Fig. 2: Species-specific methylome divergence in Lake Malawi cichlids is enriched in promoters, CpG-islands, and young transposons.
From: Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes
a Unbiased hierarchical clustering and heatmap of Spearman’s rank correlation scores for genome-wide methylome variation in Lake Malawi cichlids at conserved CG dinucleotides. Dotted boxes group samples by species within each tissue. b Observed/Expected ratios (O/E ratio, enrichment) for some genomic localisations of differentially methylated regions (DMRs) predicted between livers (green) and between muscles (purple) of three Lake Malawi cichlid species, and between tissues (within-species, grey); χ2 tests for between categories (p < 0.0001), for O/E between liver and muscle DMRs (p = 0.99) and between Liver+Muscle vs Tissues (p = 0.04). Expected values were determined by randomly shuffling DMRs of each DMR type across the genome (1000 iterations). Categories are not mutually exclusive. c Gene ontology (GO) enrichment for DMRs found between liver methylomes localised in promoters. GO terms: Kyoto Encyclopaedia of Genes and Genomes (KEGG), molecular functions (MF), cellular component (CC), and biological processes (BP). Only GO terms with FDR < 0.05 shown. N indicates the number of genes associated with each GO term. Only GO terms with p < 0.05 (Benjamini−Hochberg false discovery rate [FDR]-corrected p-values) are shown. d Genomic localisation of liver DMRs containing repeats/transposons (TE-DMRs). e. O/E ratios for species TE-DMRs for each TE family. Only O/E ≥ 2 and ≤0.5 shown. χ2 tests, p < 0.0001. f Violin plots showing TE sequence divergence (namely, CpG-adjusted Kimura substitution level as given by RepeatMasker) in M. zebra genome for species TE-DMRs, TEs outside species DMRs (‘outside’) and randomly shuffled TE-DMRs (500 iterations, ‘shuffle’). Mean values indicated by red dots, median values by black lines and shown above each graph. Total DMR counts indicated below each graph. Two-sided p-values for Kruskal–Wallis test are shown above the graph. DMR, differentially methylated region; TE, repeat/transposon regions; CGI, predicted CpG islands.
