Genome Studies in Amaranthus cruentus L. and A. hypochondriacus L. Based on Repeatomic and Cytogenetic Data

<i>Amaranthus cruentus</i> L. and <i>Amaranthus hypochondriacus</i> L. are valuable and promising food crops for multi-purpose use that are distributed worldwide in temperate, subtropical, and tropical zones. However, their karyotypes and genomic relationships still remain insufficiently studied. For the first time, a comparative repeatome analysis of <i>A. cruentus</i> and <i>A. hypochondriacus</i> was performed based on the available NGS data; bioinformatic analyses using RepeatExplorer/TAREAN pipelines; and chromosome FISH mapping of 45S rDNA, 5S rDNA, and the most abundant satellite DNAs. In the repeatomes of these species, interspecific variations in the amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were detected. In the repeatomes of both species, shared satDNAs with high sequence similarity were identified. The chromosome distribution patterns of four effective molecular markers, 45S rDNA, 5S rDNA, AmC4, and AmC9, allowed us to identify all chromosome pairs in the species karyotypes, construct unique karyograms of <i>A. cruentus</i> and <i>A. hypochondriacus</i>, and confirm the close relationship between their genomes. These results are important for comparative karyotypic studies within the genus <i>Amaranthus</i>. Our findings demonstrated that cytogenomic analyses might provide important data on genomic relationships within <i>Amaranthus</i> and increase knowledge on genome organization in these valuable crops.