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Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Open accessAbstract
Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis . The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
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In the paper
“Nearly one-fifth of the genes of the ancestor are eumetazoan novelties in the sense that they have no recognizable homologs outside of animals, or contain new protein domains and/or domain combinations that are not found in other eukaryotes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
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In the paper
“The anemone genome is surprisingly complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Abstract
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In the paper
“In contrast, only 33 genes are found in Nematostella and both Drosophila and C. elegans but not in any vertebrate, representing putative deuterostome or vertebrate loss, indicating a much lower degree of gene loss in the vertebrates than in the ecdysozoan model systems.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“Surprisingly, the human genome has many more such orthologous pairs with Nematostella (6,989) than with nonvertebrate bilaterians, including Drosophila (5,772), C. elegans (4,846), and even the invertebrate chordate Ciona intestinalis (6,313).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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“Combining homology-based and ab initio methods with sequences from over 146,000 expressed sequence tags, we predicted ~27,000 complete or partial protein-coding transcripts in the genome (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“After correcting for sampling, we estimated that each pair of haplotypes differ at 0.65% of nucleotide positions (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“Althought many eumetazoan introns are evidently of ancient eukaryotic origin (46) --for example, nearly 26% of human and Nematostella introns are conserved with Arabidopsis, and 24% with Cryptococcus --the remainder appear to be shared only by animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [46] source
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In the paper
“Of the 7,766 ancestral eumetazoan gene families, only 72% (5,626) are represented in the complete genomes of all three major modern eumetazoan lineages: cnidarians (i.e., Nematostella), protostomes (i.e., Drosophila and/or C. elegans), and deuterostomes (requiring presence of at least two of pufferfish, frog, and human).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“To approximate the gene repertoire of the eumetazoan ancestor we constructed 7,766 putatively orthologous gene families that are anchored by reciprocal best-scoring BLAST alignments between genes from anemone and one or more of fly, nematode, human, frog, or fish [S].”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“Over 500 families of them were discovered in the genome, including DNA transposons and both LTR and non-LTR retrotransposons (Table S2.3).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
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- It may state two separate claims as one. 83
- Probably not a substantial claim. 55
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In the paper
“The total assembly spans ~357 Mb, with half of this sequence in 181 scaffolds longer than ~470 Kb.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
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In the paper
“The emerging picture is one of surprising conservation in gene content, structure, and organization between Nematostella and vertebrates, even to the point of retaining chromosome-scale gene blocks whose linkage in modern genomes has been preserved from the genome of their common ancestor.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
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In the paper
“We estimate that the Nematostella genome contains ~18,000 bona fide protein-coding genes, comparable to gene counts in other animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
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In the paper
“The depth of the Nematostella-Hydra split (comparable to the protostome-deuterostome divergence) emphasizes the distant relationship between anthozoans and hydrozoans.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
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In the paper
“Althought many eumetazoan introns are evidently of ancient eukaryotic origin (46) --for example, nearly 26% of human and Nematostella introns are conserved with Arabidopsis, and 24% with Cryptococcus --the remainder appear to be shared only by animals.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [46]
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In the paper
“We found 673 gene families represented in model protostomes and vertebrates, but not in Nematostella.These are candidates for bilaterian novelties.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“We also generated ~15,000 ESTs from the ctenophore (comb jelly) Mnemiopsis leidyii to attempt to place this enigmatic phylum on the tree, but could not resolve its precise phylogenetic position with significant support (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [32]
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In the paper
“From the shotgun assembly and the analysis of alignments between shotgun reads, we measured a rate of single nucleotide polymorphism among the four haplotypes as 0.8%, or ~1/125 bp, approximately ten times the SNP rate in the human population.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
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In the paper
“Within alignable regions, nearly 81% of human introns are found in the same position and phase in Nematostella, and conversely 82% of the anemone introns are also found in orthologous positions in human genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
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In the paper
“Not only are the number of exons per gene similar between Nematostella and vertebrates, but the precise location and phase (i.e., the positioning of the splice sites relative to codon boundaries) of introns are also highly conserved between anemone and human.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
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In the paper
“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).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
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In the paper
“Intron-containing genes that are descended from the ancestral eumetazoan gene set in humans and anemones have a median of ~8 and ~6 introns per gene respectively, while those from fruit fly have only ~3.(32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [32]
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In the paper
“1,292 eumetazoan gene families have detectable descendents in anemone and at least two of the three vertebrates, but appear to be absent in both fruit fly and soil nematode, and were therefore either lost (or were highly diverged) in both of these model protostomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > The ancestral eumetazoan gene set
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In the paper
“While ~22,000 of all predicted genes have a significant alignment (BLAST e-value < 1e-10) to known proteins in SwissProt/Trembl and therefore have some homology support, analysis of a random sampling of genes suggest that some of these appear to be gene fragments, possible pseudogenes, or relics of transposable elements, leading to a discounting of the true gene count to ~18,000 (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Nematostella gene set
