The genomes of Tropheus moorii and Petrochromis trewavasae in comparison.. TMvsPT

Background With >1,000 species evolving within the past 10 million years, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known. As species flocks evolved recurrently in several lakes, they provide a model system to tackle the molecular mechanisms underlying repeated adaptive diversification within a single lineage. The database of high-quality cichlid genome reconstructions is still small, hence here we add two genome drafts for species holding a phylogenetic key position by representing the Lake Tanganyika offshoot of the modern haplochromine radiation. As most basal branch of the most species-rich cichlid lineage of the world, the Tanganyika-endemic tribe Tropheini comprises the sister of the expanding riverine clade that fuelled subsequent radiations in other African water bodies whereby stunningly similar eco-morphologies arose in parallel.ResultsAlong with the annotated genomes we provide first analysis results regarding discriminating genomic features of the two study species, each representing an extreme trophic and craniofacial morphology, one being an algae browser and the other an algae grazer. The high-quality genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbps with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, the transcriptomic sequences on one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per ~ 220 bp (interspecific), and 1 variant per 2,540 bp (PT vs PT) / 1,561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed 24 candidates which may influence phenotype modifications related to facial and jaw morphology. ConclusionThe two new draft genomes concern two phylogenetic key species, as they represent the most basal offshoot of the so-called modern haplochromine cichlids, the most species-rich lineage of East African cichlids. While they belong to the endemic Lake Tanganyika Tropheini radiation, their allies spread over several rivers to seed additional radiations such as those in Lake Malawi and Victoria, where they reached comparable eco morphological diversity via parallel evolution.