**1. Introduction**

In contrast to plastid genomes, plant mitochondrial genomes are usually large and complex. They are shaped by multiple structural changes, including rearrangements, duplications, and horizontal gene transfer (HGT) from nuclear and plastid genomes and, in rare cases, from other plant species [1,2]. This complexity leads to the under-representation of the plant mitochondrial genome sequences compared to the plastome sequences. Even in the species for which complete nuclear genomes are characterized, the information on the mitochondrial genome is often lacking or incomplete. The subject of our study, *Fagopyrum esculentum*, is an important agricultural non-cereal grain plant. Three nuclear genome assemblies of *Fagopyrum* species are available by now ([3,4], and an unpublished study, accession number GCA\_004303065), as well the number of plastid genomes [5,6]. However, not a single mitogenome sequence is available. At a larger scale, *Fagopyrum* belongs to the family Polygonaceae, an isolated group within the order Caryophyllales. By now the only species of Polygonaceae with

a sequenced mitochondrial genome is *Fallopia multiflora* [7]; this is not sufficient for the representation of this large and diverse group of plants. The availability of the mitochondrial genome of buckwheat is also important for practical applications. The cytoplasmic male sterility (CMS) is associated with rearrangements in the mitochondrial genome. They create chimeric open reading frames (ORF) whose products interfere with the functioning of the mitochondrial electron transfer chain and are thus toxic for cells (for a review, see [8]). The characterization of mitogenomes of CMS lines allowed the finding of events presumably responsible for the sterility in many agricultural plants (e.g., [9,10]). CMS was reported in buckwheat [11]; however, its genetic basis is unknown. Additionally, extranuclear genomes, due to their uniparental inheritance, are an important source of information on the maternal lineage of a species or cultivar. Interspecific hybridization is a promising tool for breeding as it would allow the transfer of beneficial traits (self-compatibility, resistance to abiotic stresses) from related species (*F. homotropicum*, *F. tataricum*) [12]. The characterization of extranuclear genomes of all species involved in breeding will help to trace the genealogy of the hybrids. In this study, we generated the reference genome sequence for the buckwheat mitochondrial genome and studied the diversity of the mitochondrial and plastid genome in 11 buckwheat cultivars (nine Russian, one Japanese, and one Canadian) and the ancestral subspecies, *F. esculentum* ssp. *ancestrale*.
