Fig 1.
The lanternshark Etmopterus spinax.
A-B, E: lateral views of the shark (2018 Shark Trust, www.sharktrust.org). B: lateral bioluminescence emission pattern. C: ventral and dorsal views of the shark. D: ventral bioluminescence emission pattern. F: Eye of the shark. G: histological section through the shark retina. H, J: histological sections through the shark skin. I: in vivo observation of ventral skin photophores, K: Schematic reconstruction of a photophore (modified from [95, 96]). Annotations: C: connective tissue, CTI: cellular type I, CTII: cellular type II, D: denticle, L: lens, G: ganglionic layer, E: epidermis, INL: inner nuclear layer, Ir: iris, ONL: outer nuclear layer, P: pigmented layer, Ph: photocyte, PS: pigmented shield, RL: reticulated layer.
Fig 2.
Methodological pipeline of the study performed on the lanternshark E. spinax.
Table 1.
Description of the output sequenced data.
Q20 percentage is the proportion of nucleotides with quality value larger than 20 in reads. GC percentage is the proportion of guanidine and cytosine nucleotides among total nucleotides.
Table 2.
Summary statistics of assemblies for E. spinax eye and ventral skin transcriptomes.
Fig 3.
Distribution of the assembled E. spinax unigenes in function of the number of reads to which they can be aligned.
The x-axis represents the « number of reads » classes.
Fig 4.
Comparative gene expression in E. spinax eye and ventral skin tissues.
Fig 5.
Species distribution, E-value distribution and annotation summary of the taxonomy-filtered reference transcriptome of E. spinax.
A. Species distributions of the top BLAST hits for all unigenes from E. spinax taxonomy-filtered reference transcriptome in the NR database. B: E-value distributions of NR annotation results. C. Distribution of annotation results. Unigenes of E. spinax, from the taxonomy-filtered reference transcriptome, were annotated using the NR, GO, PRIAM and Pfam databases (see text for details).
Fig 6.
Amino acid alignment of members of three opsin types found in E. spinax transcriptomes.
The selected alignment localizes to the border (vertical dotted line) between the 7th transmembrane domain and the C-terminal tail. The alignment also includes reference opsins for other metazoans Red asterisk demarcates the position of the lysine residue critical for Schiff base formation (i.e., K296 of the H. sapiens rhodopsin). The black frame indicates the “NPxxY(x)6F” pattern containing the amino acid triad, highlighted with black asterisks (i.e., positions 310–312 in H. sapiens rhodopsin). The “NxQ” motif within the amino acid triad is classically observed in visual c-opsins but is not conserved in encephalopsins. S. acanthias (Squalus acanthias (encephalopsin: HAGU01045094.1, peropsin: HAGW01023913.1), R. typus: Rhincodon typus (encephalopsin: XP_020368171.1, peropsin: XP_020384809), H. sapiens: Homo sapiens (rhodopsin: NP000530.1, peropsin: NP006574.1), L. erinacea: Leucoraja erinacea (rhodopsin: P79863.1), M. musculus: Mus musculus (encephalopsin: AAD32670.1), C. milli: Callorhinchus milli (encephalopsin: XP_007892106.1, peropsin: XP_007895211), G. melastomus: Galeus melastomus (rhodopsin: O93441), S. canicula: Scyliorhinus canicula (rhodopsin: O93459.1), C. conger: Conger conger.
Fig 7.
Metazoan opsin phylogenetic tree including the E. spinax opsins.
Predicted E. spinax opsin proteins were included in a large opsin phylogeny (i) to ensure their opsin status and (ii) define their belonging to known classical opsin groups. Phylogeny was constructed using the Bayesian method (MrBayes software, v.3.2.2). Branch support values are indicated by color-codes next to the branching points and correspond to posterior probabilities. Branch length scale bar indicates relative amount of amino acid change. C-opsins: Ciliary opsins, R-opsins: Rhabdomeric opsins, RGR opsin: Retinal G-protein coupled receptors, Outgroup (black): melatonin receptor.
Fig 8.
Predicted light-interacting toolkit genes within E. spinax eye and ventral skin.
Fig 9.
Encephalopsin immunodetection in E. spinax.
A. photosensitive film of immunoblotting performed on the protein extract of E. spinax ventral and dorsal skin as well as retina with an antibodies directed against extraocular opsin: anti-encephalopsin PAb from Genetex, GTX 70609, lot number 821 400 929, 1/2000. 50 μg of total protein were used in each well. B. Cryosection immunofluorescence directed against extraocular opsins in different tissues of the lanternshark, E. spinax. Visualization of a photophore paraffin section (A). Visualization of the labelling on cryosections of a ventral skin section with photophores (B), a section of the retina (C). The B and C sections were given the primary antibody GTX (primary antibody: anti-encephalopsin PAb from Genetex, GTX 70609, lot number 821 400 929, 1/50). The secondary antibody was coupled with a red fluorochrome (Alexa Fluor 594 Goat Anti-Rabbit IgG (H+L) Antibody, highly cross-adsorbed (A-11037), 1/300 from Life Technologies Limited). C, conjunctive tissue; E, epidermis; Ir: iris-like structure related pigmented cell; L, lens cell; Ph: photocyte; Ps: pigmented sheath; D: dermal denticle; R: rod, C: cone layer. Scale bar: 50 μm.