*2.3. Phylogenetic Analysis*

Mitochondrial genes, due to their low substitution rate, are a valuable source of information for phylogenetic analysis at a high taxonomic level (see, e.g., [33]). Phylogenetic analysis based on a set of core mitochondrial genes in 28 species representing all major clades of angiosperms and an outgroup resulted in a tree with a topology congruent with ones based on nuclear and plastid data. In particular, Caryophyllales are resolved as a sister group to asterids and *Fagopyrum* is a sister to *Fallopia* (Figure 2).

**Figure 2.** Phylogenetic tree based on maximum likelihood analysis of a concatenated data set of mitochondrial gene sequences. Branch lengths are proportional to the number of substitutions; bootstrap support values are equal to 100, unless otherwise specified.

While it is natural to expect the identical (or highly similar) topology of phylogenetic trees based on plastid and mitochondrial genes, this cannot be taken for granted (see, e.g., [34]). Mitochondrial genes are often acquired by horizontal gene transfer from other plant species. The most notable example is *Amborella trichopoda* [2] and parasitic plants, but the transfers of single genes and gene parts is known in many other species [35,36]. The phylogenetic analysis of single genes helps to reveal the cases of HGT via the incongruence of gene trees and species trees. In order to check for the presence of HGT, we performed phylogenetic analysis of single genes. In all of them, *Fagopyrum* was either grouped with *Fallopia* or unresolved (Figure S3); both cases are consistent with vertical transmission, thus we conclude that no buckwheat genes were subjects of HGT.
