Evolutionary and Functional Conservation of Topologically Associating Domain Boundaries in Rice Genomes

Traditional evolutionary analysis has relied primarily on one-dimensional (1D) sequencing data, but recent advances in three-dimensional (3D) genomics allow for deeper investigation of how genome architecture shapes evolutionary divergence. In this study, we analyze conserved and species-specific topologically associating domain (TAD) boundaries across multiple Oryza species to uncover both structural and functional evolutionary insights. Here, we characterize boundary conservation at different levels, from highly conserved to species-unique. We apply TCBF, a relatively novel and underutilized tool for TAD boundary conservation analysis, alongside a suite of complementary analyses, including gene ontology, RNA-seq, sequence conservation, and epigenetic profiling. Our approach not only validates canonical evolutionary relationships reflected in sequence data but also novel patterns unique to 3D genome organization. Most notably, our study uncovers strong associations between highly conserved TAD boundaries and RNA metabolism-related genes, as well as other genetic and epigenetic signatures, and a contrasting absence in minimally conserved boundaries. To our knowledge, we created the first phylogenetic reconstruction derived from topological domain data in plants, which demonstrated a strong similarity between 3D and 1D genomic evolutionary relationships. Overall, our work presents an approach that integrates the 3D genome structure into evolutionary genomics, addressing a critical and underexplored dimension of comparative plant genomics.