An example of results from phylogenetically-informed annotation (PIA). Here, we search a transcriptome generated for an eye from the squid Chiroteuthis calyx for relatives of the gene G protein-coupled receptor kinase 1 (Gprk1), a component of the rhabdomeric phototransduction pathway. Sequences marked with red squares and labeled "LANDMARK1" are homologs of Gprk1 that have been well-characterized functionally and are thought to share similar functions. In contrast, sequences labeled "LANDMARK2" are well-characterized genes that are more distantly related to Gprk1. Sequences marked with yellow circles and labeled "QUERY" are protein sequences predicted from our transcriptome for C. calyx. Based on their phylogenetic positions and branch lengths, it is likely that one hit (UN0029) represents an ortholog of Gprk1 and that two hits (UN1121 and UN2338) represent genes that are distant paralogs of Gprk1. We conclude that the eyes of C. calyx express an ortholog of Gprk1, a component of the rhabdomeric phototransduction pathway.