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. 2019 Oct 22;8:e45465. doi: 10.7554/eLife.45465

Figure 1. Phylogenetic analysis of metazoan opsins supports flatworm ciliary-like opsins as xenopsins and confirms a clade of flatworm rhabdomeric opsins.

Support for nodes is calculated using 1000 Ultrafast bootstrap replications as well as 1000 SH-aLRT replicates and approximate aBayes single Branch testing. Black dots indicate nodes with support values for three tests ≥ 95% (0.95 for SH-aLRT replicates). Gray dots indicate nodes with support values for three tests ≥ 90% (0.90 for SH-aLRT replicates). Scale bar unit for branch length is the number of substitutions per site. Branches in red correspond to flatworm opsin sequences. See Figure 1—figure supplement 1 for uncollapsed tree and Figure 1—source data 1 for gene accession numbers. The new xenopsin sequences we found in polyclad and triclad flatworms, plus a bryozoan and chaetognath, all fall within clade A of the xenopsins.

Figure 1—source data 1. Sequence data for opsins used in phylogenetic analyses for Figure 1.
elife-45465-fig1-data1.xlsx (93.7KB, xlsx)
DOI: 10.7554/eLife.45465.007

Figure 1.

Figure 1—figure supplement 1. Uncollapsed tree of IQ-TREE phylogenetic reconstruction of opsin relationships.

Figure 1—figure supplement 1.

Node support values correspond to 1000 Ultrafast bootstrap replications, 1000 SH-aLRT replicates and approximate aBayes single Branch testing. Scale bar unit for branch length is the number of substitutions per site. Note low support for all deeper nodes including those uniting xenopsin/cnidopsin with tetraopsins, and the sister relationship between this clade and the c-opsins/bathyopsins. Branches in red correspond to flatworm opsin sequences.
Figure 1—figure supplement 2. IQtree and RaxML trees showing the influence of the small opsin clades (i.e. chaopsins, bathyopsins, ctenophore and anthozoan opsins) on the position of xenopsins in relation to c-opsins and tetra-opsins (Neuropsin, Go-opsin and RRP); inclusion of these small opsin clades brings xenopsins close to tetraopsins (full dataset), their exclusion brings xenopsins close to c-opsins (reduced dataset).

Figure 1—figure supplement 2.

Figure 1—figure supplement 3. Alignment of major opsin clades showing conserved lysine in transmembrane domain VII, which binds to the retinal chromophore to form a photopigment.

Figure 1—figure supplement 3.

Some xenopsins possess a tripeptide motif, NxQ, which is also found in ciliary opsins and known to be crucial for G-protein activation. A number of flatworm xenopsin sequences in clade A have similar NxQ patterns (including Maritigrella - NAQ), while the motif differs considerably in the polyclad xenopsins of clade B, cnidopsins, bathyopsins and tetraopsins. An alignment of the C-terminal regions of ciliary opsins, xenopsins, cnidopsins, tetraopsins and bathyopsins shows, at a conserved position, similar VxPx motifs in flatworm clade A xenopsins (including Mc xenopsin - VSPQ) as well as a mollusk (A. irradiens) and brachiopod (T. transversa) xenopsin, it is also present in ciliary opsins from non-vertebrate chordates (tunicate and lamprey) and annelids, as well as in cnidopsin sequences. This motif binds the small GTPase Arf4 to direct vertebrate rhodopsin (a ciliary opsin) to the primary cilia. The presence of this motif in some ciliary opsins, xenopsins, cnidopsins may suggest a shared mechanism for the active delivery of these opsins to the cilia in CPRs.