**Mitochondrial Genome of** *Fagopyrum esculentum* **and the Genetic Diversity of Extranuclear Genomes in Buckwheat**

**Maria D. Logacheva 1,2,\*, Mikhail I. Schelkunov 1,2, Aleksey N. Fesenko 3, Artem S. Kasianov <sup>1</sup> and Aleksey A. Penin <sup>1</sup>**


Received: 22 April 2020; Accepted: 9 May 2020; Published: 12 May 2020

**Abstract:** *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 single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form 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 of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the 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 three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with *F. esculentum* ssp. *ancestrale* is much higher: 220 positions differ in the mitochondrial genome and 159 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*, and *psbH*. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.

**Keywords:** mitochondrial genome; buckwheat; plastid genome; genetic diversity; long reads; targeted assembly
