3D genome organization under extreme metabolic adaptation shows variations in genome compartmentalization and looping

The cave morphs of Astyanax mexicanus have evolved a suite of distinct adaptations to life in perpetual darkness, including the loss of eyes and pigmentation loss, as well as profound metabolic changes such as hyperphagia and starvation resilience, traits that sharply contrast with those of their river-dwelling surface counterparts. While changed gene expression is a primary driver of these adaptations, the underlying role of 3D genome organization - a key regulator of gene expression - remains unexplored. Here, we investigate the 3D genome architecture of the livers of surface fish and two cavefish morphs (Pachon and Tinaja) using Hi-C, performing the first comparative 3D genomic analysis in this species. We analyzed and identified cave-specific 3D genomic features, such as genomic compartments and loops, which were conserved in both the cave populations but absent in surface fish. Integrating the 3D genome data with transcriptomic and epigenetic datasets, linked these changes to differential expression of metabolically relevant genes, such as Arhgef19 and Endog. Additionally, our study also uncovered genomic inversions unique to cavefish, potentially tied to cave adaptation. Our findings suggest that 3D genome organization contributes to transcriptomic shifts underlying cavefish phenotypes, providing a novel intra-species and morph specific perspective on 3D chromatin evolution. This study establishes a foundation for exploring how genome architecture potentially facilitates adaptation to new environments. Comparison of morphs within the same species also establishes a foundation for better understanding of how 3D genome reorganization may drive speciation and phenotypic diversity.