What the sources say
- Not checked yetcites [32]
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In the paper
“While approximately one-third of the shotgun sequences were not assembled, they could typically be characterized as derived from long (>100 Kb) tandem-repetitive minisatellite arrays suggestive of heterochromatin, implying a total genome size of ~450 Mb (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
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In the paper
“Despite the fact that flies and nematodes share a more recent common ancestor with human than sea anemones do, we find that the anemone peptides are more similar to human than to either of the model protostomes (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
What the sources say
- Not checked yetcites [32]
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In the paper
“In contrast, the fruit fly and nematode model systems have experienced significant gene loss, intron loss, and genome rearrangement.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
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In the paper
“Some, such as Wnt, SFRP, dpp/BMP, activin and chordin are Type I novelties with no homology to proteins from outgroups”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Caveolin, a membrane adapter that couples the integrin a subunit to Fyn is present in the Nematostella genome and is a Type I novel protein”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
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In the paper
“These include important signaling factors, like the secreted wingless (Wnt) and fibroblast growth factor (FGF) families, and transcription factors, including the T-box and mothers-against-decapentaplegic (SMAD) families (Table 5b).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
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In the paper
“The 40 human segments that show conserved synteny with Nematostella cover half of the human genome; within such human segments, typically 40-50% of eumetazoan-derived genes have counterparts in syntenic Nematostella segments, and vice versa.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“Nematostella has several clusters of homeobox genes (56)(57)(58), but only those on scaffolds 3 and 61 are embedded within the ancestral eumetazoan Hox context, providing independent support for the assignment of these homeobox genes as bona fide Nematostella Hox genes (54,56,59).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
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In the paper
“type II receptors turn out to be ancient eukaryotic kinase genes that were co-opted for this function”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
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In the paper
“Tetrapods have four Hox clusters that arose by duplication on the vertebrate stem --HoxA (human chromosome 7p15.2),HoxB (17q21.32),HoxC (12q13.13),and HoxD (2q31.1)--which all appear in the same eumetazoan PAL, linked to eight Nematostella scaffolds (Figure 4d).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“consist of animal genes whose domains are all ancient (i.e., each found in other eukaryotes) but which occur in apparently unique combination in eumetazoa relative to known non-animal genes (32)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“The eumetazoan genes of ancient eukaryotic ancestry are themselves descended from approximately ~5,148 eukaryotic progenitors by nearly one thousand gene duplications along the eumetazoan stem, that is, after the early radiation of eukaryotes ~1100-1500 Mya (60) but prior to the divergence of cnidarians and bilaterians (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
What the sources say
- Not checked yetcites [60] source
- Not checked yetcites [32]
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In the paper
“Remarkably, we find that not only is the organization of the Hox cluster itself preserved, but that there is an extensive block of 225 ancestral genes (Table S7.3) that were linked to Hox in the eumetazoan ancestor and have (independently) retained that linkage in both the modern human and anemone genomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“Surprisingly, despite extensive local scrambling of gene order, we find extensive conservation of synteny between the Nematostella and vertebrate genomes, allowing the identification of ancient eumetazoan linkage groups.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
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In the paper
“Alignment 1 consists of 19,563 columns, with no missing data.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
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In the paper
“We identified 809”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
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In the paper
“There are 242 clusters of tandemly duplicated genes, comprising 2-13 members, with annotated Pfam domains, which apparently were duplicated after split of bilateria”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Troyka retrotransposons are present also in sea urchin, and the hAT5 and hAT6 transposons are wide spread in sea urchin, sea squirts and lancelet.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
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In the paper
“The large set of all predicted models was reduced to a non-redundant set of 27,273 representative models (Filtered Models), where every locus is described by a single best gene model according to the criteria of homology and EST support.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
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In the paper
“There are 5 large clusters of short proteins (around ~100aa), each comprising 55-74 members with weak similarity to hypothetical short ORFs from fungi (28)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
What the sources say
- Not checked yetcites [28]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For Nematostella, this curve shows a large excess, exceeding the human curve for values of Cmin > 0.5, while falling below human at high Cmin values.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Human Genes Sharing Ancestry with Nematostella Genes
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In the paper
“The five elements lacking notes are not identified by either of these methods.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Repeat sequences reconstructed from unassembled WGS reads
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In the paper
“10 families of tandemly repeated sequences were identified which occur in arrays longer than fosmidlength and account for 32% of the WGS data set.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Repeat sequences reconstructed from unassembled WGS reads
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In the paper
“All nodes were resolved as shown in 100% of the samples trees.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
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In the paper
“Some are novel pairings of ancient domains (such as neuropilin and Lim-homeobox genes)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
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In the paper
“In addition to olfactory and taste receptors, the human genome shows strong recent preference of C2H2 zinc finger genes with a KRAB domain, keratin, and immune defence proteins.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
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None of the sources cited for this claim have been checked yet.
