Recombination is typically suppressed in inverted chromosomal regions, leading to the accumulation of alleles important for adaptation and reproductive isolation. The 3D organization of the genome influences the location of chromosomal inversions. For example, the boundaries of chromosomal inversions often overlap with boundaries of physically interacting domains known as topologically associating domains (TADs). These observations suggest that TADs can contribute to adaptation and speciation by constraining the location of inversion breakpoints. Writing in Molecular Ecology, Yamasaki and colleagues explore the association between genome structure, inversions and gene flow in a pair of sympatric species, the Japan Sea stickleback (Gasterosteus nipponicus) and the three-spined stickleback (G. aculeatus). Comparing newly generated chromosome-scale genome assemblies for the two species, the authors found 59 inversions and showed higher levels of gene flow within the inversions when compared to those within the collinear regions, suggesting that inversions act as barriers to gene flow. The authors then used Hi-C sequencing to characterize the 3D structures of the genomes and analyse how they relate to inversions. Inversion breakpoints tended to occur at TAD boundaries, and the breakpoints of large inversions overlapped with boundaries of two genome compartments that differ in level of chromatin density and gene activity. This study shows that the 3D structure of the genome influences gene flow between two stickleback species by shaping the chromosomal location of inversions. Future work that combines genome structure analysis with population genetics can inform as to the mechanisms by which the 3D architecture of the genome influences speciation.
Original reference: Mol. Ecol. https://doi.org/10.1111/mec.17814 (2025)
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