Nutritive phagocyte incubation chambers provide a structural and nutritive microenvironment for germ cells of Strongylocentrotus droebachiensis, the green sea urchin

Hemal sinus basal laminae contact sites: a possible route between gonadal lumen and myoepithelial cells in the gonad of the sea star Patiria pectinifera

Sea stars are a group of marine invertebrates suitable for studying the hormonal regulation of reproduction and spawning. In spite of substantial progress in understanding how various substances such as 1-methyladenine act in their gonads, there are still many gaps concerning the fine details of their action. One such gap is how the gonadal wall contraction is induced. Recent literature data suggest that, upon 1-methyladenine stimulation, some cells within the gonadal lumen produce non-neuronal acetylcholine that, upon contact with the gonadal wall, induces contraction of myoepithelial cells. Our ultrastructural study of the gonads in the sea star Patiria pectinifera has shown, for the first time, that there are sites where the basal laminae bordering the hemal sinus directly contact one another and appear at this contact site as a single entity. These contact sites are often associated with hemidesmosome-like junctions that anchor male accessory cells or female follicle cells on one side of the site and myoepithelial cells on the opposite. We suggest that contraction-inducing substance is secreted from an accessory or follicle cell, passes through a basal lamina contact site, and on the opposite side of the contact site acts on a myoepithelial cell to induce its contraction.

De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq

Simple Summary

Edible red sea urchin (Loxechinus albus) is an endemic species of echinoderm distributed along the Chilean coasts. This resource has been overexploited in recent years, depleting their natural populations. At present, there are few reported gene sequences available in public databases, restricting the molecular studies associated with aquaculture for this species. The aim of this study was to present the first annotated reference transcriptome of L. albus using NGS technologies and the differential expression transcripts analysis of the evaluated tissues. The transcriptome data obtained in this study will serve as a reference for future molecular research in the edible red sea urchin and other sea urchin species.

Abstract

Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.

Quality of a fished resource: Assessing spatial and temporal dynamics

Understanding spatio-temporal variability in the demography of harvested species is essential to improve sustainability, especially if there is large geographic variation in demography. Reproductive patterns commonly vary spatially, which is particularly important for management of “roe”-based fisheries, since profits depend on both the number and reproductive condition of individuals. The red sea urchin, Mesocentrotus franciscanus, is harvested in California for its roe (gonad), which is sold to domestic and international sushi markets. The primary driver of price within this multi-million-dollar industry is gonad quality. A relatively simple measure of the fraction of the body mass that is gonad, the gonadosomatic index (GSI), provides important insight into the ecological and environmental factors associated with variability in reproductive quality, and hence value within the industry. We identified the seasonality of the reproductive cycle and determined whether it varied within a heavily fished region. We found that fishermen were predictable both temporally and spatially in collecting urchins according to the reproductive dynamics of urchins. We demonstrated the use of red sea urchin GSI as a simple, quantitative tool to predict quality, effort, landings, price, and value of the fishery. We found that current management is not effectively realizing some objectives for the southern California fishery, since the reproductive cycle does not match the cycle in northern California, where these management guidelines were originally shaped. Although regulations may not be meeting initial management goals, the scheme may in fact provide conservation benefits by curtailing effort during part of the high-quality fishing season right before spawning.

De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus

Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform. A total of 88,581 unigenes were acquired with a mean length of 1354bp, of which 66,331 (74.88%) unigenes could be annotated using six major publicly available databases. Comparative analysis revealed that 353 unigenes were differentially expressed (with log2(ratio)≥1, FDR≤0.001) between the two groups. Of these, 20 differentially expressed genes (DEGs) were selected to confirm the accuracy of RNA-seq data by quantitative real-time RT-PCR. Furthermore, gene ontology and KEGG pathway enrichment analyses were performed to find the putative genes and pathways related to ovarian maturity. Eight unigenes were identified as significant DEGs involved in reproduction related pathways; these included Mos, Cdc20, Rec8, YP30, cytochrome P450 2U1, ovoperoxidase, proteoliaisin, and rendezvin. Our research fills the gap in the studies on the S. nudus ovaries using transcriptome analysis.

