*4.4. Sequence Analysis*

NGS clusters of *C. acuminatum*, *C. bryoniifolium*, *C. ficifolium*, *C. iljinii*, *C. pamiricum*, *C. suecicum* and *C. vulvaria* falling into the CficCl-61-40 satDNA family were investigated on the intra-unit (analysis of changes in single monomer) and inter-unit (analysis of changes in array components) levels with TRF software (https://tandem.bu.edu/trf/trf.html). As a result, performance tables with data on monomer sizes, copy numbers, percent matches, percent indels and consensus patterns were obtained (supplementary data 1).

For the reconstruction of phylogenetic relationships among the analyzed monomers k-mer based distance estimation was performed [55]. We have chosen the k-mer value equal to 9, as the most optimal for the analyzed sequences. For calculation of distances method based on fractional common k-mer count was used [56]. The phylogenetic relationships among the sequences are then reconstructed from the pairwise distance matrix [57]. The distance matrix thus obtained can be used to construct a phylogenetic tree using the Minimum Evolution method. The construction of the phylogenetic tree was performed in the MEGA program (Figure 3) [58]. The ancestral monomer (root) was reconstructed as follows: nucleotide-BLAST was used to align contigs of each cluster that, according to BLAST searches, show relatedness between satellite monomers of *Chenopodium* and *Beta* species. DNA fragments with 100% similarity were selected and aligned with each other (supplementary data 2). As a result, a fragment of the ancestral monomer was reconstructed.
