Extended Data Fig. 7: Genes with functions related to haematopoiesis, hemoglobin and lipid metabolism show higher transcriptional activity in Benthic fish specifically.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Boxplot of liver gene expression (log10(tpm + 1)) for the three hemoglobin (Hb) subunit genes and for SCL/Tal1 gene, all significantly upregulated in benthic fish. False discovery rate adjusted P-values (q) using the Benjamini-Hochberg method (sleuth; Wald test; see Methods) shown for Benthic-Littoral comparison only. b. The 2kbp-long DMR is located 7kbp away from the ‘MN’ globin cluster containing the three differentially expressed hemoglobin genes (see a.). Gain-DMR in the wild Benthic fish. Littoral and river fish show intermediate and low methylation levels respectively. w, wild-caught; R, L, B, river, littoral and benthic fish, respectively. Each bar plot represents average mCG/CG levels for each population in 50bp-long windows. c. Methylation landscape over the genes fads2 (gene body DMR) and miox (promoter DMR). Each bar represents the average liver mCG/CG levels in 50bp-long windows for each population. d. Boxplot of gene expression values (log10(tpm + 1) for fads2 and miox in Benthic (n = 5), Littoral (n = 4) and River (n = 4) liver tissues. q, false discovery rate adjusted two-sided P-value, using the Benjamini-Hochberg methods (sleuth; Wald test; see Methods) are shown for all comparisons in graphs. All box plots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (single points).
