Ma, XiaoVaistij, Fabian E.Li, YiJansen van Rensburg, Willem S.Harvey, SarahBairu, Michael W.Venter, Sonja L.Mavengahama, SydneyNing, ZeminGraham, Ian A.Van Deynze, AllenVan de Peer, YvesDenby, Katherine J.2022-03-112022-03-112021-05Ma, X., Vaistij, F..E., Li, Y. et al. 2021, ' A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop', The Plant Journal, vol. 107, pp. 613–628.0960-7412 (print)1365-313X (online)10.1111/tpj.15298http://hdl.handle.net/2263/84449Traditional 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.en© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution License.Amaranthus cruentusBiosynthetic gene clustersGene annotationGenetic improvementGenome assemblyNutritionTraditional cropUnderutilized cropArticle