In the paper
“we assigned GO (25) terms to 12,786 proteins, 16,625 (78%) proteins to KOG clusters (26), and 695 distinct EC numbers were assigned to 2,822 proteins mapped to KEGG pathways (27).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
What the sources say
- Not checked yetcites [25]
- Not checked yetcites [26]
- Not checked yetcites [27]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The anemone genome is also populated by a novel superfamily of eukaryotic”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesThe quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Transposable elements (TEs) constitute more than 26% of the assembled sea anemone genome (Table S2.3) and belong to >500 families.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While the anemone 10,632-bp EnSpm-1_NV and 9,347-bp EnSpm-2_NV transposons encode transposases (TPase) similar to the plant En/Spm TPase and are flanked by 3-bp targets site duplications typical for known En/Spm elements”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of these, the first had the highest likelihood score, but it was not significantly better than the second in a Shimodaira-Hasegawa test.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
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In the paper
“the anemone genome contains several families of RTE-like elements, RTEX in Fig. S2.1, which are longer than canonical RTE elements and contain an additional ORF at their 5' terminal portion that codes for the esterase domain, analogously to elements from the CR1/L2 clade (20).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [20] source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Certain enzymes important in synaptic transmission (e.g.DOPA-beta monooxygenase) and some vesicular trafficking proteins (e.g.synaptophysin) appear as completely novel (Type I) eumetazoan proteins”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“others are novel animal genes (e.g., Hes, Gcm, netrin, semaphorins, dachsund)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Emergence of the neuromuscular system
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one. The quote only partly states this claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There are 9 neurotoxins genes, with an anemone neurotoxin domain (PF0076) previously found only in the Cnidaria, but not previously in Nematostella, and 5 copies of green fluorescent protein (PF01353), originally found in jellyfish and predominantly found in Cnidaria.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional observations on the Nematostella proteome
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“146,095 ESTs were clustered into 30,813 consensus sequences and both individual ESTs and consensus sequences were mapped onto genome assembly using BLAT (10).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
What the sources say
- Not checked yetcites [10] source
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The genome of Nematostella vectensis includes 27,273 predicted gene models built using the JGI Annotation Pipeline, described below.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Alignment 2 consists of 19,977 columns, however only 2272 columns contain Mnemiopsis sequence.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The complete set of these numbers of shared orthologous genes are shown in figure S7.3, for all scaffolds (67/147) and segments (40/98) which participated in a statistically significant shared synteny relationship.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Table S7.3 has 112 yellow cells, corresponding to 112 cases of statistically significant conservation of synteny between a Nematostella scaffold and a segment of the human genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In 2,347 cases, a human gene was found to have a mutual best hit to both a Nematostella and an Arabidopsis gene, forming a tentative cluster of orthologous genes to be studied further.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For human-Nematostella, we found no strict significant conservation of gene order, but by choosing a large value of Nmax we nonetheless detect regions of conserved linkage in which the local gene order has been scrambled.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The rows and columns of this table have been ordered to reveal 13 sets of scaffolds and chromosome segments, defined by the criterion that none can be subdivided without separating into different sets a scaffold-segment pair with significant evidence (p<0.01) for conserved synteny.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we find 26.5% of all Nematostella introns and 26.1% of all human introns are shared with Arabidopsis”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The rate of single nucleotide polymorphism observed in the assembled genome sequence is 0.8%.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Figure S2.1: Observed density of polymorphic sites
