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.