monkeys., Mubiru, James N., Yang Alice S., Olsen Christian, Nayak Sudhir, Livi Carolina B., Dick Edward J., Owston Michael, Garcia-Forey Magdalena, Shade Robert E., and Rogers Jeffrey , PloS one, 2014, Volume 9, Issue 4, p.e94522, (2014) Abstract
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis., Tu, Qiang, Cameron Andrew R., Worley Kim C., Gibbs Richard A., and Davidson Eric H. , Genome research, 2012 Oct, Volume 22, Issue 10, p.2079-87, (2012) Abstract
Bos taurus genome assembly., Liu, Yue, Qin Xiang, Song Xing-Zhi Henry, Jiang Huaiyang, Shen Yufeng, Durbin James K., Lien Sigbjørn, Kent Matthew Peter, Sodeland Marte, Ren Yanru, et al. , BMC genomics, 2009, Volume 10, p.180, (2009) Abstract
Shedding genomic light on Aristotle's lantern., Sodergren, Erica, Shen Yufeng, Song Xingzhi, Zhang Lan, Gibbs Richard A., and Weinstock George M. , Developmental biology, 2006 Dec 1, Volume 300, Issue 1, p.2-8, (2006) Abstract
The genome of the sea urchin Strongylocentrotus purpuratus., Sodergren, Erica, Weinstock George M., Davidson Eric H., Cameron Andrew R., Gibbs Richard A., Angerer Robert C., Angerer Lynne M., Arnone Maria Ina, Burgess David R., Burke Robert D., et al. , Science (New York, N.Y.), 2006 Nov 10, Volume 314, Issue 5801, p.941-52, (2006) Abstract
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