Nematostella vectensis full length opsin sequences and transcriptomes

Opsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g. jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g. corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemone Nematostella vectensis. We analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We ..., Opsin Identification and Phylogenetics (References numbered as in the paper)
Initial N. vectensis opsin sequences were collected from three published datasets [5,6,47]. All potential N. vectensis sequences were aligned in Geneious Prime v.11.0.12, and identical matches and fragments were discarded. BLAST was used with the final set of opsins as bait to search against the Nematostella vectensis Embryogenesis and Regeneration Transcriptomics database (NvERTx) [67], our own reference transcriptome (generated for this study), and two publicly available chromosome level genomes: v2 genome hosted by the Stowers Institute [50,71], and the genome from the Darwin Tree of Life Programme at the Wellcome Sanger Institute (ENA submission accession: ERA9667479) ([51] no associated publication). Hits were added inclusively and combined with a modified alignment including non-redundant sequences from Vöcking et al. 2017, Picciani et al. 2018, and Gornik et al. 2021 opsin phylogenies [5,6,29]. We then a..., Text software is needed to open the files. To view the tree any tree viewing software can be used. ,