Assembly of the guppy reference transcriptome. (A) Flowchart describing read summary, assembly strategy, and assembler comparison. The high quality paired reads from each sequenced dataset, non-barcoded (orange) and barcoded (green), were assembled using genome-independent (Trinity, GIA, red) and genome-guided (Cufflinks, GGA, blue) assemblers. Venn diagram shows the total number of protein sequence orthologs identified between at least two species using translated sequences from the two guppy assemblies (red, blue), and protein sequence databases from eight teleosts, mouse, and human (yellow); (B) Inset (dotted yellow, bottom left) shows an alternate view of the ortholog comparisons. Barplots show the number of orthologs identified in two-way reciprocal best blast-hit comparison between platyfish, tilapia, medaka, stickleback, takifugu, tetraodon, zebrafish, cod, human, and mouse proteins. The stacked bars show the number of orthologs common between GGA and GIA (purple), unique to GGA (blue) and unique to GIA (red); (C) Inset rectangle (dotted blue, bottom right) summarizes the steps for merging predicted CDS from both assemblies and functional annotation of the guppy reference transcriptome (GRT).