FIGURE 6: The overlap of RNA-seq and ATAC-seq datasets narrows the list of candidate genes. (A) In total, 89 genes were identified that were both differentially expressed (DE) and differentially accessible (DA) between species. Of these, 15 overlapped with genes identified in the pelagic dataset (light blue), 11 overlapped with genes from the benthic dataset (dark blue), and 13 were identified in both foraging environments. These overlapping datasets identified a relatively small subset of genes where expression differences may be due to differences in the cis- regulatory region. Boxes to the right of the venn diagram display the specific genes from each area of overlap. (B-D) Diagrams of genes are shown (each panel has its own scale bar), as well as the location of ATAC-seq peaks based on DA analyses, and CpG islands (from the UCSC genome browser CpG island track based on at least 50% GC content, >200 bp, and >0.6 ratio of observed number of CG dinucleotides). Shown are representative data from the benthic dataset (B, actr6 on LG7), the pelagic dataset (C, kiaa0586 on an unlinked contig), and a gene that was significantly DE and DA in both environments (D, capn1-like on LG10). Beneath each gene model, ATAC-seq peaks are colored based on concentrations, with lighter colors indicating lower concentrations and darker colors indicating higher concentrations.