Genomic sequencing of two Lake Tanganyika cichlid fish

During the last two decades cichlid fishes have been established as evolutionary model system. Genomic approaches have undergone massive innovation concerning speed and efficiency of deciphering whole genomes and become increasingly important in evolutionary biology. My research group has been studying the adaptive radiation of cichlid fishes for more than 15 years, attempting to understand the pathways of speciation and adaptation to novel ecological niches. The cichlid fishes of Lake Tanganyika represent the oldest and eco- morphologically most advanced adaptive radiation and several lineages radiated in parallel. We chose the tribe Tropheini to study adaptive evolution, as they are much more diverse in terms of ecology, morphology and behavior than any Lake Malawi and Victoria cichlid, despite being part of a monophyletic and closely related assemblage. To take our approach further in evo-devo context, we propose to decipher the genomes of two highly divergent members of the Tropheini, the epilithic algae feeder Tropheus moorii, and the unicellular algae comber Petrochromis trewavasae. We intend to use 454 sequencing technology in combination with shotgun approaches to successfully score the two genomes in reasonably complete coverage. The project is planned as cooperation between three research groups from three Universities, The Karl-Franzens University of Graz, The Medical University of Graz, and the Graz University of Technology, whereby each group contributes crucial expertise and resources. The team-members of the Department of Zoology provide the study system and the research questions and hypotheses, the partners of the Center of Medical Research of the Medical University of Graz contribute their powerful genome sequencing unit, the members of the Institute for Genomics and Bioinformatics provide their expertise in genome assembly and annotation and computing infrastructure, which can cope with the demands of sequencing large genomes. This project should not be understood as an attempt to undermine ongoing efforts in cichlid genomics, but as a valuable complement in the common goal to decipher a suite of wisely chosen cichlid genomes as "natural mutants", to understand the common pattern of cichlid adaptive evolution and its connection to speciation processes at various stages of adaptive radiation. By comparing particular structural and regulatory genes in addition to the genome sequencing effort we hope to find correlates to divergent eco-morphologies, as recently demonstrated e.g. for Lake Malawi rock cichlids. The advantage and complementary potential of the Lake Tanganyika system would be its significantly older evolutionary age and the fact of more complete genomic separation, mirrored in the completed lineage sorting among species in the mtDNA genome.

The project continued our studies on the evolution and comparative morphometry and set out to elucidate two complete vertebrate genomes and transcriptomes of two cichlid fish species, which represent an important model system for the study of the evolution of new species in tight connection to adaptation to novel ecological niches. If this process is condensed like in the Great East African Lakes, Tanganyika, Malawi and Victoria, several hundreds of species can evolve within short periods of time via a process termed adaptive radiation. Such explosive phases of speciation have repeatedly renewed or innovated the fauna of our planet. Since our research group at Graz University has concentrated on the oldest of the three species flocks in Lake Tanganyika for more than 15 years, we selected two Tanganyikan species which separated from their common ancestor about 3 million years ago and evolved two distinct diet specializations resulting in strikingly different head-, mouth- and dental morphologies. Our goal was to contribute two genomes for the elucidation of the genetic architecture of trophic specialization in the cichlid head morphology and its evolution, for which cichlid fishes have become an important model system. The project was accomplished through a collaboration between scientists from four Austrian Universities (three in Graz involving the BioTechMed platform and one in Vienna) and after four years of intensive work we can now present the two genomes and transcriptomes. These results were generated by utilizing state-of-the-art sequencing methods and extensive bioinformatics analyses, reaching and partly surpassing the quality level of the five recently published genomes. With ~918 million bases the genomes have one third of the size of the human genome, but comprise with ~24.000 a similar number of genes. Comparison of the two genomes shows more than 5 million variants of which more than 1 million reside in annotated genes, rendering them more likely to have an effect on bodily functions or physical appearance of the species. Comparisons with published genomes revealed that there are variants in genes, which were recently shown to modulate facial structures in humans (especially of the nose and the chin). Further research is necessary to substantiate these findings. The project supported four Masters- and two PhD theses and will provide the basis for a follow-up project focusing on the evolution of the genetic basis of trophic specialization. So far, 16 publications and 19 conference presentations emerged from the project the genome paper and three additional publications are currently in preparation.