Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species. [Display omitted] •Paralogs that specialize for expression in diapause are evolutionarily very ancient•The chromatin landscape at very ancient paralogs was recently rewired in diapause•Rewiring of the chromatin landscape reveals binding sites for key transcription factors•A central function affected by rewiring is lipid metabolism, which is unique in diapause The African turquoise killifish has an extreme form of diapause that lasts many months, even years. Comparing gene expression and chromatin states across species revealed gene duplicates and a shift in lipid metabolism as important contributors to the specialization of a diapause expression program, critical for long-term protection and survival.