Multi-omics analyses reveal epigenetic regulation of anthocyanin biosynthesis in <i>Disanthus cercidifolius</i> subsp. <i>longipes</i>

Abstract Disanthus cercidifolius subsp. longipes (DCL), a rare and endangered species endemic to southern China, possesses remarkable ornamental value and thus warrants enhanced conservation and utilization. However, the lack of a reference genome has hindered research progress. Here, we report a high-quality, chromosome-scale genome assembly of DCL using PacBio HiFi and Hi-C technologies, yielding a 1.05 Gb genome with a contig N50 of 121 Mb and anchoring 99.98% of sequences to eight chromosomes. Gene family analysis revealed that expanded gene families are mainly related to flavonoid biosynthesis and glycosyltransferase activity. DCL underwent only the whole-genome triplication event shared by core eudicots. Integrating ATAC-seq and ChIP-seq datasets, we generated a comprehensive epigenomic landscape comprising 45,359 accessible chromatin regions (ACRs). Highly expressed genes were consistently associated with a greater number of ACRs, a trend evident across both whole-genome duplication-derived gene pairs and tandem duplicates. Gene expression analysis indicated that H3K27ac, H3K9ac, and H3K4me3 may serve as critical histone marks for active regulatory elements. We further elucidated the epigenetic regulation of anthocyanin biosynthesis, mapping a molecular regulatory network. A key enhancer was involved in transcriptional regulation of Dcl09116 (chalcone isomerase) through recruitment of specific transcription factors. Collectively, this study provides comprehensive genomic and epigenomic resources for DCL, facilitating genetic improvement of its ornamental traits and advancing conservation efforts.