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

Xiaoping Chen¹, Qing Lu², Hao Liu², Jianan Zhang³, Yanbin Hong², Haofa Lan⁴, Haifen Li², Jinpeng Wang⁵, Haiyan Liu², Shaoxiong Li², Manish K Pandey⁶, Zhikang Zhang⁵, Guiyuan Zhou², Jigao Yu⁵, Guoqiang Zhang⁷, Jiaqing Yuan⁵, Xingyu Li², Shijie Wen², Fanbo Meng⁵, Shanlin Yu⁸, Xiyin Wang⁵, Kadambot H M Siddique⁹, Zhong-Jian Liu¹⁰, Andrew H Paterson¹¹, Rajeev K Varshney¹², Xuanqiang Liang¹³

Affiliations

¹ South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China. Electronic address: chenxiaoping@gdaas.cn.
² South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China.
³ National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
⁴ MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China.
⁵ School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.
⁶ Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
⁷ Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
⁸ Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China.
⁹ UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia.
¹⁰ Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: zjliu@fafu.edu.cn.
¹¹ Plant Genome Mapping Laboratory, University of Georgia, Athens, USA. Electronic address: paterson@uga.edu.
¹² Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. Electronic address: r.k.varshney@cgiar.org.
¹³ South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China. Electronic address: liangxuanqiang@gdaas.cn.

PMID: 30902685
DOI: 10.1016/j.molp.2019.03.005

Free article

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

Xiaoping Chen et al. Mol Plant. 2019.

Free article

. 2019 Jul 1;12(7):920-934.

doi: 10.1016/j.molp.2019.03.005. Epub 2019 Mar 19.

Authors

Affiliations

¹ South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China. Electronic address: chenxiaoping@gdaas.cn.
² South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China.
³ National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
⁴ MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China.
⁵ School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.
⁶ Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
⁷ Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
⁸ Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China.
⁹ UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia.
¹⁰ Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China. Electronic address: zjliu@fafu.edu.cn.
¹¹ Plant Genome Mapping Laboratory, University of Georgia, Athens, USA. Electronic address: paterson@uga.edu.
¹² Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India. Electronic address: r.k.varshney@cgiar.org.
¹³ South China Peanut Sub-center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China. Electronic address: liangxuanqiang@gdaas.cn.

PMID: 30902685
DOI: 10.1016/j.molp.2019.03.005

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.

Keywords: comparative genomics; cultivated peanut; de novo sequencing; genome evolution; oil metabolism.

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

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

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