Figure 7

Overview of the non-model species RNA-Seq mapping strategy for inferring ‘gene’ grouping of RNA-Seq read data. Displayed are RNA-Seq reads that are mapped to three different TA contigs. The red and green contigs (DNA) are assigned to the same gene of the GRS (protein) via BlastX. However, due to divergence between the target species and the genomic reference species (GRS), the blue contig is not, resulting in only the red and green RNA-Seq reads being assigned to this GRS ortholog. In order to compare the expression data inferred from these GRS groupings to that obtained by directly mapping RNA-Seq reads to the CCDS genes, the orthology between GRS and CCDS genes was determined using the Reciprocal Best Hit (RBH) via BLASTp. This method can be compared to the method outlined in Figure 5b.