Genetic diversity of extranuclear genomes in buckwheat

Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by SMRT CCS technology we assembled buckwheat mitochondrial genome and showed that it consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable to process long reads. The mitogenome contains all genes typical for plant mitochondrial genomes. Using this reference sequence we characterized genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: only 3-6 substitutions differ in the mitogenome and 1-2 in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher 153 positions differ in the mitochondrial genome and 111 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.