摘要Common buckwheat(Fagopyrum esculentum)and Tartary buckwheat(Fagopyrum tataricum),the two most widely cultivated buckwheat species,differ greatly in flavonoid content and reproductive mode.Here,we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb.Comparative genomic anal-ysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromo-some rearrangements after divergence from Tartary buckwheat.Moreover,multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion(MATE)and chalcone synthase(CHS)un-derwent significant expansion in buckwheat,espe-cially in common buckwheat.Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buck-wheat as being important for the differences in fla-vonoid type and content between these buckwheat species.We also identified a candidate key rutin-degrading enzyme gene(Ft8.2377)that was highly expressed in Tartary buckwheat seed.In addition,we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen,which was potentially related to self-incompatibility in common buckwheat.Our study provides important resources facilitating future functional genomics-related re-search of flavonoid biosynthesis and self-incompatibility in buckwheat.