Autophagy is required for sea urchin oogenesis and early development

Autophagy is a major intracellular pathway for the degradation and recycling of cytosolic components. Emerging evidence has demonstrated its crucial role during the embryo development of invertebrates and vertebrates. We recently demonstrated a massive activation of autophagy in Paracentrotus lividus embryos under cadmium stress conditions, and the existence of a temporal relationship between induced autophagy and apoptosis. Although there have been numerous studies on the role of autophagy in the development of different organisms, information on the autophagic process during oogenesis or at the start of development in marine invertebrates is very limited. Here we report our recent data on the occurrence of autophagy at these key phases of development. In order to investigate autophagy trends we performed in vivo assays to detect autophagolysomes, as well as in situ analysis with anti-LC3 antibody to detect autophagosomes before the fusion with lysosomes. From data generated through confocal laser scanning microscopy and quantification of autophagic signals we have drawn several unequivocal conclusions. The results showed a copious and rising number of autophagic organelles that had specific localization. Interestingly the increase in autophagy that occurred just after fertilization has been proved to be crucial for correct initiation of the developmental programme: irreversible developmental delays and morphologic anomalies were induced by short autophagic inhibition. This work focused on the sea urchin model system and corroborates evidence on the need for self-digestion during development, enriching the knowledge on autophagy, a biological mechanism belonging to evolutionarily different organisms.

Microautophagy in nutritive phagocytes of sea urchins

Two types of cells were observed in germinative epithelium of male and female sea urchins: germ cells and somatic accessory cells; the latter referred to as nutritive phagocytes. At the onset of gametogenesis, nutritive phagocytes accumulate nutrients and greatly increase in their size. As gametogenesis progresses, the accumulated nutrients are transferred from nutritive phagocytes into developing gametes, and size of the nutritive phagocytes decreases. An electron microscopic study of nutritive phagocytes in sea urchins, Strongylocentrotus intermedius, at different stages of annual reproductive cycle showed for the first time that both macro- and microautophagy take place in nutritive phagocytes. Both processes occur simultaneously and regulate size and composition of nutritive phagocytes in male and female sea urchins. Nutritive phagocytes consume redundant cytoplasm via macroautophagy. Microautophagy is probably involved in consumption of redundant membranes that appear within nutritive phagocytes due to destruction of nutrient-storing globules, macroautophagy, and phagocytosis of germ cells or their remnants.

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

The edible sea urchin Loxechinus albus (Molina, 1782) is a keystone species in the littoral benthic systems of the Pacific coast of South America. The international demand for high-quality gonads of this echinoderm has led to an extensive exploitation and decline of its natural populations. Consequently, a more thorough understanding of L. albus gonad development and gametogenesis could provide valuable resources for aquaculture applications, management, conservation and studies about the evolution of functional and structural pathways that underlie the reproductive toolkit of marine invertebrates. Using a high-throughput sequencing technology, we explored the male gonad transcriptome of this highly fecund sea urchin. Through a de novo assembly approach we obtained 42,530 transcripts of which 15,544 (36.6%) had significant alignments to known proteins in public databases. From these transcripts, approximately 73% were functionally annotated allowing the identification of several candidate genes that are likely to play a central role in developmental processes, nutrient reservoir activity, sexual reproduction, gamete generation, meiosis, sex differentiation, sperm motility, male courtship behavior and fertilization. Additionally, comparisons with the male gonad transcriptomes of other echinoderms revealed several conserved orthologous genes, suggesting that similar functional and structural pathways underlie the reproductive development in this group and other marine invertebrates.

