Haplotype-resolved genomes of two buckwheat crops provide insights into their contrasted rutin concentrations and reproductive systems

Abstract

AbstractBackgroundTwo widely cultivated annual buckwheat crops,Fagopyrum esculentumandF. tataricum, differ from each other in both rutin concentration and reproductive system. However, the underlying genetic mechanisms remain poorly elucidated.ResultsHere, we report the first haplotype-resolved chromosome-level genome assemblies of the two species. Two haplotype genomes ofF. esculentumwere assembled as 1.23 and 1.19 Gb with N50 = 9.8 and 12.4 Mb, respectively; the two haplotype genomes ofF. tataricumwere 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 ofF. 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 inF. tartaricum.ConclusionsOur results highlight the importance of high-quality genomes to identify genetic mutations underlying phenotypic differences between closely related species.F. tataricummay have been experienced stronger selection thanF. esculentumthrough 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.