*3.5. Plastid Genome Assembly*

To assemble the Dasha plastid genome, we took the largest plastid contig (found based on similarity with *F. esculentum* ssp. *ancestrale* plastome) in the Unicycler assembly described above and extended it by Elloreas, which created a circular sequence after 50 iterations of extension. Elloreas was run with parameters "sequencing\_technology hifi\_pacbio", "minimum\_length\_of\_mapped\_read\_part 8000", "minimum\_read\_similarity 100%", "contig\_edge\_size\_to\_use\_for\_mapping 15000". To find possible misassemblies, we mapped PacBio reads by minimap2 with the "asm20" parameter and performed variant calling by FreeBayes v.1.3.0, searching for variants with a variant quality at least 40 supported by more than 50% reads. We found one misassembly in a poly-A region; that misassembly was introduced by Unicycler. An alternative variant (5 adenines instead of 4) was supported by 98.6% reads mapping to this position and we fixed the genome accordingly.

A pairwise alignment by the online version of NCBI BLAST showed that this assembly was collinear with the plastid genome of *F. esculentum* spp. *ancestrale*. The plastome sequence is deposited in NCBI Genbank under accession number MT364821.
