No abstract

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 analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome 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) underwent significant expansion in buckwheat, especially 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 buckwheat as being important for the differences in flavonoid 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 research of flavonoid biosynthesis and self‐incompatibility in buckwheat.

Phylogenetic tree of Scartelaos histophorus with 19 other species. Black numbers at nodes represent divergence time. The orange numbers and blue numbers represent the numbers of expanded and contracted gene families, respectively. Author contributionsJZ supervised the study and managed the project. JZ, XL, and JQ collected the samples in-field. XL performed the genome sequencing, assembly, annotation, genetic data analyses, and writing of the draft manuscript. JQ, JBC, and JC contributed to the taxonomy and phylogeny issues. JZ, XL, and JBC finished the