Fig. 3

a Reads aligned back to the superTranscript of chicken C22orf39 (ENSGALG00000023833). The region shaded in red is a gap in the galGal4 reference genome. The gap is within the conserved coding sequence of the gene (black). Transcripts from Ensembl (red) and Cufflinks (blue) miss the gap sequence, whereas the Trinity assembly (green) recovers it. b The number of superTranscripts with novel conserved coding sequence, not found in the galGal4 version of the chicken reference genome. In most cases, the superTranscript contains one or more blocks that can be found in the genome in addition to the novel blocks (partially missing); however, some superTranscripts are missing in their entirety (fully absent). Most of the novel sequence has been gained in the latest reference genome, galGal5