dc.contributor.author |
Ma, Xiao
|
|
dc.contributor.author |
Vaistij, Fabian E.
|
|
dc.contributor.author |
Li, Yi
|
|
dc.contributor.author |
Jansen van Rensburg, Willem S.
|
|
dc.contributor.author |
Harvey, Sarah
|
|
dc.contributor.author |
Bairu, Michael W.
|
|
dc.contributor.author |
Venter, Sonja L.
|
|
dc.contributor.author |
Mavengahama, Sydney
|
|
dc.contributor.author |
Ning, Zemin
|
|
dc.contributor.author |
Graham, Ian A.
|
|
dc.contributor.author |
Van Deynze, Allen
|
|
dc.contributor.author |
Van de Peer, Yves
|
|
dc.contributor.author |
Denby, Katherine J.
|
|
dc.date.accessioned |
2022-03-11T09:00:16Z |
|
dc.date.available |
2022-03-11T09:00:16Z |
|
dc.date.issued |
2021-05 |
|
dc.description.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. |
en_ZA |
dc.description.department |
Biochemistry |
en_ZA |
dc.description.librarian |
pm2022 |
en_ZA |
dc.description.uri |
https://onlinelibrary.wiley.com/journal/1365313x |
en_ZA |
dc.identifier.citation |
Ma, 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. |
en_ZA |
dc.identifier.issn |
0960-7412 (print) |
|
dc.identifier.issn |
1365-313X (online) |
|
dc.identifier.other |
10.1111/tpj.15298 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/84449 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
Wiley |
en_ZA |
dc.rights |
© 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. |
en_ZA |
dc.subject |
Amaranthus cruentus |
en_ZA |
dc.subject |
Biosynthetic gene clusters |
en_ZA |
dc.subject |
Gene annotation |
en_ZA |
dc.subject |
Genetic improvement |
en_ZA |
dc.subject |
Genome assembly |
en_ZA |
dc.subject |
Nutrition |
en_ZA |
dc.subject |
Traditional crop |
en_ZA |
dc.subject |
Underutilized crop |
en_ZA |
dc.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 |
en_ZA |
dc.type |
Article |
en_ZA |