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nematostella has the most introns at these conserved positions, followed by human with a relative intron frequency of about 0.91, whereas nematode and in particular fly have considerably fewer introns (0.37 and 0.21).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Using Nmax = 40 and considering only segments of 9 or more participating genes, we find 33 such segments of conserved synteny between human and Nematostella, with none expected by chance, as seen by running the algorithm on the scrambled set.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Table S7.X lists the 255 ancestral gene clusters linked with the HOX clusters in PAL-A.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“At this stage we were left with 11,351 pairwise hits, involving 6,986 nematostella genes and 8,426 human genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The conclusion is that 2N = 30, the same number as in Hydra.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The genes of the HOX C cluster fall into such a large family, but have been labeled to show the position of the HOX cluster.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“integrin a and integrin b (the former being a Type I novelty and the latter a Type II novelty).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that the nematode, although having retained only ~23% of the introns since the LCA with human have ~37% of the number of human introns.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“The other Cnidarian classes are united by their pelagic medusae and uniquely linear mitochondrial genomes (9) into the Medusozoa, including Hydra and related hydroids, jellyfish, and box jellies.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [9] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Similarly, we can characterize the genome of this long-dead eumetazoan progenitor by comparing modern DNA and protein sequences and identifying conserved features in different modern lineages.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“To probe the ancestral eumetazoan genome requires sequences from even deeper branches of the animal tree, comparing bilaterian and non-bilaterian phyla.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Some of the oldest animal body fossils (e.g., the Ediacaran Charnodiscus (10) but see also (11,12)) and fossil embryos (13) are plausibly relics of stem cnidarians, suggesting a Precambrian origin for the phylum.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“This eumetazoan ancestor lived perhaps seven hundred million years ago, but is not preserved in the fossil record (3).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [3]
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Among Anthozoan cnidarians, the starlet sea anemone Nematostella vectensis is an emerging model system (14,15).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [15]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Our ability to recognize ancient genomic features depends on the availability of sequences from diverse living animals, and can only illuminate genomic characteristics that have an intrinsically slow rate of change and/or are preserved by selective pressures.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“This estuarine burrowing anemone is found on the Atlantic and Pacific coasts of North America, as well as the coast of southeast England (16) (Figure 1).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [16]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Comparison of Nematostella genes to those of other animals reveals that the ancestral eumetazoan genome must have been intron-rich, with gene structures closely resembling those of modern vertebrate and anemone genes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“The source population for the genome sequence (Rhode River, Maryland) appears typical in this regard (37).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [37] source
Strength:hedged· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Nematostella cultures are easily maintained in the laboratory.With separate sexes, inducible spawning, and external fertilization (14,17), embryos are available throughout the year.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [17]
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The relatively low level of intra-specific genetic variation in Nematostella vs. marine broadcast spawners might be explained if its estuarine habitat limited gamete dispersal and led to a smaller efective population size.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This is of course only a very rough estimate with numerous caveats, most notably that there is no guarantee that the rate of protein evolution was constant on the eumetazoan stem, but provides a rough time scale for the eumetazoan radiation.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Rests on an assumption: The rate of protein evolution was constant on the eumetazoan stem for the molecular clock estimate.
