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

Abstract

Comprehensive 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.

Acknowledgements

This research was supported by the Zhejiang Province ‘SanNongJiuFang’ project (2025SNJF034) and Zhejiang Provincial Natural Science Foundation of China (LR23C150001).

Author contributions

X.S. conceived and supervised the project. T.L. and S.X. performed experiments. S.X., J.W., and X.S. analyzed the data. J.Y., J.G., M.W., and X.H. contributed to sample preparation and processing. S.X., X.L., and X.S. wrote the manuscript.

Data availability

All sequencing data supporting this study have been deposited in public repositories. The Hi-C and CUT&Tag (seven histone modifications) datasets generated in this study are available from the China National GeneBank Database (CNGBdb; https://db.cngb.org/) under accession number CNP0007920. Chromatin accessibility (ATAC-seq) data and fruit RNA-seq data across multiple developmental stages are available from the Genome Sequence Archive (GSA; https://ngdc.cncb.ac.cn/gsa/) under accession number PRJCA024619 and PRJCA003268, respectively [73, 74]. WGBS data, along with RNA-seq data from root, stem, leaf, and flower tissues are available from NCBI BioProject under accession numbers PRJNA1039995, PRJNA328414 and PRJNA389468, respectively [75–77].

Conflicts of interest statement

The authors declare that they have no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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