Denovo assembly of a Japan Sea stickleback (Gasterosteus nipponicus) and a Japanese Pacific Ocean lineage of three-spined stickleback (Gasterosteus aculeatus)

DNA within the nucleus is organized into a well-regulated three-dimensional (3D) structure. However, it remains largely elusive how such 3D genome structures influence speciation processes. Recent studies have shown that 3D genome structures influence mutation rates, including the occurrence of chromosomal rearrangement. For example, breakpoints of chromosomal rearrangements are often enriched at topologically associating domain (TAD) boundaries. Here, we hypothesized that TAD structures may constrain the location of chromosomal inversions and thereby shape the genomic landscape of divergence between species with ongoing gene flow, because inversions can contribute to barriers to gene flow. To test this hypothesis, we used a Japanese stickleback species pair, Gasterosteus nipponicus (Japan Sea stickleback) and G. aculeatus (three-spined stickleback). We first constructed high-quality genome assemblies of both species using PacBio HiFi and Dovetail Omni-C technologies and identified several chromosomal inversions. Second, population genomic analyses revealed higher genetic differentiation in inverted regions than in colinear regions and no gene flow within inversions, which contrasts with significant gene flow in colinear regions. Third, using Hi-C data, we revealed 3D genome structures of sticklebacks, such as A/B compartments and TAD. Finally, we found that inversion breakpoints were enriched at TAD boundaries. Thus, our study demonstrate that 3D genome constrains breakpoints of inversions that can act as barriers to gene flow in the stickleback. Further integration of 3D genome analyses with population genomics has the potential to provide novel insights into the mechanisms by which 3D genome influences speciation processes.