Comprehensive histological and immunological studies reveal a novel glycoprotein hormone and thyrostimulin expressing proto-glycotrope in the sea lamprey pituitary

In the adenohypophysis (anterior pituitary) of all gnathostomes, there are six tropic cell types: corticotropes, melanotropes, somatotropes, lactotropes, gonadotropes and thyrotropes; each cell type produces specific tropic hormones. In contrast, we report in this study that there are only four tropic cell types in the sea lamprey (Petromyzon marinus) adenohypophysis. We specifically focused on the cell types that produce the glycoprotein hormones (GpHs). The gnathostome adenohypophyseal GpHs are follicle-stimulating hormone (FSH), luteinizing hormone (LH), thyroid-stimulating hormone (TSH), and thyrostimulin. However, lampreys only have two heterodimeric adenohypophyseal GpHs consisting of unique α and β subunits, lamprey GpH (lGpH) (lGpA2/lGpHβ) and thyrostimulin (lGpA2/lGpB5). We used an array of histological techniques to determine the (co)-localization and (co)-expression of the lGpH and thyrostimulin subunits in the lamprey adenohypophysis at different life stages (larval, parasitic, adult) and to identify their synthesizing cell(s). The thyrostimulin subunits (lGpA2/lGpB5) were co-expressed throughout the adenohypophysis (larval, parasitic, and adult), while the GpH β-subunit (lGpHβ) exhibited localized distribution (adult); all three subunits were co-localized and co-expressed, suggesting that both GpHs are synthesized in the same cells, novel proto-glycotropes, in specific adenohypophyseal regions at different life stages. In summary, we provide the first comprehensive study using histology, transmission electron microscopy, in situ hybridization and immunohistochemistry that strongly supports further evidence for four definitive adenohypophyseal cell types in the lamprey, including: corticotropes, somatotropes, melanotropes, and the first identification of a novel proto-glycotrope. In addition, our studies show that there is developmental and region-specific co-localization and co-expression of lGpH and thyrostimulin in the lamprey adenohypophysis.

Localization of germ plasm-related structures during sea urchin oogenesis

BACKGROUND

Animal germ cells have specific organelles that are similar to ribonucleoprotein complex, called germ plasm, which is accumulated in eggs. Germ plasm is essential for inherited mechanism of germ line segregation in early embryogenesis. Sea urchins have early germ line segregation in early embryogenesis. Nevertheless, organization of germ plasm-related organelles and their molecular composition are still unclear. Another issue is whether maternally accumulated germ plasm exists in the sea urchin eggs.

RESULTS

I analyzed intracellular localization of germ plasm during oogenesis in sea urchin Strongylocentrotus intermedius by using morphological approach and immunocytochemical detection of Vasa, a germ plasm marker. All ovarian germ cells have germ plasm-related organelles in the form of germ granules, Balbiani bodies, and perinuclear nuage found previously in germ cells in other animals. Maternal germ plasm is accumulated in late oogenesis at the cell periphery. Cytoskeletal drug treatment showed an association of Vasa-positive granules with actin filaments in the egg cortex.

CONCLUSIONS

All female germ cells of sea urchins have germ plasm-related organelles. Eggs have a maternally accumulated germ plasm associated with cortical cytoskeleton. These findings correlate with early segregation of germ line in sea urchins.

An ultrastructural study of testes permeability in sea urchins, Strongylocentrotus intermedius

Permeability of testes in sea urchins, Strongylocentrotus intermedius, was investigated by using an electron-opaque tracer, lanthanum nitrate. This tracer is able to enter the basal compartment of germinative epithelium, where developing germ cells are located. However, its ability to penetrate the gonadal lumen was reduced. An incomplete permeability barrier between the basal compartment and the gonadal lumen is supposed to exist in testes of S. intermedius.

Lipofuscin-like pigment in gonads of Sea Urchin Strongylocentrotus intermedius as a potential biomarker of marine pollution: a field study

Accumulation of lipofuscin-like pigments (LLPs) has been shown to be an appropriate index of both age and stress in some aquatic invertebrates. In the present study, LLP was quantified by measuring its autofluorescence intensity (ex 450 nm/em 512 nm) in nutritive phagocytes (NPs) of sea urchins Strongylocentrotus intermedius inhabiting polluted and relatively clean areas of Japan Sea. To avoid variations in LLP content related to sea urchin reproductive condition, only developing gonads with acini occupied mostly by NPs were used for LLP quantification as well as semiquantitative histopathological analysis. LLP concentrations ranged from 0.0 to 4.57 ± 0.53% area fraction in female gonads and from 0.0 to 4.61 ± 0.35% in male gonads. The presence of specimens with extremely high LLP concentrations (>1.5%) in all examined samples, including specimens from the reference station, as well as the absence of strong correlations between LLP concentrations and several parameters related to pollution (heavy-metal concentrations in sea urchin gonads and concentrations of heavy metals, DDT, hexachlorocyclohexane, and total petroleum hydrocarbons in sediments), allow us to conclude that LLP content in sea urchin NPs can not be used as a biomarker in marine pollution monitoring.

