Dwelling mbuna’, (5) zooplanktivorous utaka’, (6) Astatotilapia calliptera specialised for shallow weedy habitats
Dwelling mbuna’, (five) zooplanktivorous utaka’, (six) Astatotilapia calliptera specialised for shallow weedy habitats (also identified in surrounding rivers and lakes), and (7) the midwater pelagic piscivores Rhamphochromis36,37. Current large-scale genetic studies have revealed that the Lake Malawi cichlid flock is characterised by an overall very low genetic divergence amongst RORγ Inhibitor Purity & Documentation species (0.1-0.25 ), TIP60 Activator site combined using a low mutation price, a higher price of hybridisation and in depth incomplete lineage sorting (shared retention of ancestral genetic variation across species)34,36,38,39.TMultiple molecular mechanisms could be at perform to enable such an explosive phenotypic diversification. As a result, investigating the epigenetic mechanisms in Lake Malawi cichlids represents a outstanding chance to expand our comprehension with the processes underlying phenotypic diversification and adaptation. Right here we describe, quantify, and assess the divergence in liver methylomes in six cichlid species spanning 5 from the seven ecomorphological groups in the Lake Malawi haplochromine radiation by producing high-coverage whole-genome liver bisulfite sequencing (WGBS). We find that Lake Malawi haplochromine cichlids exhibit substantial methylome divergence, in spite of conserved underlying DNA sequences, and are enriched in evolutionary young transposable components. Next, we generated complete liver transcriptome sequencing (RNAseq) in 4 of the six species and showed that differential transcriptional activity is drastically connected with between-species methylome divergence, most prominently in genes involved in essential hepatic metabolic functions. Lastly, by producing WGBS from muscle tissues in 3 cichlid species, we show that half of methylome divergence between species is tissue-unspecific and pertains to embryonic and developmental processes, possibly contributing to the early establishment of phenotypic diversity. This represents a comparative evaluation of natural methylome variation in Lake Malawi cichlids and delivers initial evidence for substantial species-specific epigenetic divergence in cis-regulatory regions of ecologically-relevant genes. Our study represents a resource that lays the groundwork for future epigenomic analysis in the context of phenotypic diversification and adaptation. Final results The methylomes of Lake Malawi cichlids function conserved vertebrate qualities. To characterise the methylome variation and assess possible functional relationships in organic populations of Lake Malawi cichlids, we performed high-coverage whole-genome bisulfite sequencing of methylomes (WGBS) from liver tissues of six various cichlid species. Muscle methylome (WGBS) information for three from the six species were also generated to assess the extent to which methylome divergence was tissuespecific. Furthermore, to examine the correlation amongst transcriptome and methylome divergences, total transcriptomes (RNAseq) from each liver and muscle tissues of four species were generated. Only wild-caught male specimens (2-3 biological replicates for every tissue and every single species) have been utilized for all sequencing datasets (Fig. 1a , Supplementary Fig. 1, Supplementary Data 1, and Supplementary Table 1). The species chosen were: Rhamphochromis longiceps (RL), a pelagic piscivore (Rhamphochromis group); Diplotaxodon limnothrissa (DL), a deep-water pelagic carnivore (Diplotaxodon group); Maylandia zebra (MZ) and Petrotilapia genalutea (PG), two rock-dwelling algae eaters (Mbuna group); Aul.