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Cited by 1,132Genomics and Phylogenetic StudiesDevelopmental Biology and Gene RegulationEchinoderm biology and ecology

The Genome of the Sea Urchin Strongylocentrotus purpuratus

Open access
Sodergren, Erica, Weinstock, George M., Davidson, Eric H, Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina +220 more·2006·Science
DOI 10.1126/science.1133609PMC PMC3159423
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Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus , a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

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Written from the paper’s full text.

TL;DR

The paper reports the 814-Mb genome sequence and analysis of the sea urchin *Strongylocentrotus purpuratus*, produced by combining whole-genome shotgun and BAC sequencing. It estimates about 23,300 genes and uses the echinoderm as a deuterostome outgroup to illuminate vertebrate gene family evolution, immunity, development, and sensory biology.

Key findings

  • The final combined assembly is 814 Mb, covers more than 90% of the genome at roughly 8× base coverage, and contains 4–5% redundancy; the gene estimate is about 23,300, derived from an official set of ~28,900 models after correcting for redundancy, fragments, pseudogenes, and unrepresented transcriptionally active regions.
  • The genome contains representatives of nearly all vertebrate gene families, including some genes previously considered vertebrate-specific, while other genes found in sea urchin but not chordates suggest lineage-specific loss; gene family expansions occurred independently in sea urchin and vertebrates.
  • Innate immunity is greatly expanded: large families of TLRs, NLRs, and SRCR-domain proteins, plus 65 ABC transporters, 120 CYP genes, and 32 nuclear receptors; complement components are present, but the classical pathway and terminal C6–C9 factors appear absent.
  • Developmental and signaling analyses found ~12,000–13,000 genes expressed by mid-late gastrula (~52% of coding capacity), 353 protein kinases covering 97% of human kinase subfamilies, 11 of 13 Wnt subfamilies, ~900 rhodopsin-type GPCRs, and orthologs of Usher syndrome and biomineralization-related genes.

Methods

  • DNA came from sperm of one male; sequencing used a combined strategy of ~6× whole-genome shotgun plus ~2× BAC coverage from a minimal tiling path, with CAPSS applied to 8,248 BACs to reduce time and cost.
  • Annotation merged four gene prediction sets with GLEAN into an official gene set of ~28,900 models, followed by manual curation by more than 200 volunteers and integration of EST, tiling microarray, and other evidence.
  • Comparative analyses used InterPro/Pfam domain surveys, reciprocal BLAST orthologs, phylogenetic reconstructions, and expression profiling across embryonic stages.

Limitations

  • The paper states that high heterozygosity—single-copy DNA variation of 4–5% and at least one SNP per 100 bases—complicated assembly; the released assembly is a mosaic of two haplotypes, with haplotype resolution deferred to a future version.
  • The paper notes that linkage and cytogenetic maps are unavailable, making the genome scaffold-centric, and that the gene count depends on corrections for redundancy, invalid models, and the 10% of transcriptionally active regions not represented in the official set.
  • Evident from the text: the assembly is a high-quality draft covering more than 90% rather than a complete genome, and several comparative conclusions rely on predicted gene models and on detecting homologs that may be divergent or difficult to identify.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1126/science.1133609

Cites

42 of 42 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 74 cited sources checked · 0 supported · 0 flagged

  • Findingnone given

    An extensive defensome was identified in the sea urchin genome.

    “An extensive defensome was identified.”
    Quote in the paperSubstantial claim
  • Findingown data

    Orthologs of many human disease-associated genes are present in the sea urchin.

    “Orthologs of many human disease-associated genes were found in the sea urchin.”
    Quote in the paperSubstantial claim
  • Findingown data

    The sea urchin genome contains many genes that were previously considered vertebrate innovations or were known only outside deuterostomes.

    “including many previously thought to be vertebrate innovations or known only outside the deuterostomes.”
    Quote in the paperSubstantial claim
  • Findingown data

    The assembled genome of Strongylocentrotus purpuratus is 814 megabases.

    “The assembly size of 814 Mb is in good agreement with the previous estimate of genome size, 800 Mb ± 5% (6).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] source

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  • Findingnone given

    Distinct biomineralization genes exist in both sea urchins and vertebrates.

    “Distinct genes for biomineralization exist in the sea urchin and vertebrates.”
    Quote in the paperNot a substantial claim
  • May combine two claims. 87
  • The quote only partly states this claim. 1
  • Classified as probably not a substantial claim. 11

  • May combine two claims.

    Findingown data

    The sea urchin has representatives of nearly all vertebrate gene families, though these families are often smaller than in vertebrates.

    “The sea urchin is estimated to have 23,300 genes with representatives of nearly all vertebrate gene families, although often the families are not as large as in vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Single-copy DNA in the sea urchin varies by 4 to 5 percent for SNPs plus indels, much more than the roughly 0.5 percent in humans.

    “It was known that single-copy DNA in the sea urchin varied by as much as 4 to 5% [single nucleotide polymorphism (SNP) plus insertion/deletion (indel)], which is much greater than human (~0.5%) (3).”
    Quote in the paperSubstantial claim0 of 1 sources checked
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  • May combine two claims.

    Findingnone given

    The sea urchin has a diverse immune system with a very large repertoire of innate pathogen recognition proteins.

    “The sea urchin has a diverse and sophisticated immune system mediated by an astonishingly large repertoire of innate pathogen recognition proteins.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the 13 known Wnt subfamilies, S. purpuratus has 11 and lacks Wnt2 and Wnt11 homologs.

    “Phylogenetic analyses from cnidarian to human indicate that of the 13 known Wnt subfamilies, S. purpuratus has 11, missing Wnt2 and Wnt11 homologs (Fig. 5).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Fig. 5

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  • May combine two claims.

    Findingown data

    The average sea urchin gene length is 7.7 kb and the average primary transcript length is 8.9 kb.

    “The average gene length was 7.7 kb with an average primary transcript length of 8.9 kb.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    Eighty percent of the sea urchin regulome, excluding zinc finger genes, is expressed by 48 hours of embryogenesis, a greater genetic investment than the 52 percent total gene use.