Sea urchin tube feet are photosensory organs that express a rhabdomeric-like opsin and PAX6

All echinoderms have unique hydraulic structures called tube feet, known for their roles in light sensitivity, respiration, chemoreception and locomotion. In the green sea urchin, the most distal portion of these tube feet contain five ossicles arranged as a light collector with its concave surface facing towards the ambient light. These ossicles are perforated and lined with pigment cells that express a PAX6 protein that is universally involved in the development of eyes and sensory organs in other bilaterians. Polymerase chain reaction (PCR)-based sequencing and real time quantitative PCR (qPCR) also demonstrate the presence and differential expression of a rhabdomeric-like opsin within these tube feet. Morphologically, nerves that could serve to transmit information to the test innervate the tube feet, and the differential expression of opsin transcripts in the tube feet is inversely, and significantly, related to the amount of light that tube feet are exposed to depending on their location on the test. The expression of these genes, the differential expression of opsin based on light exposure and the unique morphological features at the distal portion of the tube foot strongly support the hypothesis that in addition to previously identified functional roles of tube feet they are also photosensory organs that detect and respond to changes in the underwater light field.

An investigation of yolk-protein localization in the testes of the starfish Pisaster ochraceus

The distribution of the yolk epitope, PY4F8, was studied in the testes of the starfish Pisaster ochraceus (Brandt, 1835). Western blots have revealed that testes only show one 180 kDa band, whereas ovaries exhibit four PY4F8 bands at 90, 110, 120, and 180 kDa. This finding suggests that male yolk is less complex than female yolk. It was shown that PY4F8-positive material abounds in the hemal sinus of testes. Moreover, this epitope was found in the basal lamina, in the lumen of the testes, and in the cytoplasm of auxiliary and spermatogenic cells. It is likely that a hemal testis barrier is absent in P. ochraceus, and this lack allows direct penetration of nutrition to sustain metabolism of both spermatogenic and auxiliary cells. Morphologically, this penetration is possible through the gaps between adjacent auxiliary cell bases. Yolk granules containing the PY4F8 epitope are located in spermatogonia and spermatocytes, but not in spermatids and sperm. Therefore, yolk may play an important role in early spermatogenesis, but it does not participate at the final stage of sperm formation.

Methods for karyotyping and for localization of developmentally relevant genes on the chromosomes of the purple sea urchin, Strongylocentrotus purpuratus

The purple sea urchin, Strongylocentrotus purpuratus, is the only non-chordate deuterostome model with a fully sequenced genome. Chromosomal localization of individual genes and resulting gene maps are unavailable for this or for any sea urchin. As a result, the purple sea urchin genome has not been mapped onto specific chromosomes and remains inaccessible to genome-wide approaches addressing questions that require positional information for particular genes. Here we describe the first successful methods for karyotyping and localizing specific gene loci on chromosomes of Strongylocentrotus purpuratus and those of the phylogenetically related Strongylocentrotus droebachiensis. Both species have 42 chromosomes in their diploid genomes (n = 21). There are 2 large, 8 medium, and 10 small pairs, plus one putative sex pair. In both species, bindin genes were localized to 2 pair of homologous chromosomes by fluorescent in situ hybridization. Fluorescently labeled bacterial artificial chromosome clones generated from S. purpuratus for the functionally related genes brachyury, foxa, and foxb were localized to different chromosomes. Our protocols provide previously unavailable tools for developing a gene map for the purple sea urchin genome.

