Comparative Analysis of Chromosome Repeat DNA Patterns in Four Amaranthus Species

<i>Amaranthus</i> L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of <i>Amaranthus tricolor</i> L., <i>Amaranthus cruentus</i> L., and <i>Amaranthus hypochondriacus</i> L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence <i>in situ</i> hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of <i>A. tricolor</i>, <i>A. cruentus</i>, <i>Amaranthus paniculatus</i> L., and <i>A. hypochondriacus</i> were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of <i>A. cruentus</i>, <i>A. paniculatus</i>, and <i>A. hypochondriacus</i> were more similar compared to <i>A. tricolor</i>, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on <i>Amaranthus</i> species relationships elucidating taxonomy and evolution of these valuable crops.