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Echinobase

Strongylocentrotus purpuratus

S. purpuratus




About S.purpuratus

Sea urchin embryo and larval development serves as a model due to the abundance of externally fertilized, transparent embryos and their evolutionary relationship to vertebrates. These features have allowed for the elucidation of gene regulatory networks and make genomic studies feasible.

The new Echinobase is a resource for the research community and incorporates information from EchinoBase (legacy.echinobase.org) and the Sea Urchin Genome Project.

The development of sea urchins has been studied for over 100 years. The fertilized eggs develop rapidly to form larvae and cell fate and lineage tracing experiments detail the development.

Skeletogenesis in S. purpuratus is well documented and an area of active research.

Echinobase also has an extensive collection of resources including reagents and protocols, literature, and contacts to facilitate research.

Genome assembly statistics for S. purpuratus are shown below.


General Information

Egg Size: Strongylocentrotus purpuratus (Sp) = 80 micrometers

Ash-free dry organic weight: 70 ng

DNA: Diploid genomic DNA content is 1.78 pg measured from sperm.

RNA: Total RNA = 2.8 ng per embryo. 
1.5% is polyA-RNA, 65% of polyA-RNA is nontranslated interspersed maternal transcript and mRNa is about 50% polyA-containing, therefore about 30 pg of mRNA per egg. 
About 30% of mRNA greater than 1400 nt is capped. Half-life of the newly synthesized zygotic transcripts is 5.7 hr (but Cabrera gets 2-2.2 hr).
 Steady state content of newly synthesized mRNA is 64 pg and maternal is replaced with zygotic by the blastula-gastrula stage. 
 Mammalian ribosomal RNA has a length of 4718 bp for 28S and 1874 for 18S. 

Protein: The total protein in the sea urchin egg is about 40-65 ng. 
The egg has 6.6X108 ribosomes.
An approximate rate of synthesis is one protein molecule per minute per mRNA template. 
During cleavage the rate of protein synthesis rises to about 400 picograms protein per hour per embryo. 
At mid-development the absolute rate is within the range of 650-250 pg per hour. 
About 0.8% per hour of the newly synthesized protein is lost by turnover during development (since the decay equals the synthesis there is little change in total protein).

Assemblies

Current Assembly: v5.0
Assembly name: Spur_5.0 | Date: 2019-09-06 | Genome coverage: 123.0x | Assembly method: Canu v. 1.8 | BioSample: SAMN00829422 | BioProject: PRJNA10736 | Sequencing technology: PacBio Sequel

Assembly: v4.2
Assembly name: Spur_4.2 | Date: 2015-3-10 | Genome coverage: 8.3x Sanger; 18x SOLiD; 40x Illumina; 8.6x PacBio | Assembly method: Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement; PBJelly2 v. 14.9.9 | BioSample: SAMN00829422 | BioProject: PRJNA10736 | Sequencing technology: Sanger; SOLiD; Illumina; PacBio RS

Assembly: v3.1
Assembly name: Spur_3.1 | Date: 2011-6-10 | Genome coverage: 8.3x Sanger; 18x SOLiD; 40x Illumina | Assembly method: Atlas v. WGS for Sanger Assembly, Atlas-Link and Atlas-GapFill for SOLiD and Illumina improvement | BioSample: SAMN00829422 | BioProject: PRJNA13728 | Sequencing technology: Sanger; SOLiD; Illumina