Extended Data Fig. 6: Transcriptional divergence among populations and negative correlation between promoter methylation and transcriptional activity.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Unbiased hierarchical clustering and heatmap of transcriptional variation among all RNAseq samples (based on Spearman’s correlation scores). Gene expression patterns segregate the populations apart, independently of sequencing read lengths. All annotated genes were used (tpm). Of note, paired-end 150bp-long reads were trimmed in silico down to paired-end 100 bp to account for different read lengths (see Methods). b. Methylation profiles (averaged mCG/CG levels for n = 3 WGBS benthic samples) along gene bodies and at promoters according to gene expression levels. Genes were split into five categories according to their gene expression activity (averaged tpm per gene for n = 5 benthic fish RNAseq samples). Spearman’s correlation tests are shown in plot and show significant negative correlation between methylation at promoters and transcriptional activity (rho = -0.33, two-sided P < 2.2E-16).
