Strongylocentrotus purpuratus

About S.purpuratus

That sea urchins eggs and embryos have long remained a popular research subject for cell and developmental biologists is one rationale for sequencing the genome. In addition, studies of embryonic development in the California Purple Sea Urchin, Strongylocentrotus purpuratus , have paralleled the emergence of molecular techniques ranging from the characterization of genomic repeat sequences in the 1970's to the elucidation of gene regulatory networks in recent times.

navigationThe parent of this site, SUGP, provided a focal point for the exchange of genomic information as the genome of the purple sea urchin was being sequenced. Over these past years it has served as a repository for small sequencing projects and a source of sequence information useful for gene discovery projects. Here one could find information on macro-array libraries of cDNAs from the purple sea urchin and genomic DNA from several species. In addition, a Sequence Tag Connector (STC) collection has been assembled from 5% of the genome sequence and a very extensive repeat sequence catalog prepared. All of the sequence data that we maintained at SUGP was incorporated into the new web site while preserving the extensive primary annotations made in conjunction with the primary sequencing of the purple sea urchin (Strongylocentrotus purpuratus) genome. Of course, these data are also available in public sequence databases such as the National Center for Biological Information. Some additional sequence information is available at the Resource Center of the German Human Genome Project.The current release of the purple sea urchin genome assembly (Spur3.1) is fourth in the series showing substantial improvements at each step.

Sequence and Scaffold statistics

Assembly Type Number N50(kb) Bases+Gaps(Mb) Bases(Mb)
Spur_v3.1 Scaffolds 32,008 401.6 936 816
Spur_v3.1 Contigs 174,772 13.4 816 816

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.