    “We found that 80% of the whole sea urchin regulome (except the zinc finger genes) was expressed by 48 hours of embryogenesis (20), an even greater genetic investment than the 52% total gene use in the same embryo.”
    Quote in the paperSubstantial claim0 of 1 sources checked
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  • May combine two claims.

    Findingown data

    The sea urchin genome has 36.9 percent GC content, and the GC content is uniformly low across domains.

    “The 36.9% GC content of the genome is uniformly low because assessment of the average GC content by domains is consistent (36.8%), and the distribution is tight (see SOM).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Combining BAC and WGS sequence produced a high-quality draft with 4 to 5 percent redundancy, covering more than 90 percent of the genome at 8x base coverage.

    “Combining the BAC-derived sequence with the WGS sequence generated a high-quality draft with 4 to 5% redundancy that covered more than 90% of the genome while sequencing to a level of 8× base coverage (table S2).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites table S2

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    Findingown data

    The number of presumed orthologous genes between ascidian and mammals is about equal but lower than between those species and sea urchin.

    “The numbers of presumed orthologous genes between the ascidian and the two mammals are about equal, but are less than the number counted between these species and the sea urchin.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Expression profiling showed that 87 percent of signaling kinases and 80 percent of the 91 phosphatases were expressed in the embryo.

    “Expression profiling showed that 87% of the signaling kinases and 80% of the 91 phosphatases were expressed in the embryo (23,24), which emphasized the importance of signaling pathways in embryonic development.”
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    • cites [24]

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    Findingown data

    About 12,000 to 13,000 genes are expressed during development up to the mid-late gastrula stage, representing about 52 percent of the protein-coding capacity.

    “Expression of about 12,000 to 13,000 genes, as conservatively assessed, was seen during this early period, indicating that ~52% of the entire protein-coding capacity of the sea urchin genome is expressed during development to the mid-late gastrula stage.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The S. purpuratus genome has 353 protein kinases, an intermediate number between the core vertebrate set of 510 and the approximately 230 in fruit fly and nematode.

    “The S. purpuratus genome has 353 protein kinases, intermediate between the core vertebrate set of 510 and the fruit fly and nematode conserved sets of ~230.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Exon lengths peak around 100 to 115 nucleotides, while intron lengths peak around 750 nucleotides.

    “A broad distribution of all exon lengths peaked at around 100 to 115 nucleotides, whereas that for introns at around 750 nucleotides.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A mismatch frequency of one per 50 bases or higher blocked merging by Atlas and Phrap and made it hard to distinguish duplicated diverged regions from heterozygous homologs.

    “This average frequency of a mismatch per 50 bases or higher prevented merging by the assembly module in Atlas, the Phrap assembler, and also made it difficult to determine if reads were from duplicated but diverged sections of the genome or heterozygous homologs.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    The sea urchin lacks gap junction proteins, consistent with the absence of morphological evidence for gap junctions.

    “In agreement with the lack of morphological evidence of gap junctions in sea urchins, there are no gap junction proteins (connexins, pannexins, and innexins).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Most sea urchin kinase subfamilies have a single member, and the kinome is largely nonredundant.

    “Most sea urchin kinase subfamilies have just a single member, although many are expanded in vertebrates; thus, the sea urchin kinome is largely nonredundant.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The assembly is a mosaic of two haplotypes, and BAC phase could be determined from mismatches in overlapping regions.

    “The assembly is a mosaic of the two haplotypes, but it was possible to determine the phase of the BACs on the basis of how many mismatches neighboring BACs had in their overlap regions.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    With 68 percent of the human kinase total, sea urchin has members of 97 percent of human kinase subfamilies, lacking only four, while Drosophila lacks 20 and nematodes lack 32.

    “Indeed, with only 68% of the total number of human kinases, the sea urchin has members of 97% of the human kinase subfamilies, lacking just four of those subfamilies (Axl, FastK, H11, and NKF3),whereas Drosophila lacks 20 and nematodes 32 (Fig. 3) (23).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [23]

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  • May combine two claims.

    Findingcitation

    The sea urchin genome lacks several insect-specific protein domains and the vertebrate KRAB domain.

    “Also missing are several protein domains unique to insects, such as insect cuticle protein, chitin-binding protein, and several pheromone-or odorant-binding proteins, as well as a vertebrate invention-the Krüppel-associated box or KRAB domain, a repressor domain in zinc finger transcription factors (12).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [12] source

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  • May combine two claims.

    Findingcitation

    S. purpuratus has WntA, which was previously reported absent from deuterostomes.

    “S. purpuratus has WntA, previously reported as being absent from deuterostomes (29).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [29] source

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  • May combine two claims.

    Findingown data

    The sea urchin gene set shares about 4000 domains with other bilaterian gene models, while 1375 domains from other bilaterian genomes are absent from sea urchin.

    “The sea urchin gene set shares with other bilaterian gene models about 4000 domains, whereas 1375 domains from other bilaterian genomes are not found in the sea urchin set.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Alignment of WGS reads to the early v0.1 assembly found at least one SNP per 100 bases and a similar frequency of indels.

    “alignment of WGS reads to the early v 0.1 WGS assembly revealed at least one SNP per 100 bases, as well as a comparable frequency of indel variants.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Two of the most abundant sea urchin domains account for 3 percent of the total and mark innate immune response genes.

    “Two of the most abundant domains make up 3% of the total and mark genes that are involved in the innate immune response.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Although many cytokine, chemokine, and receptor families were not found, several important immune signaling homologs are present in the sea urchin genome.

    “Although members of many cytokine, chemokine, and receptor families were not identified in the sea urchin genome, a number of important immune signaling homologs were present.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The ABCC multidrug transporter family is about 25 percent larger than in other deuterostome genomes, with at least 30 genes, nearly half of the sea urchin ABC transporters.

    “The ABCC family of multidrug transporters is about 25% larger than in other deuterostome genomes with at least 30 genes in this family (nearly half of the sea urchin ABC transporters)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Strongylocentrotus purpuratus has 32 nuclear receptor genes, about two-thirds the human number, including several potentially involved in chemical defense.

