title: Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens.
abstract: Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Chen
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Hongjie
authors.initials: H
authors.lastname: Li
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Manish K
authors.initials: MK
authors.lastname: Pandey
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China; College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266000, China;
authors.forename: Qingli
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605;
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Vanika
authors.initials: V
authors.lastname: Garg
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Haifen
authors.initials: H
authors.lastname: Li
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Chi
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Dadakhalandar
authors.initials: D
authors.lastname: Doddamani
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Hong
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Hari
authors.initials: H
authors.lastname: Upadhyaya
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605;
authors.forename: Hui
authors.initials: H
authors.lastname: Guo
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Aamir W
authors.initials: AW
authors.lastname: Khan
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Fanghe
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Lijuan
authors.initials: L
authors.lastname: Pan
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605;
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Pierce
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Guiyuan
authors.initials: G
authors.lastname: Zhou
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Katta A V S
authors.initials: KA
authors.lastname: Krishnamohan
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Mingna
authors.initials: M
authors.lastname: Chen
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Ni
authors.initials: N
authors.lastname: Zhong
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Gaurav
authors.initials: G
authors.lastname: Agarwal
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Shuanzhu
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authors.lastname: Li
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Annapurna
authors.initials: A
authors.lastname: Chitikineni
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen 518000, China;
authors.forename: Guo-Qiang
authors.initials: GQ
authors.lastname: Zhang
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Na
authors.initials: N
authors.lastname: Chen
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Haiyan
authors.initials: H
authors.lastname: Liu
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Pasupuleti
authors.initials: P
authors.lastname: Janila
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Shaoxiong
authors.initials: S
authors.lastname: Li
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Min
authors.initials: M
authors.lastname: Wang
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Tong
authors.initials: T
authors.lastname: Wang
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Jie
authors.initials: J
authors.lastname: Sun
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Xingyu
authors.initials: X
authors.lastname: Li
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Chunyan
authors.initials: C
authors.lastname: Li
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Mian
authors.initials: M
authors.lastname: Wang
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Lina
authors.initials: L
authors.lastname: Yu
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China;
authors.forename: Shijie
authors.initials: S
authors.lastname: Wen
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
authors.forename: Sube
authors.initials: S
authors.lastname: Singh
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Zhen
authors.initials: Z
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authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China;
authors.forename: Jinming
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authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
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authors.lastname: Zhang
authors.affiliation: Macrogen Millennium Genomics Company, Shenzhen 518000, China;
authors.forename: Yue
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authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China;
authors.forename: Jie
authors.initials: J
authors.lastname: Bi
authors.affiliation: College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266000, China;
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen 518000, China; liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Zhong-Jian
authors.identifier: 0000-0003-4390-3878
authors.initials: ZJ
authors.lastname: Liu
authors.affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605; liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.affiliation: Shandong Shofine Seed Company, Jiaxiang 272400, China; liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Shuping
authors.initials: S
authors.lastname: Wang
authors.affiliation: Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Key Laboratory for Crops Genetic Improvement, Guangzhou 510640, China; liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Xuanqiang
authors.initials: X
authors.lastname: Liang
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia; The Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266000, China; liuzj@sinicaorchid.org paterson@uga.edu wsp@shofine.com liang-804@163.com r.k.varshney@cgiar.org yshanlin1956@163.com.
authors.forename: Shanlin
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authors.lastname: Yu
mesh_terms: D010367:Arachis / Q000235:genetics / Q000378:metabolism; D018745:Genome, Plant / Q000502:physiology*; D006801:Humans; D005810:Multigene Family / Q000502:physiology*; D000074241:Peanut Oil; D010938:Plant Oils / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D057891:Tetraploidy
chemical_list: D000074241:Peanut Oil; D010938:Plant Oils; D010940:Plant Proteins
keywords: Arachis duranensis; gene duplication; gene models; genome sequence; polyploidizations