The Genome of the Sea Urchin Strongylocentrotus purpuratus

Abstract

Comparative analysis of the sea urchin genome has broad implications for the primitive state of deuterostome host defense and the genetic underpinnings of immunity in vertebrates. The sea urchin has an unprecedented complexity of innate immune recognition receptors relative to other animal species yet characterized. These receptor genes include a vast repertoire of 222 Toll-like receptors, a superfamily of more than 200 NACHT domain-leucine-rich repeat proteins (similar to nucleotide-binding and oligomerization domain (NOD) and NALP proteins of vertebrates), and a large family of scavenger receptor cysteine-rich proteins. More typical numbers of genes encode other immune recognition factors. Homologs of important immune and hematopoietic regulators, many of which have previously been identified only from chordates, as well as genes that are critical in adaptive immunity of jawed vertebrates, also are present. The findings serve to underscore the dynamic utilization of receptors and the complexity of immune recognition that may be basal for deuterostomes and predicts features of the ancestral bilaterian form.

The oyster genome reveals stress adaptation and complexity of shell formation

“…This 44% reduction in polymorphism in the inbred genome is smaller than the 59.4% predicted from four generations of brother-sister mating, indicating that selection favouring heterozygotes had occurred 19 . The polymorphism combining inbred and wild (among four haplotypes) was 2.3%, higher than that in most studied animal genomes 20,21 but comparable to that in known high-polymorphism species 7 . In inbred and wild, we found 3,094 short indels located in coding regions inferred to cause frameshift variants in 2,665 genes, providing an important source for recessive lethal mutations.…”

“…One of the main challenges, however, is the high levels of polymorphism present in oysters and many marine invertebrates [6][7][8] . To overcome this, an oyster derived from four generations of full-sibling mating (coefficient of inbreeding, F 5 0.59) was used for genome sequencing and assembly (Supplementary Text B1) through fosmid pooling, next-generation sequencing (NGS) and hierarchical assembling.…”

Living with death: the evolution of the mitochondrial pathway of apoptosis in animals

“…The genome of an echinoderm, the purple sea urchin Strongylocentrotus purpuratus, has recently been sequenced 58 and homologs of the components of the vertebrate apoptotic pathways have been identified. 59 The S. purpuratus genome contains five classes of caspases, including both apical and executioner caspases.…”

Origins of the other metazoan body plans: the evolution of larval forms

“…Most genome sequencing has concentrated on model or medically significant vertebrates, arthropods and nematodes. A sea urchin genome has now been sequenced (Sodergren et al 2006), but the genomes of lophotrochozoans, especially marine annelids and molluscs with planktotrophic larvae, are still needed.…”