Abstract:
Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but
have been neglected, with most modern agricultural systems over-reliant on a small number of internationally
traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are
nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (particularly where
diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climateresilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies, we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop
with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to
productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a
related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and
fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific
genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families,
and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome
assembly will underpin much-needed research and global breeding efforts to develop improved varieties for
economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.
