3D Atlas reveals the organization of the kiwi genome

Researchers from Zhejiang A&F University and Zhejiang University have constructed a three-dimensional atlas of the kiwi (Actinidia chinensis) genome. The work analyzed leaf and fruit tissues and related chromatin organization to epigenetic marks and gene expression.

The team produced in situ Hi-C chromosome conformation capture maps. The experiment pooled three biological repeats per tissue and generated approximately 6,51 billion paired reads. The scientists integrated the data with analyses of chromatin accessibility, DNA methylation, seven histone modifications, and RNA sequencing.

The atlas identified A and B compartments, hierarchical subcompartments, TAD-like domains, and chromatin loops. Leaves and fruits showed similar overall organization. Differences emerged at smaller scales. Fruits concentrated more short-distance contacts. Leaves recorded a higher proportion of long-distance interactions.

Type B subcompartments occupied approximately 55% to 60% of the genome. These regions concentrated transposable elements, DNA methylation, and markers associated with gene repression. Type A regions showed greater transcriptional activity and markers of active chromatin.

The study identified 68 genes with predominant expression in fruits. Of these, 63 appeared within TAD-like domains in leaves and fruits. More than 60% of these genes were located in compartment B of the fruit tissue. Only eight coincided with chromatin loop anchoring points.

The results indicate a stronger relationship between fruit-specific expression and the local organization of chromatin domains. Long-distance loops showed a limited association with expression differences between leaves and fruits. The atlas offers a reference for functional and evolutionary studies in perennial fruit trees (doi 10.1093/hr/uhag076).