Amaranthus hybridus subsp. cruentus cultivar:Arusha Genome sequencing and assembly

Here we present a high-quality genome assembly for A. cruentus, confirming the genome is n = 17 in agreement with cytogenetic studies. We demonstrate that the whole genome duplication seen in A. hypochondriacus occurred before divergence of this species and A. cruentus, and highlight intra- and inter-chromosomal rearrangements compared to A. hypochondriacus. We identify gene families contracted and expanded in the A. cruentus genome, as well as potential biosynthetic gene clusters that may play a role in the high nutritional content of this underutilised crop.