Genetic and epigenetic variations underlying flavonoid divergence in Beihua and Sijihua honeysuckles

Flavonoids are important antibacterial and antiviral active substances which are the most crucial medicinal components of honeysuckle. However, the content of medicinally active substances in different honeysuckle cultivars is significantly different. Genetic variations and epigenetics play essential roles in plant evolution and trait improvement. Here, we performed multi-omics sequencing of two honeysuckle cultivars (Beihua and Sijihua) at different stages (WB and GF). The results revealed 9,909,981 SNPs in the genomes of the two cultivars, and 12,688 high-impact SNPs were found to regulate genes involved in important biological pathways, such as plant stress resistance. Furthermore, it was found that the majority of differentially methylated cytosines (DMCs, 81%) between Beihua and Sijihua were associated with SNPs. SNP-related DMCs were associated with 76% of the genes, among which 3,325 DEGs (e.g., LjPAL, LjCHI, and LjFLS) were significantly enriched in the flavonoid biosynthesis pathway. The presence of a large number of SNP-related DMCs in the flanking and gene regions of these genes may have led to the overexpression of the genes in Beihua, which increased the accumulation of flavonoids in Beihua. In summary, the present study provides theoretical and technical support for improving the genetic and epigenetic traits of honeysuckle.