@article{8710599,
  abstract     = {{Traditional crops 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 (especially where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient 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 realisation of the benefits to global nutrition security and agrobiodiversity.}},
  author       = {{Ma, Xiao and Vaistij, Fabián E. and Li, Yi and Jansen van Rensburg, Willem S. and Harvey, Sarah and Bairu, Michael W. and Venter, Sonja L. and Mavengahama, Sydney and Ning, Zemin and Graham, Ian A. and Van Deynze, Allen and Van de Peer, Yves and Denby, Katherine J.}},
  issn         = {{0960-7412}},
  journal      = {{PLANT JOURNAL}},
  keywords     = {{Plant Science,Genetics,Cell Biology,Amaranthus cruentus,biosynthetic gene clusters,gene annotation,genetic improvement,genome assembly,nutrition,traditional crop,underutilized crop,PIGMENT EVOLUTION,LEAFY VEGETABLES,ANNOTATION,IDENTIFICATION,DIVERSITY,EFFICIENT,ALIGNMENT,PROGRAM,GENERATION,SOFTWARE}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{613--628}},
  title        = {{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}},
  url          = {{http://dx.doi.org/10.1111/tpj.15298}},
  volume       = {{107}},
  year         = {{2021}},
}

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