Improvement in Amphimedon queenslandica gene annotations. A) Increase in the number of exons (x-axis) per gene (y-axis) between Aqu1 (gray) and Aqu2 (black) for all genes with less than 30 exons. B) Increase in the number (y-axis) and size of coding (CDS - blue) and non-coding (3’ UTR – pink, 5’ UTR – green) transcript regions (x-axis) between Aqu1 (left panel) and Aqu2 (right panel). The transcript region size is displayed in log-scale. C) Genome browser example of improvements in gene annotations between ab initio (Augustus, SNAP and GenomeScan – purple track), Aqu1 (dark green-blue track), EVM models with annotated UTRs (bright blue) and Aqu2 (orange track). The gene on the right side of the panel is GATA and the one on the left has no significant match in other organisms. Thick blocks represent coding exons, thin blocks non-coding exons and lines introns. Small arrows on introns denote the direction of transcription. Scaffold number and position, and scale bar shown on top. D) Distribution of the intergenic distance between annotated genes of Amphimedon queenslandica (Aqu2) displayed in log-scale. The median intergenic distance (587 bp) is shown as a vertical line (red).