Dwelling mbuna’, (five) zooplanktivorous utaka’, (six) Astatotilapia calliptera specialised for shallow weedy habitats
Dwelling mbuna’, (5) zooplanktivorous utaka’, (6) Astatotilapia calliptera specialised for shallow weedy habitats (also identified in surrounding rivers and lakes), and (7) the midwater pelagic piscivores Rhamphochromis36,37. Recent large-scale genetic studies have revealed that the Lake Malawi cichlid flock is characterised by an general quite low genetic divergence amongst species (0.1-0.25 ), TLR8 Agonist Synonyms combined with a low mutation rate, a high price of hybridisation and substantial incomplete lineage sorting (shared retention of ancestral genetic variation across species)34,36,38,39.TMultiple molecular mechanisms may be at operate to enable such an explosive phenotypic diversification. For that reason, investigating the epigenetic mechanisms in Lake Malawi cichlids represents a remarkable opportunity 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 in the seven ecomorphological groups from the Lake Malawi haplochromine radiation by generating high-coverage whole-genome liver bisulfite sequencing (WGBS). We discover that Lake Malawi haplochromine cichlids exhibit substantial methylome divergence, despite conserved underlying DNA sequences, and are enriched in evolutionary young transposable elements. Subsequent, we generated whole liver transcriptome sequencing (RNAseq) in 4 of the six species and showed that differential transcriptional activity is drastically associated with between-species methylome divergence, most prominently in genes involved in key hepatic metabolic functions. Finally, by generating 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 for the early establishment of phenotypic diversity. This represents a comparative analysis of all-natural methylome variation in Lake Malawi cichlids and provides initial proof 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 study in the context of phenotypic diversification and adaptation. Outcomes The methylomes of Lake Malawi cichlids function conserved vertebrate characteristics. To MMP-3 Inhibitor custom synthesis characterise the methylome variation and assess feasible functional relationships in natural populations of Lake Malawi cichlids, we performed high-coverage whole-genome bisulfite sequencing of methylomes (WGBS) from liver tissues of six unique cichlid species. Muscle methylome (WGBS) data for 3 of your six species were also generated to assess the extent to which methylome divergence was tissuespecific. Additionally, to examine the correlation in between transcriptome and methylome divergences, total transcriptomes (RNAseq) from each liver and muscle tissues of four species had been generated. Only wild-caught male specimens (2-3 biological replicates for every tissue and every species) were utilised 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.