    “Strongylocentrotus purpuratus has 32 nuclear receptor (NR) genes (20), two-thirds the number in humans, including several with potential roles in chemical defense (42).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [20]

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    • cites [42] source

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  • May combine two claims.

    Findingnone given

    Metal-complexing proteins include three metallothionein genes and three phytochelatin synthase homologs.

    “The metal-complexing proteins include three metallothionein genes and three homologs of phytochelatin synthase genes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingnone given

    Two thioester proteins, SpC3 and SpC3-2, are expressed in coelomocytes and in embryos and larvae, respectively.

    “Two of the thioester proteins, SpC3 and SpC3-2, are known to be expressed, respectively, in coelomocytes and in embryos and larvae.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Present immune signaling homologs include TNF ligand and receptor superfamily members, an IL-1 receptor and accessory proteins, two IL-17 receptor-like genes, 30 IL-17 family ligands, and nine MIF-like genes.

    “These included members of the tumor necrosis factor (TNF) ligand and receptor superfamilies, an IL-1 receptor and accessory proteins, two IL-17 receptor-like genes and 30 IL-17 family ligands, and nine macrophage inhibitory factor (MIF)-like genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Antioxidant protein genes include three SOD genes, an ovoperoxidase gene, one catalase, four glutathione peroxidase genes, and at least three thioredoxin peroxidase genes.

    “Genes for antioxidant proteins include three superoxide dismutase (SOD) genes and a gene encoding ovoperoxidase (an unusual peroxidase with SOD-like activity), along with one catalase, four glutathione peroxidase, and at least three thioredoxin peroxidase genes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The sea urchin genome contains homologs of CYP26, CYP51, CYP27, and CYP46.

    “In addition to the CYPs in families 1 to 4, the sea urchin genome contains homologs of proteins involved in developmental patterning (CYP26), cholesterol synthesis (CYP51), and metabolism (CYP27, CYP46).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    One sea urchin AHR homolog is more closely related to vertebrate AHR, while the other is most similar to Drosophila spineless.

    “One of the sea urchin AHR homologs was more closely related to the vertebrate AHR; the other shared greatest sequence identity with the Drosophila AHR homolog spineless.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Twenty-eight gene models encode MAC-perforin domains, but none have the additional domains expected for terminal complement factors C6 through C9.

    “Twenty-eight gene models were identified that encode MAC-perforin domains, but none of these had the additional domains expected for terminal complement factors (C6 through C9).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    PU.1, the Ikaros-like gene, and homologs of Gata1/2/3, E2A/HEB/ITF2, and SCL are expressed at substantial levels in coelomocytes.

    “Transcript prevalence measurements showed that PU.1, the Ikaros-like gene and homologs of Gata1/2/3, E2A/HEB/ITF2, and Stem Cell Leukemia (SCL) were all expressed at substantial levels in coelomocytes (41).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [41] source

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  • May combine two claims.

    Findingcitation

    Absent Wnt targets include vertebrate adhesion molecules, which are frequently missing from the sea urchin genome, and signaling receptors that are more divergent.

    “The absent Wnt targets include vertebrate adhesion molecules, which were frequently missing from the sea urchin genome (32), as well as signaling receptors, which are more divergent and thus more difficult to identify.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [32]

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  • May combine two claims.

    Findingown data

    The diversity of genes for xenobiotic-sensing transcription factors in the sea urchin is comparable to that in other invertebrates but generally lower than in vertebrates.

    “The diversity of genes encoding xenobiotic-sensing transcription factors that regulate biotransformation enzymes and transporters was similar to other invertebrate genomes, but in most cases lower than vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Several collectin, C1q, and MBP genes are present in the sea urchin genome, but MASP/C1r/C1s family members were not identified.

    “Several genes encoding collectins, C1q and MBP, have been predicted (39) and were present in the genome; however, members of the MASP/C1r/ C1s family were not identified.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [39]

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  • May combine two claims.

    Findingown data

    Eleven CYP1-like genes are present in the sea urchin genome, more than twice the number in chordates.

    “Eleven CYP1-like genes are present in the sea urchin genome, more than twice the number in chordates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    The sea urchin genome includes two PPAR-like genes and one NR1H gene that is coorthologous with both LXR and FXR.

    “The sea urchin genome also contains two peroxisome proliferator-activated receptor (PPAR, NR1C) homologs and an NR1H gene coorthologous to both liver X receptor (LXR) and farnesoid X receptor (FXR) (42).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [42] source

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  • May combine two claims.

    Findingown data

    The sea urchin has two hypoxia-inducible factor alpha subunit genes and one ARNT gene.

    “Sea urchins also had two genes encoding hypoxia-inducible factors (HIFα subunits), which regulate adaptive responses to hypoxia, and a gene encoding ARNT, a PAS protein that is a dimerization partner for both AHRs and HIFs.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Much ABCC expansion is in the Sp-ABCC5 and Sp-ABCC9 families, and orthologs of vertebrate ABCC2 are absent.

    “Much of the expansion is in the Sp-ABCC5 and Sp-ABCC9 families, whereas orthologs of the vertebrate gene ABCC2 (also called MRP2) are absent.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The basic metazoan basement membrane ECM tool kit is present in the sea urchin: two alpha-IV collagen genes, perlecan, laminin subunits, nidogen, and collagen XV/XVIII.

    “The basic metazoan basement membrane extracellular matrix (ECM) tool kit was presenttwo alpha-IV collagen genes, perlecan, laminin subunits, nidogen, and collagen XV/XVIII.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Cannabinoid, lysophospholipid, and melanocortin receptors are absent in sea urchins, but orthologs are found in ascidians.

    “Cannabinoid, lysophospholipid, and melanocortin receptors are not present in urchins, but orthologs were found in ascidians (4,47).”
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  • May combine two claims.

    Findingown data

    The sea urchin has 200 to 700 putative chemosensory genes that form large clusters and lack introns, features of vertebrate chemosensory genes but not of Caenorhabditis elegans and Drosophila melanogaster.

