Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

Xiaoping Chen, Qing Lu, Hao Liu, Jianan Zhang, Yanbin Hong, Haofa Lan, Haifen Li, Jinpeng Wang, Haiyan Liu, Shaoxiong Li, Manish K. Pandey, Zhikang Zhang, Guiyuan Zhou, Jigao Yu, Guoqiang Zhang, Jiaqing Yuan, Xingyu Li, Shijie Wen, Fanbo Meng, Shanlin Yu & 6 others Xiyin Wang, Kadambot H.M. Siddique, Zhong Jian Liu, Andrew H. Paterson, Rajeev K. Varshney, Xuanqiang Liang

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

Original languageEnglish
Pages (from-to)920-934
Number of pages15
JournalMolecular Plant
Volume12
Issue number7
DOIs
Publication statusPublished - 1 Mar 2019

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Arachis hypogaea
peanuts
Oils
Genome
Arachis
oils
genome
seed development
genes
genomics
gene targeting
desiccation (plant physiology)
Genes
transcriptomics
transposons
dominance (genetics)
tetraploidy
genetic improvement
diploidy
Seeds

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Chen, Xiaoping ; Lu, Qing ; Liu, Hao ; Zhang, Jianan ; Hong, Yanbin ; Lan, Haofa ; Li, Haifen ; Wang, Jinpeng ; Liu, Haiyan ; Li, Shaoxiong ; Pandey, Manish K. ; Zhang, Zhikang ; Zhou, Guiyuan ; Yu, Jigao ; Zhang, Guoqiang ; Yuan, Jiaqing ; Li, Xingyu ; Wen, Shijie ; Meng, Fanbo ; Yu, Shanlin ; Wang, Xiyin ; Siddique, Kadambot H.M. ; Liu, Zhong Jian ; Paterson, Andrew H. ; Varshney, Rajeev K. ; Liang, Xuanqiang. / Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. In: Molecular Plant. 2019 ; Vol. 12, No. 7. pp. 920-934.
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Chen, X, Lu, Q, Liu, H, Zhang, J, Hong, Y, Lan, H, Li, H, Wang, J, Liu, H, Li, S, Pandey, MK, Zhang, Z, Zhou, G, Yu, J, Zhang, G, Yuan, J, Li, X, Wen, S, Meng, F, Yu, S, Wang, X, Siddique, KHM, Liu, ZJ, Paterson, AH, Varshney, RK & Liang, X 2019, 'Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement' Molecular Plant, vol. 12, no. 7, pp. 920-934. https://doi.org/10.1016/j.molp.2019.03.005

Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. / Chen, Xiaoping; Lu, Qing; Liu, Hao; Zhang, Jianan; Hong, Yanbin; Lan, Haofa; Li, Haifen; Wang, Jinpeng; Liu, Haiyan; Li, Shaoxiong; Pandey, Manish K.; Zhang, Zhikang; Zhou, Guiyuan; Yu, Jigao; Zhang, Guoqiang; Yuan, Jiaqing; Li, Xingyu; Wen, Shijie; Meng, Fanbo; Yu, Shanlin; Wang, Xiyin; Siddique, Kadambot H.M.; Liu, Zhong Jian; Paterson, Andrew H.; Varshney, Rajeev K.; Liang, Xuanqiang.

In: Molecular Plant, Vol. 12, No. 7, 01.03.2019, p. 920-934.

Research output: Contribution to journalArticle

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T1 - Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement

AU - Chen, Xiaoping

AU - Lu, Qing

AU - Liu, Hao

AU - Zhang, Jianan

AU - Hong, Yanbin

AU - Lan, Haofa

AU - Li, Haifen

AU - Wang, Jinpeng

AU - Liu, Haiyan

AU - Li, Shaoxiong

AU - Pandey, Manish K.

AU - Zhang, Zhikang

AU - Zhou, Guiyuan

AU - Yu, Jigao

AU - Zhang, Guoqiang

AU - Yuan, Jiaqing

AU - Li, Xingyu

AU - Wen, Shijie

AU - Meng, Fanbo

AU - Yu, Shanlin

AU - Wang, Xiyin

AU - Siddique, Kadambot H.M.

AU - Liu, Zhong Jian

AU - Paterson, Andrew H.

AU - Varshney, Rajeev K.

AU - Liang, Xuanqiang

PY - 2019/3/1

Y1 - 2019/3/1

N2 - Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

AB - Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.

KW - comparative genomics

KW - cultivated peanut

KW - de novo sequencing

KW - genome evolution

KW - oil metabolism

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