Workflow of transcriptome assembly through annotation and differential expression analyses. Raw reads from three normalized libraries were filtered based on quality score and separately mapped to unpublished genomic scaffolds of H. symbiolongicarpus using TopHat 2.0.6, assembled using Cufflinks 2.1.1, merged into a single assembly using cuffmerge, and filtered by transcript size, removing assembled transcripts less than 200 bp in length. Blast2GO, CEGMA, HMMscan, and orthoMCL were used to annotate the transcriptome. Differential expression began with mapping 12 non-normalized libraries to the final transcriptome assembly with Bowtie2. DE was then assessed with DESeq and edgeR and polyp-specific DEs were compared to the annotated transcriptome.