    “There were 200 to 700 putative chemosensory genes that formed large clusters and lacked introns, which are features of chemosensory genes in vertebrates, but not in Caenorhabditis elegans and Drosophila melanogaster.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Some gene sets thought to be chordate-specific have sea urchin orthologs, including insulin and IGFs that are more similar to chordate counterparts than those of other invertebrates.

    “some sets of genes thought to be chordate-specific have sea urchin orthologs, for example, insulin and insulin-like growth factors (IGFs) that are more similar to their chordate counterparts than those of other invertebrates (47).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
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  • May combine two claims.

    Findingown data

    The sea urchin cadherin repertoire is small relative to vertebrates (about a dozen versus over a hundred), with many chordate-specific expansions missing.

    “The cadherin repertoire was also small relative to vertebrates (a dozen or so instead of over a hundred), and many chordate-specific expansions were missing.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    S. purpuratus has a number of LRP receptors, although it is unclear whether they are reelin receptors, lipoprotein receptors, or something else.

    “Receptors for reelin are believed to include low-density lipoprotein receptor-related proteins (LRPs), and there are a number of these receptors in S. purpuratus although it is as yet unclear whether they are reelin receptors, lipoprotein receptors, or something else.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The sea urchin neurotransmitter repertoire is large, but melatonin and adrenalin are lacking, as they are in ascidians.

    “The repertoire of sea urchin neurotransmitters is large, but melatonin and adrenalin are lacking, as they are in ascidians (4,47).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
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    • cites [47]

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  • May combine two claims.

    Findingown data

    The sea urchin integrin family is intermediate in size between protostomes and vertebrates; several chordate-specific expansions are absent and some expansions are unique to echinoderms.

    “The integrin family was intermediate in size between those of protostomes and vertebrates-several chordate-specific expansions of the integrin repertoire were absent, and there were some expansions unique (so far) to echinoderms.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Both the secretin and rhodopsin GPCR superfamilies show marked lineage-specific expansions in the sea urchin.

    “Both the secretin and rhodopsin superfamilies display marked lineage-specific expansions (13,47).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
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    • cites [47]

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  • May combine two claims.

    Findingown data

    Specialized large cadherins shared by protostomes and vertebrates are present in the sea urchin, as are some previously thought chordate-specific, but overall the cadherin repertoire is more invertebrate than vertebrate.

    “Specialized large cadherins shared by protostomes and vertebrates were present, as well as some specialized large cadherins previously thought to be chordate-specific, but overall, the cadherin repertoire was more invertebrate than vertebrate in character.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Key neural adhesion systems for axonal outgrowth (netrin/Unc5/DCC, Slit/Robo, semaphorins/plexins) and for synaptogenesis (Agrin/MUSK, neurexin/neuroligins) are present in the sea urchin.

    “The key neural adhesion systems involved in regulating axonal outgrowth were present (netrin/Unc5/ DCC; Slit/Robo; and semaphorins/plexins), as were adhesion molecules involved in synaptogenesis (Agrin/MUSK; and neurexin/neuroligins).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    These photoreceptor genes include many transcription factors regulating retinal development and a photorhodopsin gene.

    “These included many genes encoding transcription factors regulating retinal development and a photorhodopsin gene.”
    Quote in the paperNot a substantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    These Usher network orthologs include usherin, VLGR-1, cadherins, myosin 7 and 15, harmonin, whirlin, SANS, NBC, and TrpA1.

    “These include the very large membrane proteins, usherin and VLGR-1 and large cadherins (Cadh23 and possibly Pcad15), all of which participate in forming links between stereocilia in mammalian hair cells, as well as myosin 7 and 15, two PDZ proteins (harmonin and whirlin) and another adaptor protein (SANS), which participate in linking these membrane proteins to the cytoskeleton.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingcitation

    Echinoderm synapses are structurally unusual because they lack direct synaptic contacts.

    “However, structurally, the synapses of echinoderms are unusual because there are no direct synaptic contacts (49).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
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  • May combine two claims.

    Findingown data

    The S. purpuratus genome contains representatives of all standard metazoan adhesion receptors, but the emphasis on different receptor classes differs substantially from vertebrates.

    “The S. purpuratus genome contained representatives of all the standard metazoan adhesion receptors (table S7), but the emphasis on different classes of receptors differed substantially from that used by vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    Sea urchin spicule matrix proteins are encoded by a family of 16 genes organized in small clusters and likely proliferated by gene duplication.

    “The sea urchin spicule matrix proteins were encoded by a family of 16 genes that are organized in small clusters and likely proliferated by gene duplication.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Most S. purpuratus dynein heavy chain genes map one-to-one to mammalian homologs, but Sp-DNAH9 maps one-to-three, being equidistant between DNAH9, DNA11, and DNAH17.

    “although most S. purpuratus dynein heavy chain genes mapped one-to-one to mammalian homologs, Sp-DNAH9 mapped one-to-three, as it was equidistant between the closely similar mammalian genes DNAH9, DNA11, and DNAH17 (52).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
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  • May combine two claims.

    Findingown data

    Many more human genes have shared ancestry across deuterostomes, and bilaterian genes are more broadly shared than had been inferred from comparison of previously limited genome sequences.

    “Many more human genes have shared ancestry across the deuterostomes, and in fact, bilaterian genes are more broadly shared than had been inferred from comparison of the previously limited genome sequences.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    Deuterostomes share 9 protein kinase subfamilies absent from C. elegans and Drosophila, and the sea urchin has not lost any of the 158 metazoan primordial kinase classes, unlike insects or nematodes.

    “Deuterostomes share 9 protein kinase subfamilies absent from C. elegans and Drosophila, and the sea urchin has not lost any of the 158 metazoan primordial kinase classes, unlike insects or nematodes.[From (23)]”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [23]

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Gene-specific duplications increased sea urchin GTPase numbers, resulting in complexity comparable to vertebrates.

    “The pink boxes highlight gene-specific duplications that increased sea urchin GTPase numbers, resulting in a complexity comparable to vertebrates.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [28] source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Many genes described in the paper fall into the human disease gene ortholog category and cover nervous, endocrine, blood, muscle, and skeletal systems, as exemplified by Huntington and muscular dystrophy genes.

