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
© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd..
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 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 realization of the benefits to global nutrition security and agrobiodiversity.
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| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:107 |
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| Enthalten in: |
The Plant journal : for cell and molecular biology - 107(2021), 2 vom: 07. Juli, Seite 613-628 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Ma, Xiao [VerfasserIn] |
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| Links: |
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| Themen: |
Amaranthus cruentus |
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| Anmerkungen: |
Date Completed 29.11.2021 Date Revised 25.06.2022 published: Print-Electronic ErratumIn: Plant J. 2022 Jun;110(6):1829. - PMID 35751495 Citation Status MEDLINE |
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| doi: |
10.1111/tpj.15298 |
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| funding: |
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| 100 | 1 | |a Ma, Xiao |e verfasserin |4 aut | |
| 245 | 1 | 2 | |a 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 |
| 264 | 1 | |c 2021 | |
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| 500 | |a Date Completed 29.11.2021 | ||
| 500 | |a Date Revised 25.06.2022 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a ErratumIn: Plant J. 2022 Jun;110(6):1829. - PMID 35751495 | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. | ||
| 520 | |a 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 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 realization of the benefits to global nutrition security and agrobiodiversity | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Amaranthus cruentus | |
| 650 | 4 | |a biosynthetic gene clusters | |
| 650 | 4 | |a gene annotation | |
| 650 | 4 | |a genetic improvement | |
| 650 | 4 | |a genome assembly | |
| 650 | 4 | |a nutrition | |
| 650 | 4 | |a traditional crop | |
| 650 | 4 | |a underutilized crop | |
| 700 | 1 | |a Vaistij, Fabián E |e verfasserin |4 aut | |
| 700 | 1 | |a Li, Yi |e verfasserin |4 aut | |
| 700 | 1 | |a Jansen van Rensburg, Willem S |e verfasserin |4 aut | |
| 700 | 1 | |a Harvey, Sarah |e verfasserin |4 aut | |
| 700 | 1 | |a Bairu, Michael W |e verfasserin |4 aut | |
| 700 | 1 | |a Venter, Sonja L |e verfasserin |4 aut | |
| 700 | 1 | |a Mavengahama, Sydney |e verfasserin |4 aut | |
| 700 | 1 | |a Ning, Zemin |e verfasserin |4 aut | |
| 700 | 1 | |a Graham, Ian A |e verfasserin |4 aut | |
| 700 | 1 | |a Van Deynze, Allen |e verfasserin |4 aut | |
| 700 | 1 | |a Van de Peer, Yves |e verfasserin |4 aut | |
| 700 | 1 | |a Denby, Katherine J |e verfasserin |4 aut | |
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