The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development

Abstract

Apricot (Prunus armeniaca L.) is an economically significant fruit crop worldwide with remarkable germplasm diversity, and its fruit quality is primarily determined by key metabolites (e.g., sugars, organic acids, and flavonoids). However, current apricot genome assemblies remain incomplete, with substantial unanchored regions that hamper analyses of genomic evolution and the regulatory mechanisms underlying fruit quality. Here, we generated the first gap-free telomere-to-telomere (T2T) de novo assembly of the P. armeniaca genome (248.3 Mb) and annotated 22 786 protein-coding genes across eight chromosomes. Combined analyses of metabolomic and transcriptomic data, we characterized the transcriptomic and metabolic landscape of apricot across five developmental stages and assigned 3198 metabolites and their co-expressed genes to five functional metabolic-gene modules. DNA methylome profiling further revealed dynamic epigenetic reprogramming during fruit development, characterized by decreases in CG and CHG methylation and an increase in CHH methylation. Notably, higher CHH DNA methylation in promoter regions was associated with the upregulation of leucoanthocyanidin reductase (PaLAR) and dihydroflavonol 4-reductase (PaDFR), contributing to anthocyanin biosynthesis during ripening. Moreover, we identified PaTT2 as a potential regulator of proanthocyanidin biosynthesis and directly activates PaLAR, as evidenced by Y1H and dual-luciferase assays. Our study sheds light on the epigenetic and metabolic regulatory networks of apricot, serving as a valuable foundation for molecular breeding and genetic enhancement.