    “Many of the genes described in the preceding sections fall into this category (see tables S8 and S9) and cover a surprising diversity of systems such as nervous, endocrine, and blood systems, as well as muscle and skeleton, as exemplified by the Huntington and muscular dystrophy genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    Newly identified motor protein genes include members of four more myosin classes and eight more kinesin families.

    “Newly identified motor protein genes include members of four more classes of myosin, and eight more families of kinesins.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductreasoning

    BAC clones provided an assembly framework that helped assemble repeats and addressed high heterozygosity without extremely high sequencing coverage.

    “The use of BACs provided a framework for localizing the assembly process, which aided in the assembly of repeated sequences and solved problems associated with the high heterozygosity of the sea urchin genome, without our resorting to extremely high coverage sequencing.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductreasoning

    The CAPSS strategy reduced BAC sequencing time to one-fifth and cost to one-tenth.

    “This allowed the BAC sequencing to be performed in 1/5th the time and at 1/10th the cost.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The sea urchin has orthologs of vertebrate genes for vision, hearing, balance, and chemosensation, suggesting previously unknown sensory capabilities.

    “The sea urchin has orthologs of genes associated with vision, hearing, balance, and chemosensation in vertebrates, which suggests hitherto unknown sensory capabilities.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Euechinoids became the dominant echinoid form after the Permian-Triassic extinction about 250 million years ago.

    “These evolved to become the dominant echinoid form after the great Permian-Triassic extinction 250 million years ago.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Stem group echinoderms appear in Lower Cambrian fossil assemblages dated to 520 Ma.

    “Stem group echinoderms appear in the Lower Cambrian fossil assemblages dating to 520 Ma.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Some genes thought to be vertebrate-specific are present in sea urchin, and others found in sea urchin but not chordates suggest gene loss in vertebrates.

    “Some genes thought to be vertebrate-specific were found in the sea urchin (deuterostome-specific); others were identified in sea urchin but not the chordate lineage, which suggests loss in the vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    The failure to find chemosensory GPCRs likely reflects independent evolution rather than absence of chemoreceptive molecules, because the genome encodes close to 900 rhodopsin-type GPCRs, some expressed in sensory structures.

    “However, this failure more likely reflects the independent evolution of these receptors, rather than a lack of chemoreceptive molecules, because the sea urchin genome encodes close to 900 GPCRs of the same superfamily (rhodopsin-type GPCRs), several of which are expressed in sensory structures (13).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [13]

      Not checked in the free run.

  • May combine two claims.

    Study design and conductreasoning

    The heterozygosity problem was addressed by adding Atlas components and using BAC data, since each BAC represented a single haplotype.

    “This challenge was met by adding components to Atlas to handle local regions of heterozygosity and to take advantage of the BAC data, because each BAC sequence represented a single haplotype (see SOM).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    The smaller average intron size in sea urchin relative to human is consistent with the trend that intron size correlates with genome size.

    “The smaller average intron size relative to humans' was consistent with the trend that intron size is correlated with genome size.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    High heterozygosity has been observed in Ciona genomes and is likely to become common as fewer inbred organisms are sequenced.

    “High heterozygosity has been seen in the past with the Ciona genomes (4,5) and is likely to be the norm in the future as fewer inbred organisms are sequenced.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [4]

      Not checked in the free run.

    • cites [5]

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    A small number of sea urchin kinases are more similar to insect than vertebrate homologs, indicating loss of kinase classes in vertebrates.

    “A small number of kinases were more similar to insect than to vertebrate homologs (including the Titin homolog Projection, the Syk-like tyrosine kinase Shark, and several guanylate cyclases), which indicated for the first time the loss of kinase classes in vertebrates (23).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [23]

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    More than 90 percent of small GTPases are expressed during sea urchin embryogenesis, suggesting comparable signaling complexity between sea urchins and vertebrates.

    “More than 90% of the small GTPases are expressed during sea urchin embryogenesis, which suggests that the complexity of signaling through GTPases is comparable between sea urchins and vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    The quinoprotein amine dehydrogenase domain is ten times more abundant in sea urchin than in other representative genomes and may be used in quinone-containing pigments.

    “The quinoprotein amine dehydrogenase domain seen in the sea urchin set is 10 times as abundant as in other representative genomes and may be used in the systems of quinone-containing pigments known to occur in these marine animals.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The shared genes form a bilaterian common set, while additional sea urchin-mouse pairs are unique to deuterostomes.

    “Thus, these genes constitute a set of genes common to the bilaterians, whereas the additional sea urchin-mouse pairs are unique to the deuterostomes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    About 90 percent of 126 Wnt signal transduction machinery genes have sea urchin homologs, indicating high conservation of all three Wnt pathways.

    “Of 126 genes described as components of the Wnt signal transduction machinery, homologs of ~90% were present in the sea urchin genome, which indicates a high level of conservation of all three Wnt pathways (30).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [30]

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The sea urchin has kinase diversity comparable to vertebrates without the same complexity.

    “The sea urchin therefore possesses a kinase diversity surprisingly comparable to that of vertebrates without the complexity.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    The CAPSS approach makes BAC sequencing more manageable for large genomes.

    “Moreover, the CAPSS approach makes BAC sequencing more manageable for large genomes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductown data

    Over 9000 gene models were manually curated, and 159 novel models were added to the official set.

    “Over 9000 gene models were manually curated by the consortium with 159 novel models (gene models not represented in the OGS) added to the official set.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    ABCC efflux activity has been described in sea urchin embryos, and the major early embryo efflux activity is consistent with the genomic expansion of the ABCC family.

    “ABCC efflux activity has been described in sea urchin embryos and, consistent with the genomic expansion of the ABCC family, the major activity in early embryos ensues from an ABCClike efflux mechanism.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    Reactive oxygen detoxification genes may be important for the long sea urchin life span, because oxidative damage is thought to be a major factor in aging.

