*3.6. Annotation*

For the mitochondrial genome, the annotation of protein-coding genes and rRNA genes was performed based on the BLAST search of genes encoded in the mitochondrial genomes of other Caryophyllales (*Beta vulgaris*, *Nepenthes* × *ventrata*, *Fallopia multiflora*). For the plastid genome, the annotation was transferred from the sequence of *F. esculentum* ssp. *ancestrale* plastome (NCBI accession NC\_010776) using GATU [53] with manual correction. Annotation of tRNAs was performed using the tRNA-scan-SE server with sequence source = other mitochondrial for mitogenome and mixed for plastid genome and search mode = default.

The maps of mitochondrial and plastid chromosomes were drawn by a custom script, which utilized Circos 0.69 [54]. Repeats in the mitochondrial genome were found by BLASTN 2.9.0 without a requirement for the maximum e-value but with requirements for the minimum length (500 bp) and percent identity (95%). MIPTs were found by the same method with an identity cut-off of 90% and length cut-off of 100 bp. Since mitochondrial genomes are known to have tRNAs of plastid origin and genes with homologs in the plastid genome (*atp*, *rrn*), only hits that do not overlap with annotated mitochondrial protein-coding or RNA genes were reported.
