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Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis

Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first refe...

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Autores principales: Wang, Hengchao, Xu, Dong, Wang, Sen, Wang, Anqi, Lei, Lihong, Jiang, Fan, Yang, Boyuan, Yuan, Lihua, Chen, Rong, Zhang, Yan, Fan, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847342/
https://www.ncbi.nlm.nih.gov/pubmed/36473054
http://dx.doi.org/10.1093/dnares/dsac050
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author Wang, Hengchao
Xu, Dong
Wang, Sen
Wang, Anqi
Lei, Lihong
Jiang, Fan
Yang, Boyuan
Yuan, Lihua
Chen, Rong
Zhang, Yan
Fan, Wei
author_facet Wang, Hengchao
Xu, Dong
Wang, Sen
Wang, Anqi
Lei, Lihong
Jiang, Fan
Yang, Boyuan
Yuan, Lihua
Chen, Rong
Zhang, Yan
Fan, Wei
author_sort Wang, Hengchao
collection PubMed
description Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi–C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution.
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spelling pubmed-98473422023-01-20 Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis Wang, Hengchao Xu, Dong Wang, Sen Wang, Anqi Lei, Lihong Jiang, Fan Yang, Boyuan Yuan, Lihua Chen, Rong Zhang, Yan Fan, Wei DNA Res Resource Article: Genomes Explored Amaranthus tricolor is a vegetable and ornamental amaranth, with high lysine, dietary fibre and squalene content. The red cultivar of A. tricolor possesses a high concentration of betalains, which has been used as natural food colorants. Here, we constructed the genome of A. tricolor, the first reference genome for the subgenus Albersia, combining PacBio HiFi, Nanopore ultra-long and Hi–C data. The contig N50 size was 906 kb, and 99.58% of contig sequence was anchored to the 17 chromosomes, totalling 520 Mb. We annotated 27,813 protein-coding genes with an average 1.3 kb coding sequence and 5.3 exons. We inferred that A. tricolor underwent a whole-genome duplication (WGD) and that the WGD shared by amaranths occurred in the last common ancestor of subfamily Amaranthoideae. Moreover, we comprehensively identified candidate genes in betalain biosynthesis pathway. Among them, DODAα1 and CYP76ADα1, located in one topologically associated domain (TAD) of an active (A) compartment on chromosome 16, were more highly expressed in red leaves than in green leaves, and DODAα1 might be the rate-limiting enzyme gene in betalains biosynthesis. This study presents new genome resources and enriches our understanding of amaranth evolution, betalains production, facilitating molecular breeding improvements and the understanding of C4 plants evolution. Oxford University Press 2022-12-06 /pmc/articles/PMC9847342/ /pubmed/36473054 http://dx.doi.org/10.1093/dnares/dsac050 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Resource Article: Genomes Explored
Wang, Hengchao
Xu, Dong
Wang, Sen
Wang, Anqi
Lei, Lihong
Jiang, Fan
Yang, Boyuan
Yuan, Lihua
Chen, Rong
Zhang, Yan
Fan, Wei
Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title_full Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title_fullStr Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title_full_unstemmed Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title_short Chromosome-scale Amaranthus tricolor genome provides insights into the evolution of the genus Amaranthus and the mechanism of betalain biosynthesis
title_sort chromosome-scale amaranthus tricolor genome provides insights into the evolution of the genus amaranthus and the mechanism of betalain biosynthesis
topic Resource Article: Genomes Explored
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847342/
https://www.ncbi.nlm.nih.gov/pubmed/36473054
http://dx.doi.org/10.1093/dnares/dsac050
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