Reannotation strategy and comparison of the new gene models (Aqu2) of the Amphimedon queenslandica genome with previous gene models (Aqu1, ab initio and NCBI). A) Diagram of de novo transcriptome assembly and annotation strategy. Boxes represent sets of data while arrows denote specific computational steps in the annotation pipeline. Steps involving Trinity have been omitted for brevity. B) Venn diagram showing overlap of Aqu2 models with previous annotations including ab initio (Augustus, SNAP and GenomeScan), NCBI and Aqu1 at 80% similarity to account for missing UTR regions in previous annotations. Intersections were done in a hierarchical fashion with the following order of precedence: Aqu2; Aqu1; ab initio; and NCBI.