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].

More recently the S. purpuratus genome assembly was improved and several echinoderms were sequenced for comparative analysis including Strongylcentrotus franciscanus, Allocentrotus fragilis, Patiria miniata, Lytechinus variegatus, Ophiothrix spiculata, Parastichopus parvimensis, and Eucidaris tribuloides. A recent review describes these assemblies.1

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, “primitive” sea urchin (E. tribuloides), the sea star (O. spiculata), the sea cucumber (P. parvimensis) and the hemichordate outgroup, the acorn worm (Saccoglossus kowalevskii).

Assembly Description
Spur_v2.1 [NCBI build 2.1] - assembly of BAC plus WGS sequence
Spur_v2.6 improved with addition of SOLiD WGS sequence
Spur_v3.1 improved with addition of Illumina WGS sequence
Spur_v4.2 improved with addition of Pacific Biosciences WGS sequence

 

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.

The preliminary genome assembly, as well as published version Spur_v2.1 [NCBI build 2.1], and the later versions with additional improvements, are available from NCBI.

Species
 
Distance to S. purpuratus cDNA Genome Assembly
Strongylocentrotus purpuratus
 
   
Strongylocentrotus fransciscanus
 
20 mya    
Allocentrotus fragilis 20 mya   Planned comparative Illumina for indels
Lytechinus variegatus 50 mya
 
Lvar_0.4
Lvar_2.2
Eucidaris tribuloides 250 mya   Etri_1.0
Parastichopus parvimensis
 
500 mya   Ppar_1.0
Patiria miniata
 
500 mya Pmin_1.0
Ophiothrix spiculata 500 mya   Ospi.un_1.0
Saccoglossus kowalevskii Hemichordate
 
  Skow_1.1

 

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.

Funding

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.

Genomic Resources

Genome Assembly

The genome assemblies are available for download from NCBI. 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

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

Reference

1Cameron RA, Kudtarkar P, Gordon SM, Worley KC, Gibbs RA. Do echinoderm genomes measure up? Mar Genomics. 2015 Aug;22:1-9

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