    “Reactive oxygen detoxification genes may be important in conferring the long life-span of sea urchins, because oxidative damage is thought to be a major factor in aging.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Oxidative damage is a major factor in aging.

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    If the sea urchin complement system uses multiple lectin and alternative pathways without terminal lytic function, its major activity is expected to be opsonization.

    “If the complement system in the sea urchin functions through multiple lectin and alternative pathways in the absence of the lytic functions of the terminal pathway, the major activity of this system is expected to be opsonization.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    Most Wnt pathway transcription factor targets are present in the sea urchin genome, reflecting higher conservation of transcription factor families.

    “In contrast, most transcription factor targets of the Wnt pathway are present in the genome, which reflects a higher degree of conservation of transcription factor families (20).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [20]

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Echinoderm larval and adult nervous systems are dispersed but are not simple nerve nets.

    “The nervous systems of echinoderm larvae and adults are dispersed, but they are not simple nerve nets.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [47]

      Not checked in the free run.

    • Rests on an assumption: The echinoderm nervous system is the least studied among the major metazoan phyla.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The Rag1/2-like cluster and other findings suggest these genes have been part of animal genomes longer than previously thought.

    “The presence of this cluster, along with other recent findings (37), suggested the possibility that these genes had been part of animal genomes for longer than previously considered.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [37] source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Because ABCC transporters generally move more hydrophilic compounds, sea urchins may have an increased need to transport such compounds.

    “Because the ABCC family is known to generally transport more hydrophilic compounds than other transporter families, such as the ABCB genes, sea urchins may have increased need for transport of these compounds.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationcitation

    The sea urchin has 120 CYP genes, with 80 percent related to families 1 to 4, suggesting selective pressure to expand these functions.

    “The sea urchin has 120 CYP genes, and those related to CYP gene families 1 to 4 constitute 80% of the total, which suggests that there has been selective pressure to expand functionality in these gene families (42).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [42] source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The peripheral appendages of adult sea urchins are connected to each other and to radial nerves, which provide overall control and coordination.

    “These peripheral appendages are connected to each other and to radial nerves, which provide overall control and coordination (47,48).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [47]

      Not checked in the free run.

    • cites [48]

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The neurotrophin-Trk receptor system has a deuterostome origin and was potentially lost in urochordates.

    “which suggests a deuterostome origin and a potential loss in urochordates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Sea urchins respond to light, touch, and displacement and probably use some of the same sensory genes used by vertebrates.

    “Sea urchins respond to light, touch, and displacement and probably use some of same sensory genes used by vertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Sea urchins lack ears and eyes, so they must deploy these sensory proteins in other sensory processes.

    “Sea urchins do not have ears or eyes, so they must deploy these proteins in other sensory processes.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Sea urchins lack ears and eyes.

  • May combine two claims.

    Interpretationnone given

    The diversity of pathogen-binding motifs encoded in the sea urchin genome provides a resource for antimicrobial applications and identification of new deuterostome immune functions relevant to human health.

    “The immense diversity of pathogen-binding motifs encoded in the sea urchin genome provides an invaluable resource for antimicrobial applications and the identification of new deuterostome immune functions with direct relevance to human health.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Duplications in the chordate lineage contributed to increased complexity of vertebrates, but regional expansions also play a large role in animal evolution.

    “Thus, whereas the duplications of the chordate lineage were a contributor to the increased complexity of vertebrates, regional expansions clearly play a large role in the evolution of these animals.”
    Quote in the paperSubstantial claim
95 of 95

  • The authors state this as an assumption.

    The manually curated gene models are not biased in a way that affects the estimate of novel gene models.

    “If we assume no bias in the curated gene models”

  • The paper relies on this without support.

    The need to cope with environmental physical, chemical, and biological challenges drives the evolution of defense gene families and pathways.

    “The need to deal with physical, chemical, and biological challenges in the environment underlies the evolution of an array of defense gene families and pathways.”

  • The paper relies on this without support.

    Oxidative damage is a major factor in aging.

    “oxidative damage is thought to be a major factor in aging.”

  • The paper relies on this without support.

    The echinoderm nervous system is the least studied among the major metazoan phyla.

    “The echinoderm nervous system is the least well studied of all the major metazoan phyla.”
    “For a number of technical reasons, the structure and function of echinoderm nerves have been neglected.”

  • The paper relies on this without support.

    Sea urchins lack ears and eyes.

    “Sea urchins do not have ears or eyes”

  • The paper relies on this without support.

    Among deuterostomes, only echinoderms and vertebrates produce extensive skeletons.

    “Among the deuterostomes, only echinoderms and vertebrates produce extensive skeletons.”
6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Comparisons among fruit fly, nematode, and vertebrate genomes show greater genomic complexity in vertebrates as measured by gene content and structure, while many genes and networks are shared across bilaterians.

    “Comparisons (4-6) between fruit fly, nematode, and vertebrate genomes reveal greater genomic complexity in the vertebrates (and other deuterostomes (7,8)) as measured by gene content and structure, but at the same time show that many genes and networks are shared across bilaterians.”

    From Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization (2007) · cites this paper as [8]

  • The parental anemones have somewhat less allelic variation than sea squirts, sea urchins, or Populus, but comparable to pufferfish.

    “Thus the parental anemones whose genomes we sampled have somewhat less allelic variation than broadcast spawning invertebrates such as sea squirts (~2%) (7) and sea urchins (5-10%) (8), or outbreeding plants like Populus (~2%) (34), but a comparable amount to the pufferfish (0.5%) (35).”

    From Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization (2007) · cites this paper as [8]

  • In echinoderms regulatory genes are generally not 2- or 4-fold paralogous, as in mammals, so the process of cis-regulatory changes in input cannot be explained by functional diversification of duplicated genes.

    “We note that in echinoderms regulatory genes are generally not 2- or 4-fold paralogous (31), as in mammals, so the process of cis -regulatory changes in input cannot be explained by functional diversification of duplicated genes.”