In the paper
“To avoid contamination from commensal microbes common to adult anemones and minimize the impact of haplotypic variation, we prepared genomic DNA from the larvae of a single mating pair originally isolated from the same lagoon (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
In the paper
“Genetic fingerprinting of wild Nematostella populations indicates a high degree of genetic structuring at fine spatial scales, implying extremely low levels of gene flow between neighboring estuaries (36).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
What the sources say
- Not checked yetcites [36]
Strength:hedged· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Currently there are no physical or genetic maps of Nematostella, so we could not reconstruct the genome as chromosomes.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The egg mass may be a derived feature of Nematostella that is related to its colonization of the estuarine environment.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Genome Sequencing and Assembly
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Analysis of the Nematostella genome in the context of sequences from other eukaryotes reveals the genomic complexity of this last common cnidarian-bilaterian ancestor, and begins to illuminate the rich history of genes and gene networks already present at the base of the animal tree of life.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Introduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Intron conservation can be unambiguously assessed by identifying well-aligned regions of orthologous proteins that are interrupted by introns in one or more species (Figure 3a).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This supports the paleontological evidence that the radiation of the cnidarian phylum is quite ancient, and suggests that significant variation in gene content and gene family diversity may be found when the anemone genome is compared with that of the hydrozoan Hydra.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Molecular evolution of the Eumetazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Between animal phyla, however, no significant large-scale conserved synteny has been identified, suggesting that signals of the ancestral eumetazoan genome organization were erased by subsequent chromosomal breaks and translocations along the various lineages.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“Cell-cell adhesion mediated by cell-ECM interactions is a hallmark of animal multicellularity (63)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
What the sources say
- Not checked yetcites [63]
Strength:boosted· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Animals rely on cell-cell signaling for cellular coordination during and after development (64)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Signaling Pathways
What the sources say
- Not checked yetcites [64] source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These are evidently members of ancient eukaryotic gene families that were already established in the unicellular ancestors of the metazoa, and are involved in core eukaryotic cellular functions including amino acid, carbohydrate, and lipid metabolism; small molecule and ion transport; DNA replication, core transcriptional machinery, RNA processing, and translation; intracellular vesicular Traffick”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Origins of eumetazoan genes
Load-bearingStrength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The human genome was selected as a reference since it is known to have a slow rate of chromosome evolution relative to other mammals (52), and has preserved chromosomal segments relative to teleost fish (48).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [52]
- Not checked yetcites [48]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“In Bilateria, the integrin pathway mediates signaling from the extracellular matrix (ECM) that elicits various responses to modulate cell adhesion, motility, and the cell cycle”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Cell Adhesion
What the sources say
- Not checked yetcites Giancotti and Caveolin
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“to generate organismal novelty such new genes must be integrated with other novel and existing genes to evolve expanded or modified biochemical pathways and/or regulatory networks”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Eumetazoan networks and pathways
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“We can rule out ancient loss in the protostome lineage based on the results of Raible et al. (2005) for Platynereis, which in combination with our analysis shows that the ancestral protostome genome was also intron-rich.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites Raible et al. (2005)
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Conserved linkage groups representing ancestral vertebrate chromosomes can be defined by comparing fish and mammalian genomes and genetic maps, despite the presence of only modest segments of conserved gene order (48,49).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [48]
- Not checked yetcites [49] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Thus assuming ~8 introns per ancestral gene, ~1 novel intron has been introduced in a typical modern animal gene since the eumetazoan radiation, a rate of approximately ~10 -9 introns/gene/year, which is comparable to the rate of nucleotide substitution and gene duplication (47).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
What the sources say
- Not checked yetcites [47]
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Five PALs link Nematostella scaffolds to single human chromosome regions, which suggests that the vertebrates specific duplicates of these segments have been lost or fused and dispersed among other chromosomes (32).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [32]
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We cannot rule out the possibility, however, that such apparently animal-specific introns were in fact present in the last common ancestor of plants, fungi, and animals, but were convergently lost in both plants and fungi.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan introns
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Similarly, limited conservation of synteny is recognizable within insects (e.g., between flies and bees (50)).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
What the sources say
- Not checked yetcites [50] source
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The surprising extent of this conserved linkage suggests that either the neutral rate of inter-chromosomal translocations is low (on the order of a few breaks/fusions per chromosome since the eumetazoan ancestor, excluding intra-chromosomal rearrangements), or that selection has acted to maintain linkage of large groups of genes for unknown reasons.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Conservation of ancient eumetazoan linkage groups
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Modern animal genomes retain features inherited from the eumetazoan ancestor that have been elaborated on, and sometimes overwritten by, subsequent evolutionary elaborations and simplifications”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: Processes conserved between living species were likely functional in their common ancestor.
None of the sources cited for this claim have been checked yet.
