Transcriptional divergence during cichlid embryogenesis

Abstract

Cichlid fishes have undergone rapid speciation, making them one of the largest vertebrate families and among the most striking examples of adaptive radiation. Cichlid research has largely focused on diverging phenotypes of adults despite many of these variable traits likely being established during early embryogenesis. A central question that remains is how variation is generated during development. Moreover, cichlids are shown to have very low average nucleotide diversity within and between species. This low variation at the genomic level cannot fully explain the great diversity at the phenotypic level. Transcriptomes can thus serve as an intermediate phenotype to understand how variation is manifested at the gene expression levels. This project aims to link cichlid early development to species diversification with the use of comparative transcriptomics. The study focuses on two Lake Malawi cichlid species representing distinct eco- morphological groups: the ancestral-like generalist Astatotilapia calliptera and the specialized mbuna (rock-dwelling) algae-scraper Tropheops sp. ‘mauve’. Transcriptomic data are generated and analyzed at multiple resolutions, including bulk RNA sequencing and single-cell RNA sequencing, to address this research question comprehensively. The analysis of gene expression across 12 developmental stages, from fertilization to the larval stage, reveals that transcriptional variation emerges early in development despite the highly similar developmental trajectories of the two species. These differences likely arise not only from variations in maternal contributions at the 2-cell stage but also from zygotic gene expression, with the gastrula stage showing the highest number of differentially expressed genes. Heterochronic genes are largely enriched for protein synthesis-related functions, which are expressed earlier in the generalist species, potentially contributing to its accelerated development. Additional expression changes, including differences in exon usage, the expression of transposable elements and paralogs are also explored. These molecular changes may act in concert to shape species-specific transcriptional patterns. Furthermore, both species exhibit transcriptional profiles that align with the hourglass model, showing peak conservation at mid- embryogenesis. These patterns mirror those observed in zebrafish based on untransformed transcriptomic data, when factors such as phyletic age, sequence divergence, and pleiotropy are considered. The single-cell transcriptomic data provides the first developmental atlas for cichlids, covering four developmental stages: gastrula, somitogenesis, pharyngula, and larval. The single-cell profiles also highlight early divergence in gene expression, with genes showing species-specific expression patterns predominantly expressed during the gastrula and somitogenesis stages. These genes demonstrate cell- type-dependent expression especially in early periderm and neural cell types, highlighting potential functional roles. In addition, the two species of interest produce fertile hybrids, which can help with understanding the observed transcriptional variation. Hybrid transcriptomes revealed an abundance of dominant genes associated with generalist species and relatively few misexpressed genes at the embryonic stage. Using long-read sequencing, parental alleles can be distinguished, enabling the examination of allelic expression to assess the relative contributions of cis- and trans-regulation to gene expression variation during early cichlid development. This analysis shows an enrichment of genes with compensatory expression and stronger influence of trans-regulation over cis-regulation, highlighting regulatory divergence of these genes. In summary, this project offers a comprehensive view of interspecific variation in the transcriptional landscape during cichlid embryogenesis at both bulk and single-cell resolution. The findings suggest that early changes in gene expression play a role in driving the diversification of species and offer insights into the genes that may underlie this diversity. Additionally, this study establishes a valuable database in the form of baseline reference transcriptomes for understanding developmental processes during cichlid embryogenesis. This resource serves as a foundation for generating new hypotheses and guiding targeted functional studies.