The pan-plastome of Tartary buckwheat. The pan-plastome of Tartary buckwheat (Fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

Buckwheat (Polygonaceae family, Fagopyrum genus) is called as the pseudocereal, however, it has also been recognized as an important food and medicine crop, which has been cultivated for about 4000 years. Its nuclear genome had been sequenced, but their organelle genome has been systematically studied within population level. In this study, we used the resequencing data of Tartary buckwheat population to newly assemble 513 complete chloroplast genomes (plastomes), and combined with the 8 complete plastomes of buckwheat from NCBI database to construct the pan-plastome variations of Fagopyrum species. On this basis, the highly variable regions, population structure, genetic diversity and phylogenetic relationships were further analyzed by using the genomic variations. Based on the reference genome, the phylogenetic relationship and divergence time of Fagopyrum were analyzed, and the possible domestication pathways and population history of Fagopyrum were discussed. These results will provide important reference for the classification of new species, molecular breeding and genetic improvement of buckwheat in the future.