In the paper
“We see from Figure 2b that the cnidarian-bilaterian split lies ~30% of the way between these two nodes (adopting the midpoint rooting as shown), suggesting that the eumetazoan ancestor lived between 670 and 820 Mya.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“gene regulatory changes can also play a central role in generating novelties, allowing co-option of ancestral genes and networks to new functions (67)”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
What the sources say
- Not checked yetcites [67]
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We compared the results obtained with this set with those obtained using Nematostella rather than human as the anchor for identifying orthologs, and found that it did not change the results.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“All known RTE elements, including those in plants, insects, nematodes, and vertebrates, contain only one ORF and are characterized by extremely frequent 5' truncations of the RTE elements during their retrotransposition.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
- Not checked yetcites [19]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Among DNA transposons, the hAT superfamily is well-known for TSDs that are always 8 bp long (14).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
Strength:boosted· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“these may have arisen by sequence divergence from ancient eukaryotic genes, but the trail is obscured by deep time”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Concluding remarks
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“FGENESH was trained on this set to achieve sensitivity and specificity of 81% and 80%, respectively.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S3
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. The quote only partly states this claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Multiple runs from different starting topologies all converged on the same topology, branch lengths and posterior probabilities for protein evolution model parameters within approximately 10,000 monte carlo iterations.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Phylogenetic analysis of metazoa
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
In the paper
“all known LTR retrotransposons, including retroviruses, are defined by 4-6 bp TSDs (14).”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Transposable elements in the sea anemone genome
What the sources say
- Not checked yetcites [14]
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that this analysis is biased towards vertebrates, for which more domains have been characterized.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Lineage Specific Expansions
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This approach enriches the set for orthologous gene pairs while removing weak super-family similarities from the analysis.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Since we compared 147 scaffolds with 98 segments, we applied a Bonferroni correction factor of 1/14406.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Construction and Significance Testing of Putative Ancestral Linkage groups (PALs)
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
- The authors state this as an assumption: The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These large genes families are more likely to have members showing spurious conserved synteny, since they may have members in many regions of the genome.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The number of chromosomes was determined by analysing over 90 metaphase plates in spreads.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > 1: Four-way intron conservation comparison
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which translate into maximum intron gains of ~9% in human and ~7% in Nematostella.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In a similar fashion, we estimate a loss of almost 22% along the human lineage, twice the amount of introns lost in the Nematostella lineage.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Strength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: Intron losses have occurred independently in the human and Nematostella lineages.
- The authors state this as an assumption: The probability of independent intron insertion events at the same location is negligible.
In the paper
“The parsimony assignment of characters to internal nodes is independent of this gain/loss weight ratio.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Methods for Intron Gain/Loss tree
What the sources say
- Not checked yetcites [40]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: The phylogenetic topology onto which intron characters were projected is correct.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Note that this method does not require strict conservation of gene order: inversions on scales smaller than Nmax are tolerated.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“For both Panther Pathways and Pather Ontology, we limited our tests to the 100 ontology terms which had the greatest number of inferred ancestral genes assigned to them, and applied a Bonferroni correction for 100 tests, even though this is somewhat conservative, since the categories have significant overlap.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Functional annotation of ancestral gene clusters
What the sources say
- Not checked yetcites [44]
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“After traversing all alignments, we have a set of conserved regions, on which we can impose a minimum member limit (typical 3 pairs) to remove potentially spurious regions.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“From these numbers we estimate the intron losses in fly, nematode, and human since their LCA to be 82% , 77%, and 12% respectively.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“In order to detect the significance of these regions, we randomly scrambled the order of the genes on each chromosome or scaffold and applied, for the same sequence alignment data, the algorithm to the scrambled data set.This allows us to choose parameters to minimize false positive detection.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Additional information
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To the extent that the introns in highly conserved peptide regions studied here are representative of introns in general, the above analysis suggests that the Nematostella genome has only lost 11% of its introns since the LCA with human, and gained at most 7%.”
§ Sea anemone genome reveals the gene repertoire and genomic organization of the eumetazoan ancestor > Supplement S6 Intron Splice Site Conservation
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- The authors state this as an assumption: The introns in highly conserved peptide regions studied are representative of introns in general.
The paper relies on this without support.
The rate of protein evolution was constant on the eumetazoan stem for the molecular clock estimate.
“there is no guarantee that the rate of protein evolution was constant on the eumetazoan stem”
The paper relies on this without support.
The null model in which scaffolds and human segments have gene content independently drawn from the ancestral set is appropriate for testing conserved linkage.
“This number of shared orthologous genes was compared to a null model in which the scaffolds and segments have gene content independently drawn from the ancestral set.”
The authors state this as an assumption.
Processes conserved between living species were likely functional in their common ancestor.
“using the basic principle of evolutionary developmental biology: processes that are conserved between living species were likely functional in their common ancestor”
The paper relies on this without support.
The eumetazoan ancestor was the progenitor of all extant animals with nervous systems.
“The eumetazoan ancestor was the progenitor of all extant animals with nervous systems”
The paper relies on this without support.
