Dwelling mbuna’, (5) zooplanktivorous utaka’, (6) Astatotilapia calliptera specialised for shallow weedy habitats
Dwelling mbuna’, (5) zooplanktivorous utaka’, (six) Astatotilapia calliptera specialised for shallow weedy habitats (also found in surrounding rivers and lakes), and (7) the midwater pelagic piscivores Rhamphochromis36,37. Current large-scale genetic research have revealed that the Lake Malawi cichlid flock is characterised by an overall really low genetic divergence amongst species (0.1-0.25 ), combined with a low mutation price, a high price of hybridisation and comprehensive incomplete lineage sorting (shared retention of ancestral genetic variation across species)34,36,38,39.TMultiple molecular mechanisms could be at operate to enable such an explosive phenotypic diversification. Therefore, investigating the epigenetic mechanisms in Lake Malawi cichlids represents a outstanding opportunity to expand our comprehension on the processes underlying phenotypic diversification and adaptation. Here we describe, quantify, and assess the divergence in liver methylomes in six cichlid species spanning five on the seven ecomorphological groups in the Lake Malawi haplochromine radiation by creating high-coverage whole-genome liver bisulfite sequencing (WGBS). We find that Lake Malawi haplochromine cichlids exhibit substantial methylome divergence, despite conserved underlying DNA sequences, and are enriched in evolutionary young transposable elements. Next, we generated entire liver transcriptome sequencing (RNAseq) in four of the six species and showed that differential transcriptional activity is substantially connected with between-species methylome divergence, most prominently in genes involved in key hepatic metabolic functions. Lastly, by creating WGBS from muscle tissues in 3 cichlid species, we show that half of methylome divergence amongst species is tissue-unspecific and pertains to embryonic and developmental processes, possibly contributing to the early establishment of phenotypic diversity. This represents a comparative analysis of natural methylome variation in Lake Malawi cichlids and provides 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 investigation in the context of phenotypic diversification and adaptation. Outcomes The methylomes of Lake Malawi cichlids function conserved vertebrate characteristics. To characterise the methylome variation and assess possible functional relationships in all-natural 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) data for three on the six species were also generated to assess the extent to which methylome divergence was tissuespecific. In addition, to examine the correlation amongst transcriptome and methylome PLD Inhibitor list divergences, total transcriptomes (RNAseq) from both liver and muscle tissues of four species had been generated. Only PARP1 Inhibitor Formulation wild-caught male specimens (2-3 biological replicates for every tissue and each species) had been utilised for all sequencing datasets (Fig. 1a , Supplementary Fig. 1, Supplementary Data 1, and Supplementary Table 1). The species selected 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.
