Acanthaster is starfish with eyes located on its terminal tube feet. In efforts to study the development of vision and light sensing in a opsin dependent manner, we sequenced tissues for A. planci eyes, radial nerves, tube feet and a mix of other organ tissue (w/ 3 replicates each) for differential expression (DE) analysis using Illimina sequencers.

The preprint for this analysis and results can be found on biorxiv

The raw data for the reads has been uploaded to NCBI under the accession number TBD. Scripts used for this analysis are located in the scripts folder.

Phylogenomic analysis

• opsin sequences were idenified by reciprical best hit blast using sequences collected from various sources. The
• opsin sequences were then aligned using MAFFT v7.215 and phylogenomic trees were then generated using FastTree (v1.4.3) to better classify the retrived opsins.
• Additional trees were then generated using iqtree to confirm the placement of the opsin sequences. Tree support was 10,000 Ultrafast Bootstrap Approximation with a LG+F+L6 amino acid substution model identifed by ModelFinder.

Read quanification

• reads were quasi-mapped using salmon against the gbr Acanthaster transcriptome.
• Differentially expressed transcripts were identified using DESeq2.
• Additional visualization was done using the karyoploteR R package.