Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika

C Fischer,S Koblmüller,C Börger,G G Thallinger,C Sturmbauer,G Michelitsch,C Guelly,S Trajanoski,C Schlötterer

doi:10.1038/s41598-021-81030-z

Abstract

With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.

Highlights

With 1727 described species[1], cichlid fishes are among the most species-rich teleost fish families
The evolutionary success of East African cichlids has been attributed to particular key innovations including (1) the functional decoupling of oral and pharyngeal jaws facilitating the exploitation of diverse trophic n iches[22], (2) the adaptation of the visual system to different water turbidity[23], and (3) parental care and male mating coloration driven by sexual selection facilitating reproductive isolation[24]
Meta-assembly of a set of primary assemblies yielded high quality genome drafts with 918 and 911 Mbp for Petrochromis trewavasae and Tropheus moori, respectively. This is in line with the sizes between 900 and 1000 Mbp reported for other cichlid g enomes[21,30] and with the ~ 940 Mbp estimated by our assembly validation with REAPR38

Summary

Introduction

With 1727 described species[1], cichlid fishes are among the most species-rich teleost fish families. The evolutionary success of East African cichlids has been attributed to particular key innovations including (1) the functional decoupling of oral and pharyngeal jaws facilitating the exploitation of diverse trophic n iches[22], (2) the adaptation of the visual system to different water turbidity[23], and (3) parental care and male mating coloration driven by sexual selection facilitating reproductive isolation[24] At this stage, the suite of genetic mechanisms modifying the genomic substrate underlying the enormous phenotypic eco-morphospace covered by cichlids remains largely unknown ( see[25] for a recent review). The study revealed genome-wide diversifying selection on coding and regulatory variants, some of which recruited from ancient polymorphisms

Methods

Results

Conclusion