An integrative 3D-genome database for plants

Plant Commun. 2025 Apr 29:101346. doi: 10.1016/j.xplc.2025.101346. Online ahead of print.

ABSTRACT

High-throughput sequencing technologies have revolutionized studies of 3D-genome structures, revealing unprecedented insights into the complexity of genome-wide gene regulation in eukaryotes. To analyze and compare 3D-genome structures, we developed the 3D-genome database for plants, 3D-GDP, for interspecies comparative functional genomics (http://www.3d-gdp.com/). 3D-GDP encompasses all publicly available plant 3D-genome sequences. It offers detailed analyses and comparisons of 3D-genome structures among 26 plant species, with comprehensive information on topologically associating domains (TADs), loops and compartments, as well as gene annotations. 3D-GDP also provides a range of bioinformatic tools such as genome browser, TAD function prediction, and specialized modules for predicting and systematically comparing chromatin structures across species to identify conserved TADs and loop structures. Taken together, the 3D-genome database for plants (3D-GDP) represents a resourceful integrating database and innovative platform that can be used to reveal evolutionary conservation of 3D-genome structures and their relevance to genome-wide gene regulation in plants and beyond.

PMID:40308064 | DOI:10.1016/j.xplc.2025.101346