The major yolk protein is synthesized in the digestive tract and secreted into the body cavities in sea urchin larvae

Major yolk protein (MYP), a transferrin superfamily protein contained in yolk granules of sea urchin eggs, also occurs in the coelomic fluid of male and female adult sea urchins regardless of their reproductive cycle. MYP in the coelomic fluid (CFMYP; 180 kDa) has a zinc-binding capacity and has a higher molecular mass than MYP in eggs (EGMYP; 170 kDa). CFMYP is thought to be synthesized in the digestive tract and secreted into the coelomic fluid where it is involved in the transport of zinc derived from food. To clarify when and where MYP synthesis starts, we investigated the expression of MYP during larval development and growth in Pseudocentrotus depressus. MYP mRNA was detected using RT-PCR in the early 8-arm pluteus stage and its expression persisted until after metamorphosis. Real-time RT-PCR revealed that MYP mRNA increased exponentially from the early 8-arm stage to metamorphosis. Western blotting showed that maternal EGMYP disappeared by the 4-arm stage and that newly synthesized CFMYP was present at and after the mid 8-arm stage. In the late 8-arm larvae, MYP mRNA was detected in the digestive tract using in situ hybridization, and the protein was found in the somatocoel and the blastocoel-derived space between the somatocoel and epidermis using immunohistochemistry. These results suggest that CFMYP is synthesized in the digestive tract and secreted into the body cavities at and after the early 8-arm stage. We assume that in larvae, CFMYP transports zinc derived from food via the body cavities to various tissues, as suggested for adults.

FRAP analysis of secretory granule lipids and proteins in the sea urchin egg

Cortical granules of the sea urchin are secreted at fertilization in response to sperm fusion. Approximately 15,000 of these vesicles are tightly tethered to the cytoplasmic face of the egg plasma membrane prior to insemination such that the vesicle-plasma membrane complex may be isolated and manipulated in vitro. Furthermore, this complex remains fusion competent and can thus be used for in vitro biochemical studies of secretion on a per-vesicle or a population scale. We document approaches to study the dynamics of membrane lipids and proteins in these secretory vesicles. Their large size (1.3-microm diameter), vast number, and ease of manipulation enable several unique approaches to study general secretion mechanisms.

Exogonadal oogenesis in a temperate holothurian

Unusual structures were detected on the visceral peritoneum of the ovarian tubules in about 5%-10% of female sea cucumbers (Cucumaria frondosa) collected off Newfoundland, eastern Canada. The condition varied from mild to severe, with localized castration observed in the most heavily affected tubule sections. Investigation of the structures using histology, transmission electron microscopy (TEM), and gene analysis revealed that they were oocytes at different stages of development, growing singly or in groups of up to six. Their size and composition were consistent with those of oocytes found in the lumen of the ovaries, although "exogonadal" oocytes were devoid of a vitelline coat and presented few cortical granules. TEM sections suggest that the atypical oocytes emerged from the peritoneum and grew toward the coelomic cavity, and that they were not in direct contact with the basal lamina or the inner germinal layers. Similar masses have been observed in C. frondosa from the Gulf of St. Lawrence (Québec, Canada) and the Barents Sea (Russia), and in C. japonica from Russia and Psolus fabricii from Canada. The possibility that exogonadal oogenesis is attributable to anthropogenic disturbances should be investigated even though some of the affected specimens originate from presumably pristine locations.

Zinc-binding property of the major yolk protein in the sea urchin − implications of its role as a zinc transporter for gametogenesis

Major yolk protein (MYP), a transferrin superfamily protein that forms yolk granules in sea urchin eggs, is also contained in the coelomic fluid and nutritive phagocytes of the gonad in both sexes. MYP in the coelomic fluid (CFMYP; 180 kDa) has a higher molecular mass than MYP in eggs (EGMYP; 170 kDa). Here we show that MYP has a zinc-binding capacity that is diminished concomitantly with its incorporation from the coelomic fluid into the gonad in the sea urchin Pseudocentrotus depressus. Most of the zinc in the coelomic fluid was bound to CFMYP, whereas zinc in eggs was scarcely bound to EGMYP. Both CFMYP and EGMYP were present in nutritive phagocytes, where CFMYP bound more zinc than EGMYP. Saturation binding assays revealed that CFMYP has more zinc-binding sites than EGMYP. Labeled CFMYP injected into the coelom was incorporated into ovarian and testicular nutritive phagocytes and vitellogenic oocytes, and the molecular mass of part of the incorporated CFMYP shifted to 170 kDa. Considering the fact that the digestive tract is a major production site of MYP, we propose that CFMYP transports zinc, essential for gametogenesis, from the digestive tract to the ovary and testis through the coelomic fluid, after which part of the CFMYP is processed to EGMYP with loss of zinc-binding site(s).