Present-day cnidarians lack a clear mesoderm.
“present-day cnidarians lack a clear mesoderm”
The paper relies on this without support.
Many genes involved in mesoderm development are associated with basic patterning and/or regulation of cell migration and fate.
“many of these genes are associated either with basic patterning functions and/or the regulation of cell migration and fate”
The paper relies on this without support.
Cnidarians and ctenophores are the earliest branching metazoan phyla with a nervous system.
“Cnidarians and ctenophores are the earliest branching metazoan phyla that have a nervous system”
The authors state this as an assumption.
The estimates of tandem array sizes depend on normal cloning behavior for repetitive sequences.
“These estimates depend on the assumptions of”
The authors state this as an assumption.
Any gene has an equal probability of getting duplicated and fixed in the population.
“We then formulated a neutral-evolution hypothesis that any gene has an equal probability of getting duplicated and fixed in the population.”
The authors state this as an assumption.
Intron losses have occurred independently in the human and Nematostella lineages.
“Assuming that intron losses have occurred independently in the human and nematostella lineages”
The authors state this as an assumption.
The probability of independent intron insertion events at the same location is negligible.
“and that the probability of independent intron insertion events at the same location is negligible”
The authors state this as an assumption.
The introns in highly conserved peptide regions studied are representative of introns in general.
“To the extent that the introns in highly conserved peptide regions studied here are representative of introns in general”
The paper relies on this without support.
The phylogenetic topology onto which intron characters were projected is correct.
“projecting these characters onto the (known) topology.”
The authors state this as an assumption.
The null model treats the genes in scaffolds and segments as independently drawn from the 7,766 ancestral genes.
“a null model in which scaffolds and segments comprise genes descending from genes drawn independently from the set of 7,766 ancestral genes.”
The authors state this as an assumption.
The centroid sequence is a surrogate for the peptide sequence ancestral to each orthologous cluster.
“This provides a surrogate for the peptide sequence that is ancestral to each cluster.”
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Cnidarians seem to possess almost the complete bilaterian regulatory gene tool kit, including anterior and posterior hox genes (Finnerty et al. 2004; Putnam et al. 2007) and generate many of the ectodermal, neuronal, endodermal, and mesodermal differentiated cell types also found in bilaterians.”
From An integrated view of precambrian eumetazoan evolution (2009) · cites this paper as Putnam et al. 2007
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“scaffold-level genome assemblies revealed surprising syntenic conservation over hundreds of millions of years of evolution, spanning the divergence between cnidarians, chordates, sponges, and placozoans”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [40]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“in development of the most basal cnidarian clade, anthozoans, regulatory genes are expressed in bilateral axial patterns that indicate an underlying set of bilateral regulatory states.”
From An integrated view of precambrian eumetazoan evolution (2009) · cites this paper as Putnam et al. 2007
The cited source says what the claim attributes to it.
In the citing paper
“Genome sequences of some animal clades very distantly related to humans, including sponges (37), placozoans (flat animals) (38), and cnidarians (i.e., true jellyfish, corals) (39, 40), suggested that many genes thought to define vertebrates were, in fact, present even in earlier ancestral animals”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [40]
In the citing paper
“The publication of several cnidarian genomes has shown that much of the molecular architecture underlying neurogenesis and neuron functioning is conserved between bilaterians and cnidarians [17,47–51].”
From Evolution of eumetazoan nervous systems: insights from cnidarians (2015) · cites this paper as [17]
In the citing paper
“The sequencing in recent years of the whole genome of different cnidarian species, most notably those of the anthozoan Nematostella vectensis and the hydrozoan Hydra magnipapillata (Figure 1) [50,51], has offered the exciting possibility to quickly gather an overview on the entire complement of receptors in these species.”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [50]
In the citing paper
“Reflecting this ancestral core, cnidarian genes are often more similar to vertebrate genes than vertebrate genes are to those of more diverged animals like Caenorhabditis or Drosophila [50,109].”
From Back to the Basics: Cnidarians Start to Fire (2017) · cites this paper as [50]
In the citing paper
“Morphological and phylogenetic evidence makes the cnidarian polyps an ideal proxy to the 'prebilaterian eumetazoan' body organization, and cnidarian model systems reveal evolutionary ancestry of bilaterian characters 15,16 .”
From Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans (2014) · cites this paper as [16]
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.
