*2.1. Clustering Results and Identification of satDNA Clusters*

Application of the RE pipeline clustering tool for Illumina reads of seven diploid *Chenopodium* species (Table 1) (genome coverage 41.3–58.2%) resulted in the identification of clusters that represent different families of TEs, their derivatives and satDNAs. The latter was the main aim of our research. Several valuable outcomes from the present study are shown in Table 2. *C. vulvaria* and *C. acuminatum* possess the smallest genomes in the group, while those of *C. ficifolium* and *C. suecicum* are the largest. *C. vulvaria* exceeds all investigated species in the number of RE clusters and RE singlets, which emphasizes for its genome diversity.

**Table 1.** The accessions and geographic origin of *Chenopodium* diploid species used for satDNA cluster analysis (NGS), probe preparation (cloning) and fluorescent in situ hybridization (FISH).



**Table 2.** Summary of chromosome parameters, genome size, RE clusters and percentage of CficCl-61-40 satDNA family in the genomes of *C. album* aggregate diploid species.

The satellite monomer of ~40 bp was found during the RE analysis of satDNA in each genome of analyzed species. According to BLAST results, these monomers were related to each other and to the tribe-specific repetitive sequence (GenBank ID HM641822.1), found in *Chenopodium quinoa* by Kolano et al. [29], and to the satellite sequence with the GenBank ID AJ288880.1, which was found in *Beta corolliflora* by Gao et al. [28] (S1). It was thus assumed that in the genomes of the several *Chenopodium* diploids under study, the most abundant and the evolutionarily oldest component (*Chenopodium* and *Beta* diverged approximately in the Paleogene) is present. In the remainder of this paper, tandem arrays from the genomes of *Chenopodium* diploid species related to GenBank accession HM641822.1 will be termed the "CficCl-61-40 satDNA family". This refers to the analysis of NGS data from the *C. ficifolium* genome, RE Cluster #61 (the single cluster in genome of *C. ficifolium* that contains the basic repeat unit), with a length of 40 bp. A further thorough analysis of the interspecies divergence of the sequences of this family was also conducted to identify the main phases of transformation over time.