    From Evolutionary plasticity of developmental gene regulatory network architecture (2007) · cites this paper as [31]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Wnt target count differs between text and figure caption

    Minor

    The main text counts 94 reported Wnt target genes, but the caption for Fig. 6 counts 93.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 9

  1. C. G. Elsik A. J. Mackey J. T. Reese N. V. Milshina D. S. Roos G. M. Weinstock Genome Biol . in press.
  2. F. Raible et al. Dev. Biol. in press.
  3. K. Grobben, Verh. Zool. Bot. Ges. Wien58, 491 (1908).
  4. E. H. Davidson in Gene Regulatory Networks in Development and Evolution (Academic Press/Elsevier San Diego CA 2006).
  5. M. Howard-Ashby C. T. Brown S. C. Materna L. Chen E. H. Davidson Dev. Biol. in press.
  6. C. Byrum et al. Dev. Biol. in press.
  7. J. Croce et al. Dev. Biol. in press.
  8. J. L. S. Cobb, in Nervous Systems of Invertebrates, M. A. Ali, Ed. (Plenum, New York, 1987), pp. 483–525.
  9. We gratefully acknowledge the following support: BCM-HGSC National Human Genome Research Institute (NIH) grant 5 U54 HG003273; Naples Workshop Stazione Zoologica Naples and the Network of Excellence “Marine Genomics Europe” (GOCE-04-505403); M. Elphick Biotechnology and Biological Sciences Research Council (BBSRC) UK grant S19916; J. Rast laboratory Natural Sciences and Engineering Research Council (NSERC) of Canada Canadian Institutes of Health Research (CIHR) and the Uehara Memorial Foundation; J. A. Coffman Mount Desert Island Biological Laboratory (MDIBL) NIH grant GM070840; M. C. Thorndyke K. H. Wilson F. Hallböök R. P. Olinski Swedish Science Research Council Network of Excellence Marine Genomics Europe (GOCE-04-505403) European Union Research Training Networks FP5 Trophic Neurogenome HPRN-ct-2002-00263 and the Royal Swedish Academy of Sciences STINT; E. H. Davidson R. A. Cameron the Center for Computational Regulatory Genomics (E. H. Davidson principal investigator) was supported by the NIH grant RR-15044 NSF IOB-0212869 and the Beckman Institute; also support for the E. H. Davidson laboratory is from NIH grants HD-37105 and GM61005 and U.S. Department of Energy (DOE) grant DE-FG02-03ER63584; P. Oliveri Camilla Chandler Frost Fellowship; G. M. Wessel laboratory supported by NSF IOB-0620607 and NIH grant R01 HD028152; B. Brandhorst K. Bergeron and N. Chen NSERC; K. R. Foltz NSF IBN-0415581; M. Hahn NIH grant R01ES006272; D. Burgess NIH grant GM058231; L. C. Smith NSF (MCB-0424235); R. O. Hynes Howard Hughes Medical Institute and National Cancer Institute (NCI) (MIT Cancer Center core grant P30-CA14051); D. McClay NIH grants GM61464 HD039948 and HD14483; V. D. Vacquier (group leader) G. W. Moy H. J. Gunaratne M. Kinukawa M. Nomura A. T. Neill and Y.-H. Su NIH grant R37-HD12896; R. D. Burke NSERC and CIHR; L. M. Angerer National Institute of Dental and Craniofacial Research (NIDCR) R. C. Angerer (NIDCR) Z. Wei (NIDCR) G. Humphrey National Institute of Child Health and Human Development (NICHD) M. Landrum National Center for Biotechnology Information (NCBI) O. Ermolaeva (NCBI) P. Kitts (NCBI) K. Pruitt (NCBI) V. Sapojnikov (NCBI) A. Souvorov (NCBI) W. Hiavina (NCBI) S. Fugmann National Institute on Aging (NIA) M. Dean National Cancer Institute–Frederick (NCIFCRF) Intramural Research Program of the NIH; P. Cormier Association pour la Recherche contre la Cancer (ARC) France grants 4247 and 3507 to P.C. Ligue Nationale contre le Cancer to P.C. Conseil Régional de Bretagne and Conseil Général du Finistère; W. H. Klein National Eye Institute NIH grant EY11930 NICHD HD66219 and the Robert A. Welch Foundation (G-0010); N. Adams NSF grant IBN 0417003 and the Department of the Navy Office of Naval Research under Award N00014-05-1-0855; D. Epel NSF 0417225; A. Hamdoun F32-HD47136; C. Byrum American Heart Association grant 0420074Z; K. Walton U.S. Army Medical Research and Materiel Command grant W81XWH-04-1-0324; J. Stegeman NIH 2P42 ESO7381; and J. Goldstone NIH F32 ESO12794.

