**5. Conclusions**

Application of the RE pipeline for analysis of whole genome shotgun Illumina reads from the genomes of seven diploid plant species from divergent lineages allowed us to distinguish three types of satDNA family evolutionary development: (i) concerted evolution with mutation and recombination events (most conserved); (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer (HOR formation); and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/5/ 1201/s1. **Supplementary data 1.** Occurrence of CficCl-61-40 satDNA family in genomes of *Chenopodium* diploid species revealed by RepeatExplorer pipeline and formations of high order repeat (HOR) units. **Supplementary data 2.** Reconstruction of the major part of the ancestral monomer. **Supplementary data 3.** Repetitive elements selected for sequence characterization and in situ hybridization and primers used for amplification. **Supplementary data 4.** Pairwise comparison of sequence variation within the CficCl-61-40 (**A**,**B**), and proposed HOR units CacuCl-1-117 (**C**,**D**), CvulCl-28-118 (**E**,**F**), CvulCl-28-397 (**G**,**H**), CvulCl-112-117 (**I**,**J**), CvulCl-134-117 (**K**,**L**) and Cvul-145-129 (**M**,**N**). **Supplementary data 5.** Chromosomal distribution CficCl-61-40 satDNA family sequences. CficCl-61-40 is labelled red; *C. acuminatum*-specific HOR unit CacuCl-1-117 of 117 bp is labelled green.

**Author Contributions:** A.B. conceived the idea for the study. B.M., K.K. collected plant material. A.B., K.K., R.K, M.J., J.J. performed or supervised the wet lab work. A.B., K.K., R.K. analyzed the data. A.B., B.M., K.K. wrote the manuscript and supplements.

**Funding:** This work was supported by the Czech Science Foundation (grant no. 13-02290S) and as part of a long-term research development project RVO 67985939. This work was also supported for R.K. by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan in the framework of program funding for research (AP05130266, BR05236574 and BR06349586).

**Acknowledgments:** We thank Gary Benson for helpful comments. English language in original version was edited by Springer Nature Language Services (certificate number 2ZF7JW42), and in reversed version by "Kielentarkistuksen tilauslomake/Work Order for Revisions" University of Helsinki.

**Conflicts of Interest:** The authors declare no conflicts of interest.
