The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

In the paper

“The cell signaling components present in the M. leidyi genome include the RTK family, which predates the origin of Metazoa (40); the TGF-β signaling pathway (33), thought to have evolved in the metazoan common ancestor (39); and the canonical Wnt signaling pathway (34).”

What the sources say

• ?Not checked — no full text of the sourcecites [40] source
• Supported

  Citation 33 is attached to the TGF-β pathway, not the separately cited RTK and Wnt claims. The Ligand diversity section reports a near-complete TGF-β signaling pathway in the Mnemiopsis genome, including ligands, receptors, and Smads. Page numbers were not provided in the passages. (LLM, conf=0.94)

  cites [33] source
• Supported

  The citation to this paper is attached to the canonical Wnt signaling pathway, not the RTK or TGF-β claims. The Background reports a near-complete Wnt signaling pathway in the M. leidyi genome, while the Results identify its ligands, receptors and downstream components. The paper notes that some components are missing. (LLM, conf=0.93)

  cites [34] source

In the paper

“An exception to this shared pattern with sponges is the presence of two definitive opsin genes in M. leidyi, but not A. queenslandica, that are expressed in photocytes (light producing cells), as well as in putative photosensory cells in the apical sense organ (12).”

What the sources say

• Partly supported

  The 'Mnemiopsis opsin mRNA expression' section reports expression of two opsin homologs in photocytes and the apical sense organ, and the 'Sequence retrieval for opsin phylogeny' section reports no opsin hits in Amphimedon. However, the paper identifies three putative opsin genes in M. leidyi, not two definitive ones; it demonstrates photopigment function for only MleiOpsin2. Page numbers are unavailable in our copy. (LLM, conf=0.88)

  cites [12] sourceExperimental — accuracy not yet measured

In the paper

“The pattern of presence and absence of gene families and signaling pathway components seen in previous studies is consistent with these results (32–36).”

What the sources say

• ?Not checked — no full text of the sourcecites [32] source
• Supported

  The Introduction (page not available) reports that core TGF-β pathway components occur across the metazoans studied, while receptors and ligands have not been found outside metazoans. The Pathway members section (page not available) also identifies components present and others not identified in Mnemiopsis, supporting the citation as an example of a presence-and-absence pattern. The citing paper’s own comparison with “these results” cannot be assessed from this source alone. (LLM, conf=0.85)

  cites [33] source
• Supported

  The Discussion’s ‘Ancestral metazoan gene complement’ section compares the presence and absence of Wnt-family genes and signaling components across animal groups in Table 2. It also discusses how those patterns relate to earlier analyses. This supports citing the paper as a previous study of such patterns, although the citing document’s own results are not provided for a direct comparison. (LLM, conf=0.84)

  cites [34] source
• Partly supported

  The Results (page unavailable) compare the presence of nuclear-receptor subfamilies across ctenophores, sponges and other animals, including receptors identified in previous studies. The Discussion says their limited diversity in ctenophores and sponges provides evidence for those lineages’ early branching. The paper does not address a broader pattern of signaling-pathway components, so it supports only the gene-family part of the attributed claim. (LLM, conf=0.82)

  cites [35] sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion’s ParaHoxozoa section (page unavailable) says that the presence and absence of homeodomain gene families supports a clade uniting cnidarians, bilaterians and placozoans, and relates this pattern to previous studies. The paper does not establish a corresponding pattern for signaling-pathway components, so that part of the attributed claim is unsupported. (LLM, conf=0.82)

  cites [36] sourceExperimental — accuracy not yet measured

In the paper

“This interpretation is compatible with a recent report that striated musculature evolved independently in bilaterians, cnidarians, and in the ctenophore Euplokamis dunlapae (49).”