Cited by

Sorted by citations

Authors
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., Coffman, J. A., Dean, M., Elphick, M. R., Ettensohn, C. A., Foltz, K. R., Hamdoun, A., Hynes, R. O., Klein, W. H., Marzluff, W., McClay, D. R., Morris, R. L., Mushegian, A., Rast, J. P., Smith, L. C., Thorndyke, M. C., Vacquier, V. D., Wessel, G. M., Wray, G., Zhang, L., Elsik, C. G., Ermolaeva, O., Hlavina, W., Hofmann, G., Kitts, P., Landrum, M. J., Mackey, A. J., Maglott, D., Panopoulou, G., Poustka, A. J., Pruitt, K., Sapojnikov, V., Song, X., Souvorov, A., Solovyev, V., Wei, Z., Whittaker, C. A., Worley, K., Durbin, K. J., Shen, Y., Fedrigo, O., Garfield, D., Haygood, R., Primus, A., Satija, R., Severson, T., Gonzalez-Garay, M. L., Jackson, A. R., Milosavljevic, A., Tong, M., Killian, C. E., Livingston, B. T., Wilt, F. H., Adams, N., Bellé, R., Carbonneau, S., Cheung, R., Cormier, P., Cosson, B., Croce, J., Fernandez-Guerra, A., Genevière, A.-M., Goel, M., Kelkar, H., Morales, J., Mulner-Lorillon, O., Robertson, A. J., Goldstone, J. V., Cole, B., Epel, D., Gold, B., Hahn, M. E., Howard-Ashby, M., Scally, M., Stegeman, J. J., Allgood, E. L., Cool, J., Judkins, K. M., McCafferty, S. S., Musante, A. M., Obar, R. A., Rawson, A. P., Rossetti, B. J., Gibbons, I. R., Hoffman, M. P., Leone, A., Istrail, S., Materna, S. C., Samanta, M. P., Stolc, V., Tongprasit, W., Tu, Q., Bergeron, K.-F., Brandhorst, B. P., Whittle, J., Berney, K., Bottjer, D. J., Calestani, C., Peterson, K., Chow, E., Yuan, Q. A., Elhaik, E., Graur, D., Reese, J. T., Bosdet, I., Heesun, S., Marra, M. A., Schein, J., Anderson, M. K., Brockton, V., Buckley, K. M., Cohen, A. H., Fugmann, S. D., Hibino, T., Loza-Coll, M., Majeske, A. J., Messier, C., Nair, S. V., Pancer, Z., Terwilliger, D. P., Agca, C., Arboleda, E., Chen, N., Churcher, A. M., Hallböök, F., Humphrey, G. W., Idris, M. M., Kiyama, T., Liang, S., Mellott, D., Mu, X., Murray, G., Olinski, R. P., Raible, F., Rowe, M., Taylor, J. S., Tessmar-Raible, K., Wang, D., Wilson, K. H., Yaguchi, S., Gaasterland, T., Galindo, B. E., Gunaratne, H. J., Juliano, C., Kinukawa, M., Moy, G. W., Neill, A. T., Nomura, M., Raisch, M., Reade, A., Roux, M. M., Song, J. L., Su, Y.-H., Townley, I. K., Voronina, E., Wong, J. L., Amore, G., Branno, M., Brown, E. R., Cavalieri, V., Duboc, V., Duloquin, L., Flytzanis, C., Gache, C., Lapraz, F., Lepage, T., Locascio, A., Martinez, P., Matassi, G., Matranga, V., Range, R., Rizzo, F., Röttinger, E., Beane, W., Bradham, C., Byrum, C., Glenn, T., Hussain, S., Manning, G., Miranda, E., Thomason, R., Walton, K., Wikramanayke, A., Wu, S.-Y., Xu, R., Brown, C. T., Chen, L., Gray, R. F., Lee, P. Y., Nam, J., Oliveri, P., Smith, J., Muzny, D., Bell, S., Chacko, J., Cree, A., Curry, S., Davis, C., Dinh, H., Dugan-Rocha, S., Fowler, J., Gill, R., Hamilton, C., Hernandez, J., Hines, S., Hume, J., Jackson, L., Jolivet, A., Kovar, C., Lee, S., Lewis, L., Miner, G., Morgan, M., Nazareth, L. V., Okwuonu, G., Parker, D., Pu, L.-L., Thorn, R., & Wright, R.
Affiliations
  • California Institute of Technology (US)
  • University of North Carolina at Chapel Hill (US)
  • Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Corresponding author
  • Weinstock, George M.
  • Mackey, Aaron J.
  • Obar, Robert A.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2006-11-10
Volume
314
Issue
5801
Pages
941-952
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1133609
PMC
PMC3159423
OpenAlex
W2154403718
Semantic Scholar
2753e3ffb9df83c17ee33b08b73f8d348f53a49c
Cited by
1,132
References
42
Citations by year
2026: 22 · 2025: 16 · 2024: 44 · 2023: 24 · 2022: 48 · 2021: 51 · 2020: 30 · 2019: 49 · 2018: 59 · 2017: 57 · 2016: 65 · 2015: 63 · 2014: 62 · 2013: 67 · 2012: 82
FWCI
36.39
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Deep Blue (University of Michigan) (submittedVersion)
  • CaltechAUTHORS (California Institute of Technology) (submittedVersion)
  • KiltHub Repository (submittedVersion)
  • Journal of International Crisis and Risk Communication Research (submittedVersion)
  • HAL AMU (submittedVersion)
  • HAL (submittedVersion)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • IRIS UniPA (University of Palermo) (submittedVersion, other-oa)
  • Lund University Publications (Lund University) (submittedVersion)
  • KiltHub Repository
Funders
  • National Science Foundation (0424235, 0212869, 0415581, 0417003)
  • American Heart Association
  • Conseil Régional de Bretagne
  • National Institutes of Health (1f32es012794-01, 5p01hd037105-20, P40OD010959)
  • Directorate for Biological Sciences
  • Canadian Institutes of Health Research
  • Natural Sciences and Engineering Research Council of Canada
  • Biotechnology and Biological Sciences Research Council (S19916)
  • National Human Genome Research Institute (U54HG003273)
  • National Eye Institute (R01EY011930, EY11930)
  • National Cancer Institute (R44CA093106, R43CA093106, P30CA014051, P30-CA-14051)
  • National Institute on Deafness and Other Communication Disorders (R01DC020052)
  • National Institute of General Medical Sciences (GM 61005, R01GM061464, T32GM007601, GM61464, GM058231, R01GM070840, R01GM061005, R01GM058231, GM070840)
  • National Institute of Environmental Health Sciences (R01ES006272, P42ES007381, F32-ES012794)
  • National Center for Research Resources (P40RR015044, RR15044)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (F32HD047136, P01-HD037105, HD039948, F32-HD-47136, HD14483, HD66219, HD37105, R37-HD12896, R01HD066219, R01HD028152, P01HD039948, R01HD014483)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Echinoderm biology and ecology
Keywords
Strongylocentrotus purpuratus, sea urchin genome, genome sequencing, bacterial artificial chromosome clones, heterozygosity, gene content, deuterostome evolution, echinoderm evolution
MeSH terms
Animals, Calcification, Physiologic, Complement Activation, Genes, Immunity, Innate, Immunologic Factors, Male, Nervous System Physiological Phenomena, Proteins, Transcription Factors, Signal Transduction, Cell Adhesion Molecules, Genome, Sequence Analysis, DNA, Gene Expression Regulation, Developmental, Evolution, Molecular, Computational Biology, Embryonic Development, Strongylocentrotus purpuratus

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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