Fig 1.
Structure of coelenterazine showing the incorporation of the amino acids phenylalanine and tyrosine.
Table 1.
List of ctenophores.
Fig 2.
Survey of conserved genes across ctenophore transcriptomes.
Dashed line indicates the maximum number of genes in this set, 248. The dotted line indicates the number of genes found in the Mnemiopsis leidyi genome. Most of the transcriptomes recovered a comparable number of genes as the genome. Species abbreviations are as follows: Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; Mlei, Mnemiopsis leidyi; Omac, Ocyropsis maculata; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
Table 2.
Percent Identity Matrix of Mnemiopsis genes and proteins.
Fig 3.
Multiple sequence alignment of Mnemiopsis proteins.
ML032920-35201 is the putative full-length protein that connects ML032920a and ML35201a. MLRB263549-p indicates it is a partial sequence, as exons are missing in the scaffolds. The consensus sequence is indicated below, where identical residues are shown by ‘*’ and similar residues are shown by ‘.’. Black boxes indicate the highly conserved residues putatively involved in iron and 2-oxoglutarate binding.
Table 3.
Top BLAST hits for FYY proteins in nr.
Table 4.
Top BLAST hits for FYY proteins in Swissprot.
Fig 4.
Multiple sequence alignment of all FYY proteins.
Alignment of all FYY proteins across ctenophores. Partial sequences were excluded to show the high degree of identity, though they were used for subsequent analysis. The iron-binding residues are indicated by the black box above the consensus line. Species abbreviations are as follows: Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Omac, Ocyropsis maculata; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
Fig 5.
Maximum-likelihood tree of all putative ctenophore non-heme oxygenase protein sequences.
Maximum-likelihood tree of all ctenophore non-heme oxygenase proteins including both FYY-containing (blue branches) and two non-FYY groups (green and purple branches). Outgroups from top BLAST hits (gold branches) and model enzymes (brown and red branches) show long branches compared to the FYY proteins. Sequence names are grayed out to emphasize branch lengths and clustering of the proteins. Scale bar indicates substitutions per site. Partial or incomplete sequences are indicated by -p as in Fig 4. Species abbreviations are as follows: Anid, Aspergillus nidulans; Bfos, Bathocyroe fosteri; Bchu, Bathyctena chuni; Baby, Beroe abyssicola; Bfor, Beroe forskalii; Binf, Bolinopsis infundibulum; Cfug, Charistephane fugiens; Cgig, Crassostrea gigas; Dgla, Dryodora glandiformis; Edun, Euplokamis dunlapae; Hrub, Haeckelia rubra; Hcal, Hormiphora californensis; Llac, Lampea lactea; Lcru, Lampocteis cruentiventer; ML, Mnemiopsis leidyi; Odio, Oikopleura dioica; Omac, Ocyropsis maculata; Otri, Oxytricha trifallax; Pbac, Pleurobrachia bachei; Scla, Streptomyces clavuligerus; Tinc, Thalassocalyce inconstans; spB, Undescribed ctenophore B; spC, Undescribed ctenophore C; spN1, Undescribed ctenophore N1; spN2, Undescribed ctenophore N2; spT, Undescribed ctenophore T; spV, Undescribed ctenophore V; Vpar, Velamen parallelum
Fig 6.
Maximum-likelihood tree of putative ctenophore photoprotein-like proteins.
Maximum-likelihood tree of recovered ctenophore photoprotein-like genes and a set of verified cnidarian and ctenophore photoproteins from Schnitzler et al. (2012) [23]. Bootstrap values above 90 are shown. Abbreviations are as in Fig 5 with a few changes and additions: Ac, Aequorea coerulescens; Aque, Amphimedon queenslandica; Am, Aequorea macrodactyla; Ap, Aequorea parva; Av, Aequorea victoria; Ba, Beroe abyssicola; Bi, Bolinopsis infundibulum; Cg, Clytia gregaria; Mc, Mitrocoma cellularia; Nvec, Nematostella vectensis; Og, Obelia geniculata; Ol, Obelia longissima
Table 5.
Percent Identity Matrix of all FYY proteins.
Table 6.
Percent Identity Matrix of all 2-oxoglutarate Fe-Group 1 proteins.
Table 7.
Percent Identity Matrix of all 2-oxoglutarate Fe-Group 2 proteins.
Table 8.
Base substitution ratios for Mnemiopsis genes.