Fig. 1.

Cone and rod opsin gene expression in larval and adult deep-sea fishes. (A) Simplified phylogeny of the 20 deep-sea fish species for which the retinal transcriptomes were sequenced (topology after Betancur et al. 2017). Boxes highlight the five species for which both larval and adult samples were available. (B) Proportional opsin gene expression for each individual (horizontal bars) at different developmental stages. Different colors correspond to cone (colors) or rod (shades of grey) opsin genes, depicted as the proportional expression over the total sum of visual opsins expressed. Different shades of the same color represent multiple copies of the same gene class. Based on the opsin gene expression, the larvae (left column) show a pure-cone or cone-dominated retina, while the adults (right column) have a pure-rod or rod-dominated visual system. Juvenile specimens in two species had an adult expression profile. Note that some species expressed multiple RH1 copies (Scopelarchus, Howella brodiei, and Ceratoscopelus warmingii adults) or multiple RH2 copies (Gyrinomimus sp. larva, Hygophum reinhardtii larva). Notably, adults and larvae of Scopelarchus sp. and Coccorella atlantica expressed different copies of RH2 (more details in fig. 2). Details about the samples and expression levels are listed in table 1. (C) The genomic repertoire of the visual opsins is shown for five species: Idiacanthus fasciola, Chauliodus sloani, Coccorella atlantica, Scopelarchus michaelsarsi (all this study), and Anoplogaster cornuta (Musilova et al. 2019a). The rod RH1 opsin and the cone RH2 opsin genes are present in all studied species in one or multiple (up to seven) copies. The SWS2 opsin gene was found only in the fangtooth, and the SWS1 and LWS are missing from all five studied genomes.