The PROTGAMMALGF evolutionary model was used to infer the tree with branch support estimated with 100 bootstrap replicates. Robust and complex corals are shown in brown and green text, respectively, …
Coral genomic data compiled in this study and their attributes.
Here, in (A) Biomineralization, 1 = carbonic anhydrases (orange); 2 = bicarbonate transporter (green); 3 = calcium-ATPase (purple); 4 = organic matrix proteins (shown as protein structures).
Major components of the human ion trafficking system identified in the coral genomic data.
Bayesian posterior probabilities are indicated when greater than 50%. For this analysis and for the trees shown in Figure 2—figure supplements 2–4, MrBayes v3.1.2 was used with a random starting …
Bayesian posterior probabilities (×100) are indicated when greater than 50%.
Bayesian posterior probabilities (×100) are indicated when greater than 50%.
Bayesian posterior probabilities (×100) are indicated when greater than 50%.
(A) Maximum likelihood (RAxML) tree showing extensive history of duplication of genes encoding CARP 5 that predates the split of robust (brown text) and complex (green text) corals. (B) RAxML tree …
(A) ML tree of best galaxin hits from 19 coral species (brown for robust corals and green for complex corals) and 11 non-coral species (blue text). (B) ML tree of best amgalaxin hits from 13 coral …
The average composition and standard deviation of D + E is shown for the two cut-offs of these estimates. On average, corals contain >2-fold more acidic residues than non-corals. This acidification …
(A) The genome region showing the position of the HGT candidate (PNK3P) and its flanking genes. (B) Maximum likelihood trees of PNK3P (polynucleotide kinase 3 phosphatase, pfam08645) …
The bacterium-derived DEAD-like helicase genes in coral are nested within bacterial sequences, whereas the upstream host-derived gene (encoding mannosyl-oligosaccharide 1,2-alpha-mannosidase IB) is …
Robust and complex corals are shown in brown and green text, respectively, and non-coral metazoan and choanoflagellate species are shown in blue text. Photosynthetic lineages, regardless of …
Robust and complex corals are shown in brown and green text, respectively, and non-coral metazoan and choanoflagellate species are shown in blue text. Photosynthetic lineages, regardless of …
The coral glyoxalase gene gene was derived from a bacteria-specific gene type. Robust and complex corals are shown in brown and green text, respectively, and non-coral metazoan and choanoflagellate …
Robust and complex corals are shown in brown and green text, respectively, and non-coral metazoan and choanoflagellate species are shown in blue text. Photosynthetic lineages, regardless of …
The list of non-redundant anthozoan genes derived via HGT.
No. | Ancestor | Genes | Protein products | Support | Source(s) |
---|---|---|---|---|---|
1 | Coral | A. digitifera_2036 | PNK3P | 100 | CA |
2 | Coral | A. digitifera_8849 | SDR | 100 | CA |
3 | Coral | Seriatopora_31861 | DEAD-like helicase | 100 | Bact |
4 | Coral | Seriatopora_16594 | glyoxalase | 100 | CA |
5 | Coral | Seriatopora_17147 | acyl- dehydrogenase | 100 | Bact |
6 | Coral | Seriatopora_17703 | carbonic anhydrase | 96 | Dino |
7 | Coral | Seriatopora_19477 | fatty acid or sphingolipid desaturase | 100 | CA |
8 | Coral | Seriatopora_3957 | atpase domain-containing protein | 100 | Bact |
9 | Coral | Seriatopora_7060 | sam domain-containing protein | 100 | Bact |
10 | Coral | Seriatopora_7928 | atp phosphoribosyltransferase | 100 | CA/Fungi |
11 | Coral | Seriatopora_8296 | glyoxalase | 98 | Bact |
12 | Coral | Seriatopora_22596 | 2-alkenal reductase | 92 | Bact |
13 | Coral | Seriatopora_28321 | histidinol-phosphate aminotransferase | 96 | Unclear |
14 | Anthozoa | A. digitifera_418 | duf718 domain protein | 100 | CA |
15 | Anthozoa | A. digitifera_15871 | peptidase s49 | 96 | Algae/Bact |
16 | Anthozoa | A. digitifera_14520 | predicted protein | 100 | CA/Bact |
17 | Anthozoa | A. digitifera_7178 | rok family protein/fructokinase | 93 | Red algae |
18 | Anthozoa | A. digitifera_10592 | Phospholipid methyltransferase | 100 | CA/Viri |
19 | Anthozoa | A. digitifera_13390 | predicted protein | 100 | Bact |
20 | Anthozoa | A. digitifera_313 | malate synthase | 98 | CA/Bact |
21 | Anthozoa | A. digitifera_1537 | hypothetical protein | 100 | Bact |
22 | Anthozoa | A. digitifera_13577 | gamma-glutamyltranspeptidase 1-like | 100 | Unclear |
23 | Anthozoa | A. digitifera_5099 | Isocitrate lyase (ICL) | 100 | Bact |
24 | Anthozoa | A. digitifera_13467 | uncharacterized iron-regulated protein | 100 | CA |
25 | Anthozoa | A. digitifera_6866 | 3-dehydroquinate synthase | 98 | CA |
26 | Anthozoa | A. digitifera_11675 | intein c-terminal splicing region protein | 100 | Bact |
27 | Anthozoa | Seriatopora_10994 | penicillin amidase | 100 | Bact |
28 | Anthozoa | Seriatopora_14009 | nucleoside phosphorylase-like protein | 100 | Bact |
29 | Anthozoa | Seriatopora_14494 | phosphonoacetaldehyde hydrolase | 100 | Dino |
30 | Anthozoa | Seriatopora_15303 | exonuclease-endonuclease-phosphatase | 99 | CA/Viri |
31 | Anthozoa | Seriatopora_15772 | fmn-dependent nadh-azoreductase | 99 | Dino |
32 | Anthozoa | Seriatopora_19888 | had family hydrolase | 97 | Algae/Bact |
33 | Anthozoa | Seriatopora_20039 | chitodextrinase domain protein | 92 | Dino |
34 | Anthozoa | Seriatopora_20146 | glutamate dehydrogenase | 100 | CA/Bact |
35 | Anthozoa | Seriatopora_20479 | thif family protein | 100 | Bact |
36 | Anthozoa | Seriatopora_21195 | ATP-dependent endonuclease | 100 | Dino |
37 | Anthozoa | Seriatopora_8585 | chitodextrinase domain protein | 92 | Bact |
38 | Anthozoa | Seriatopora_24047 | aminotransferase | 100 | Bact |
39 | Anthozoa | Seriatopora_25961 | d-alanine ligase | 99 | Bact |
40 | Anthozoa | Seriatopora_26478 | quercetin 3-o-methyltransferase | 100 | Viri |
41 | Anthozoa | Seriatopora_29443 | diaminopimelate decarboxylase | 100 | CA |
Bact: Bacteria; CA: chlorophyll c-containing algae; Dino: dinoflagellates; Viri: Viridiplantae.
Taxonomic compilation and presence/absence in each taxon for genes involved in oxidative stress, DNA repair, cell cycle and apoptosis.
The values in parentheses show the number of taxa in which the gene sequence was recovered in the genomic database.