- Click on any colour tile in the legend to toggle visibility of that feature on/off
- The radius of the central plot represents the length of the longest scaffold in the assembly
- The angle subtended by the first (red) segment within this plot indicates the percentage of the assembly that is in the longest scaffold
- The radial axis originates at the circumference and indicates scaffold length, this is on a square-root scale
- Subsequent (grey) segments are plotted from the circumference and the length of segment at a given percentage indicates the cumulative percentage of the assembly that is contained within scaffolds of at least that length
- The N50 and N90 scaffold lengths are indicated respectively by dark and light orange arcs that connect to the radial axis for ease of comparison
- The cumulative number of scaffolds within a given percentage of the genome is plotted in purple originating at the centre of the plot
- White scale lines are drawn at successive orders of magnitude from 10 scaffolds onwards
- The fill colour of the circumferential axis indicates the percentage base composition of the assembly: AT = light blue; GC = dark blue; N = grey
- Contig length (off by default) is indicated by darker grey segments overlaying the scaffold length plot
- Contig count (off by default) may be toggled on to be shown in place of the scaffold count plot
- Partial and complete BUSCO values are shown in light and dark green, respectively in the smaller plot in the upper right corner
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.
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).