Comparative analysis of canonical and noncanonical rhodopsins in Amphidinium carterae and Karlodinium veneficum

Rhodopsins are ancient and versatile light-sensitive proteins, widely distributed across microbial life. In dinoflagellates, however, their diversity and function remain poorly understood, owing to the lineage's extreme genomic divergence. Here, we surveyed the rhodopsin complements of two dinoflagellates, Amphidinium carterae and Karlodinium veneficum, using iterative profile-based searches, structural modeling, and motif-guided annotation. From the two species, 18 and 10 putative rhodopsin sequences were identified, respectively, with highly conserved retinal binding residues and a pocket. Of these sequences, several belonged to canonical families, including a finding of a heliorhodopsin in dinoflagellates. However, the majority were highly divergent sequences bearing noncanonical motifs and extensive accessory domains. The predicted ion-pumping capacities for both species were divergent based on helix C functional motifs, with K. veneficum rhodopsins maintaining canonical ion-pumping capacity, whereas A. carterae rhodopsins showed no functional similarity with canonical ion pumps. These results suggest functional innovation beyond ion-pumping, potentially toward signaling or light-dependent enzymatic activity in these two species.