Intron analysis gives two sample sizes
MajorThe main-text figure description reports 5,175 introns for the seven-species analysis, whereas the methods report 4,342 introns at the same 2,645 aligned positions across seven genomes.
“Based on a sample of 5175 introns at highly conserved protein sequence positions from Arabidopsis thaliana (Plant), Crytococcus neoformans (Fungus), C. elegans (Nematode), D. melanogaster (Fly), Ciona intestinalis (Sea squirt), Homo sapiens (Human), and Nematostella (32).”
“4342 introns from the seven genomes at 2645 aligned positions which contain an intron in at least one of the seven orthologs.”
Hox-linked ancestral cluster count differs
MinorThe text and the Table S7.3 caption give 225 ancestral genes or clusters linked to the Hox region, but a supplemental description gives 255 for that linkage group.
“there is an extensive block of 225 ancestral genes (Table S7.3) that were linked to Hox in the eumetazoan ancestor”
“Table S7.X lists the 255 ancestral gene clusters linked with the HOX clusters in PAL-A.”
Supplement assigns two different contents to Table S7.3
MinorOne passage describes Table S7.3 as a colored synteny grid with 112 significant cells; its caption instead identifies it as a list of 225 Hox-linked ancestral gene clusters.
“Table S7.3 has 112 yellow cells, corresponding to 112 cases of statistically significant conservation of synteny between a Nematostella scaffold and a segment of the human genome.”
“Table S7.3:The 225 ancestral gene clusters linked with the HOX clusters in PAL-A:”
Table S7.2 is described as both complete and limited to three groups
MinorThe text says Table S7.2 shows all 13 ancestral linkage groups, while its caption says the grid covers only groups A, B, and C.
“The complete Oxford grid showing all 13 PALs is shown in Table S7.2.”
“Table S7.2:Complete Oxford Grid for Human-Nematostella comparison "Oxford grid" which tabulates the number of ancestral gene clusters shared between the 22 Nematostella scaffolds (columns) and 14 segments of the human genome (rows) that are assigned to PALs A, B and C.”
KOG annotation percentage uses an inconsistent denominator
MinorThe stated 16,625 KOG-assigned proteins are 61.0% of the 27,273 representative models, not 78%. No alternative denominator is identified for this percentage.
Reported 78 · recomputed 60.957724
“For this set of representative gene models we assigned GO (25) terms to 12,786 proteins, 16,625 (78%) proteins to KOG clusters (26), and 695 distinct EC numbers were assigned to 2,822 proteins mapped to KEGG pathways (27).”
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Metadata
- Authors
- Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., Jurka, J., Genikhovich, G., Grigoriev, I. V., Lucas, S. M., Steele, R. E., Finnerty, J. R., Technau, U., Martindale, M. Q., & Rokhsar, D. S.
- Affiliations
- Genetic Information Research Institute (US)
- Corresponding author
- Rokhsar, Daniel S.
- ORCID
- Venue
- Science
- Published
- 2007-07-06
- Volume
- 317
- Issue
- 5834
- Pages
- 86-94
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2067558229
- Semantic Scholar
- 0b61b3a2a55b156bb026a4c83d26d9b95c5af753
- Cited by
- 1,555
- References
- 71
- Citations by year
- 2026: 27 · 2025: 30 · 2024: 52 · 2023: 48 · 2022: 66 · 2021: 49 · 2020: 73 · 2019: 72 · 2018: 84 · 2017: 81 · 2016: 89 · 2015: 97 · 2014: 89 · 2013: 83 · 2012: 110
- FWCI
- 103.09
- Type
- journal article
- Language
- en
- Open access
- green
- www.osti.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- Funders
- U.S. Public Health Service (THL007279F)
- U.S. National Library of Medicine (P41LM006252)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- 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
- Keywords
- Nematostella vectensis, Cnidaria, genome evolution, gene repertoire, exon-intron structure, genetic linkage, comparative genomics, signal transduction, adhesion, synaptic transmission, animal evolution
- MeSH terms
- Animals, Cell Adhesion, Biological Evolution, Genes, Multigene Family, Humans, Introns, Genetic Linkage, Muscles, Nervous System Physiological Phenomena, Phylogeny, Sea Anemones, Signal Transduction, Genome, Human, Genome, Sequence Analysis, DNA, Evolution, Molecular, Genomics, Synteny, Metabolic Networks and Pathways
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.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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.
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