What the sources say

• Partly supported

  The Results and discussion (page not specified) conclude that striated muscles in bilaterians and hydrozoan cnidarians very likely evolved convergently. For the ctenophore, the paper says only that this *may* apply to Euplokamis sp.; it does not identify the species as Euplokamis dunlapae or establish its independent origin. (LLM, conf=0.87)

  cites [49] sourceExperimental — accuracy not yet measured

In the paper

“We found no support in any of these analyses for Coelenterata (Cn, Ct), Diploblastica (Bi,), or Placozoa being the sister lineage to the rest of animals (Tr,) (Table 1; Fig. S1).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Table 1
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Fig. S1

In the paper

“we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi.”

In the paper

“The M. leidyi genome is among the smallest 7% of genomes when compared to those catalogued in the Animal Genome Size Database (26)”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [26]

In the paper

“The average length of an unspliced M. leidyi transcript is 5.8 kilobases.”

In the paper

“The final assembly consists of 5,100 scaffolds, resulting in 160-fold physical coverage and an N50 of 187 kilobases (SOM S3).”

In the paper

“It encodes 16,545 predicted protein-coding loci, which comprises 58% of the genome”

In the paper

“We were able to identify putative snail genes in T. inconstans and E. dunlapae, and putative GATA genes in five of the seven species.”

In the paper

“We have found instead that the branch lengths in the phylogenetic analyses of our concatenated protein matrices show M. leidyi branches to be of similar length to those of Drosophila melanogaster, therefore exhibiting high (but not extreme) amino acid replacement rates (Tables S12–13).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Tables S12–13

In the paper

“Relatively few components of the Notch pathway (Tables S15–16) are present and many of those lack key diagnostic domains.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Tables S15–16

In the paper

“The conflict between the maximum-likelihood and Bayesian analysis of the amino acid matrix make it difficult to determine from these analyses whether Ctenophora or Porifera are the sister group to the rest of the Metazoa, but there is substantial support for ctenophore as sister group to the rest of animals (Table 1).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Table 1

In the paper

“sponges and ctenophores lack a similar set of synaptic scaffolding genes (Tables S17–18), all of which are present in cnidarians and bilaterians (Fig. 5).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Tables S17–18
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Fig. 5

In the paper

“We recovered broad support for a sister relationship between Cnidaria and Bilateria (Cn, Bi) and for a clade of Placozoa, Cnidaria, and Bilateria (Tr, Cn, Bi).”

In the paper

“With a ctenophore genome in hand, we show that gene content data supports Ctenophora as the sister group to all other animals and statistically reject competing hypotheses.”

In the paper

“Notably absent from both the TGF-β and Wnt pathways are the major bilaterian antagonists; members of the Wnt/PCP pathway, such as Flamingo and Strabismus, are not present.”

In the paper

“The result of this analysis was a tree supporting Ctenophora as the sister group to all other animals (Ct,) (Fig. 4) and the rejection of all other alternative topologies (in Fig. 2) at the 5% confidence level by likelihood-based statistical hypothesis testing (Table S14).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Fig. 4
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Table S14

In the paper

“Ionotropic glutamate receptors are absent from A. queenslandica, but are present in the transcriptomes of eight other sponges (48).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [48]

In the paper

“These numbers suggest that the assembly is both complete and accurately assembled.”

In the paper

“The inconsistency of reports as to the phylogenetic position of ctenophores (Table S1) has made it difficult to evaluate morphological, developmental, and experimental data involving these animals in an evolutionary context, complicating efforts to understand the early evolution of animals.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites Table S1

In the paper

“The phylogenetic relationship of ctenophores to other animals has been a source of long-standing debate.”

In the paper

“we suspect the result is due to poor taxon sampling in the Genome Set.”

In the paper

“Nevertheless, this result is congruent with the structure and inventory of a variety of gene families and signaling pathways, as well as with genes essential to neural and mesodermal cell types.”

In the paper

“This pattern suggests that a less elaborate nervous system was present in the metazoan ancestor and was secondarily reduced in placozoans and sponges.”

In the paper

“These results indicate that, within ctenophores, the majority of absences are not specific to the M. leidyi lineage, but also that there are some intriguing differences in gene content between ctenophores”