Membrane hemifusion is a stable intermediate of exocytosis

Membrane fusion during exocytosis requires that two initially distinct bilayers pass through a hemifused intermediate in which the proximal monolayers are shared. Passage through this intermediate is an essential step in the process of secretion, but is difficult to observe directly in vivo. Here we study membrane fusion in the sea urchin egg, in which thousands of homogeneous cortical granules are associated with the plasma membrane prior to fertilization. Using fluorescence redistribution after photobleaching, we find that these granules are stably hemifused to the plasma membrane, sharing a cytoplasmic-facing monolayer. Furthermore, we find that the proteins implicated in the fusion process-the vesicle-associated proteins VAMP/synaptobrevin, synaptotagmin, and Rab3-are each immobile within the granule membrane. Thus, these secretory granules are tethered to their target plasma membrane by a static, catalytic fusion complex that maintains a hemifused membrane intermediate.

Oogenesis: Single cell development and differentiation

Oocytes express a unique set of genes that are essential for their growth, for meiotic recombination and division, for storage of nutrients, and for fertilization. We have utilized the newly sequenced genome of Strongylocentrotus purpuratus to identify genes that help the oocyte accomplish each of these tasks. This study emphasizes four classes of genes that are specialized for oocyte function: (1) Transcription factors: many of these factors are not significantly expressed in embryos, but are shared by other adult tissues, namely the ovary, testis, and gut. (2) Meiosis: A full set of meiotic genes is present in the sea urchin, including those involved in cohesion, in synaptonemal complex formation, and in meiotic recombination. (3) Yolk uptake and storage: Nutrient storage for use during early embryogenesis is essential to oocyte function in most animals; the sea urchin accomplishes this task by using the major yolk protein and a family of accessory proteins called YP30. Comparison of the YP30 family members across their conserved, tandem fasciclin domains with their intervening introns reveals an incongruence in the evolution of its major clades. (4) Fertilization: This set of genes includes many of the cell surface proteins involved in sperm interaction and in the physical block to polyspermy. The majority of these genes are active only in oocytes, and in many cases, their anatomy reflects the tandem repeating interaction domains essential for the function of these proteins. Together, the expression profile of these four gene classes highlights the transitions of the oocyte from a stem cell precursor, through stages of development, to the clearing and re-programming of gene expression necessary to transition from oocyte, to egg, to embryo.

The S. purpuratus genome: a comparative perspective

The predicted gene models derived from the sea urchin genome were compared to the gene catalogs derived from other completed genomes. The models were categorized by their best match to conserved protein domains. Identification of potential orthologs and assignment of sea urchin gene models to groups of homologous genes was accomplished by BLAST alignment and through the use of a clustering algorithm. For the first time, an overview of the sea urchin genetic toolkit emerges and by extension a more precise view of the features shared among the gene catalogs that characterize the super-clades of animals: metazoans, bilaterians, chordate and non-chordate deuterostomes, ecdysozoan and lophotrochozoan protostomes. About one third of the 40 most prevalent domains in the sea urchin gene models are not as abundant in the other genomes and thus constitute expansions that are specific at least to sea urchins if not to all echinoderms. A number of homologous groups of genes previously restricted to vertebrates have sea urchin representatives thus expanding the deuterostome complement. Obversely, the absence of representatives in the sea urchin confirms a number of chordate specific inventions. The specific complement of genes in the sea urchin genome results largely from minor expansions and contractions of existing families already found in the common metazoan "toolkit" of genes. However, several striking expansions shed light on how the sea urchin lives and develops.