A high-resolution 3D genome map of kiwifruit provides insights into chromatin architecture and transcriptional activity

Abstract Comprehensive three-dimensional (3D) genome maps are essential for understanding transcriptional regulation, yet such resources remain limited for perennial woody crops. Here, we present a high-resolution, tissue-resolved 3D genome atlas of kiwifruit (Actinidia chinensis). Using in situ Hi-C, we generated chromatin contact maps from leaf and fruit tissues and integrated these data with epigenomic and transcriptomic datasets, including chromatin accessibility, whole-genome DNA methylation, seven histone modifications, and RNA-seq profiles spanning multiple tissues and fruit developmental stages. This integrated dataset enables systematic annotation of genome architecture across multiple spatial scales, including A/B compartments, hierarchical subcompartments, TAD-like domains, and chromatin loops. Global features of 3D genome organization are broadly similar between tissues, while quantitative variation is observed at finer scales, such as subcompartment rank, domain insulation strength, and loop detection frequency. Integration with genomic and epigenomic features reveals consistent associations between chromatin states and spatial organization, providing a reference framework for interpreting plant genome architecture in a perennial context. We further map tissue-specific gene sets onto the 3D genome landscape and describe their spatial distributions relative to compartments, domains, and loop anchors, offering a view of how transcriptional programs relate to higher-order chromatin organization. Together, this work establishes an integrative, high-resolution 3D genome resources for a woody perennial fruit crop, and supports future functional, evolutionary, and applied research in kiwifruit and other perennial species.