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Abstract Background Two widely cultivated annual buckwheat crops, Fagopyrum esculentum and F. tataricum, differ from each other in both rutin concentration and reproductive system. However, the underlying genetic mechanisms remain poorly elucidated. Results Here, we report the first haplotype-resolved chromosome-level genome assemblies of the two species. Two haplotype genomes of F. esculentum were assembled as 1.23 and 1.19 Gb with N50 = 9.8 and 12.4 Mb, respectively; the two haplotype genomes of F. tataricum were 453.7 and 446.2 Mb with N50 = 50 and 30 Mb, respectively. We further annotated protein-coding genes of each haplotype genome based on available gene sets and 48 newly sequenced transcriptomes. We found that more repetitive sequences, especially expansion of long terminal repeat retrotransposons (LTR-RTs), contributed to the large genome size of F. esculentum. Based on the well-annotated sequences, gene expressions, and luciferase experiments, we identified the sequence mutations of the promoter regions of two key genes that are likely to have greatly contributed to the high rutin concentration and selfing reproduction in F. tartaricum. Conclusions Our results highlight the importance of high-quality genomes to identify genetic mutations underlying phenotypic differences between closely related species. F. tataricum may have been experienced stronger selection than F. esculentum through choosing these two non-coding alleles for the desired cultivation traits. These findings further suggest that genetic manipulation of the non-coding promoter regions could be widely employed for breeding buckwheat and other crops.

Abstract Background Mitogen-activated protein kinases (MAPKs) plays essential roles in the development, hormone regulation and abiotic stress response of plants. Nevertheless, a comprehensive study on MAPK family members has thus far not been performed in Tartary buckwheat. Results Here, we identified 16 FtMAPKs in the Fagopyrum tataricum genome. Phylogenetic analysis showed that the FtMAPK family members could be classified into Groups A, B, C and D, in which A, B and C members contain a Thr-Glu-Tyr (TEY) signature motif and Group D members contain a Thr-Asp-Tyr (TDY) signature motif. Promoter cis-acting elements showed that most Pro FtMAPks contain light response elements, hormone response elements and abiotic stress response elements, and several Pro FtMAPks have MYB-binding sites, which may be involved in the regulation of flavonoid biosynthesis-related enzyme gene expression. Synteny analysis indicated that FtMAPKs have a variety of biological functions. Protein interaction prediction suggested that MAPKs can interact with proteins involved in development and stress resistance. Correlation analysis further confirmed that most of the FtMAPK genes and transcription factors involved in the stress response have the same expression pattern. The transient transformation of FtMAPK1 significantly increased the antioxidant enzymes activity in Tartary buckwheat leaves. In addition, we also found that FtMAPK1 can respond to salt stress by up-regulating the transcription abundance of downstream genes. Conclusions A total of 16 MAPKs were identified in Tartary buckwheat, and the members of the MAPK family containing the TDY motif were found to have expanded. The same subfamily members have relatively conserved gene structures and similar protein motifs. Tissue-specific expression indicated that the expression of all FtMAPK genes varied widely in the roots, stems, leaves and flowers. Most FtMAPKs can regulate the expression of other transcription factors and participate in the abiotic stress response. Our findings comprehensively revealed the FtMAPK gene family and laid a theoretical foundation for the functional characterization of FtMAPKs.