The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal-Bertioli, Soraya C.  M.; Ren, Longhui; Farmer, Andrew D.; Pandey, Manish K.; Samoluk, Sergio S.; Abernathy, Brian; Agarwal, Gaurav; Ballén-Taborda, Carolina; Cameron, Connor; Campbell, Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; El Baidouri, Moaine; Guo, Baozhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher G.; Mirouze, Marie; Moretzsohn, Márcio C.; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, Erez L.; Michelmore, Richard; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K.  S.; Scheffler, Brian E.; Grimwood, Jane; Ozias-Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz, Jeremy

doi:10.1038/s41588-019-0405-z

Title: The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Journal Article · 01 May 2019 · Nature Genetics

DOI: https://doi.org/10.1038/s41588-019-0405-z · OSTI ID:1616085

^[1];

^[2]; Clevenger, Josh ^[1];

^[3]; Gao, Dongying ^[1]; Seijo, Guillermo ^[4]; Leal-Bertioli, Soraya C. M. ^[5]; Ren, Longhui ^[6]; Farmer, Andrew D. ^[7];

^[8]; Samoluk, Sergio S. ^[4]; Abernathy, Brian ^[1]; Agarwal, Gaurav ^[9]; Ballén-Taborda, Carolina ^[1]; Cameron, Connor ^[7];

^[6]; Chavarro, Carolina ^[1]; Chitikineni, Annapurna ^[8]; Chu, Ye ^[9]; Dash, Sudhansu ^[7] more »

Univ. of Georgia, Athens, GA (United States)
HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
Baylor College of Medicine, Houston, TX (United States)
Univ. Nacional de Nordeste, Corrientes (Argentina)
Univ. of Georgia, Athens, GA (United States); Univ. of Georgia, Tifton, GA (United States)
Iowa State Univ., Ames, IA (United States)
National Center for Genome Resources, Santa Fe, NM (United States)
International Crops Research Inst. for the Semi-Arid Tropics (ICRISAT), Hyderabad (India)
Univ. of Georgia, Tifton, GA (United States)
Centre National de la Recherche Scientifique (CNRS), Perpignan (France); Univ. of Perpigan (France)
US Dept. of Agriculture (USDA)., Tifton, GA (United States)
Univ. of Georgia, Athens, GA (United States); LG Chem, Seoul (South Korea)
Univ. of Perpigan (France); Research Inst. Development (IRD), Montpellier (France); Montpellier Univ. (France)
Embrapa Genetic Resources and Biotechnology, Brasilia (Brazil)
Kazusa DNA Research Inst., Kisarazu (Japan)
National Inst. of Plant Genome Research, New Delhi (India)
US Dept. of Agriculture (USDA), Ames, IA (United States)
Henan Academy of Agricultural Sciences, Zhengzhou (China); Ministry of Agriculture and Rural Affairs, Zhengzhou (China)
Univ. of California, Davis, CA (United States)
US Dept. of Agriculture (USDA), Tifton, GA (United States)
US Dept. of Agriculture (USDA), Stoneville, MS (United States)
HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); The Peanut Foundation; National Science Foundation (NSF); USDA; Ministry of Science and Technology, India

Grant/Contract Number:: AC02-05CH11231; 04-852-14; 04-805-17; 1339194; BT/RLF/Re-entry/41/2013

OSTI ID:: 1616085

Journal Information:: Nature Genetics, Vol. 51, Issue 5; ISSN 1061-4036

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 317 works

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Additional file 1 of QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing Liu, Hua; Sun, Ziqi; Zhang, Xinyou figshare https://doi.org/10.6084/m9.figshare.12421808	dataset	January 2020
Additional file 3 of QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing Liu, Hua; Sun, Ziqi; Zhang, Xinyou figshare https://doi.org/10.6084/m9.figshare.12421823	dataset	January 2020
Additional file 4 of QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing Liu, Hua; Sun, Ziqi; Zhang, Xinyou figshare https://doi.org/10.6084/m9.figshare.12421832.v1	dataset	January 2020
Additional file 13 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut Yuan, Cuiling; Li, Chunjuan; Lu, Xiaodong figshare https://doi.org/10.6084/m9.figshare.13047392	image	January 2020
Additional file 14 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut Yuan, Cuiling; Li, Chunjuan; Lu, Xiaodong figshare https://doi.org/10.6084/m9.figshare.13047395	image	January 2020
Additional file 8 of Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut Yuan, Cuiling; Li, Chunjuan; Lu, Xiaodong figshare https://doi.org/10.6084/m9.figshare.13047422.v1	image	January 2020
Additional file 1 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141832.v1	image	January 2020
Additional file 2 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141835.v1	image	January 2020
Additional file 3 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141838	dataset	January 2020
Additional file 4 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141841	dataset	January 2020
Additional file 5 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141844.v1	dataset	January 2020
Additional file 6 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141847	dataset	January 2020
Additional file 7 of Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development Zhao, Xiaobo; Li, Chunjuan; Zhang, Hao figshare https://doi.org/10.6084/m9.figshare.13141850	dataset	January 2020
Additional file 10 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535576	image	January 2021
Additional file 11 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535579.v1	image	January 2021
Additional file 12 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535582.v1	image	January 2021
Additional file 13 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535585.v1	image	January 2021
Additional file 14 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535588.v1	image	January 2021
Additional file 15 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535591	image	January 2021
Additional file 16 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535600.v1	image	January 2021
Additional file 9 of Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L Xiong, Yi; Lei, Xiong; Bai, Shiqie figshare https://doi.org/10.6084/m9.figshare.13535633	image	January 2021
Additional file 1 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069267	image	January 2021
Additional file 2 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069270.v1	image	January 2021
Additional file 3 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069273.v1	image	January 2021
Additional file 4 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069276.v1	image	January 2021
Additional file 5 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069279	image	January 2021
Additional file 6 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069282	dataset	January 2021
Additional file 7 of Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut Fu, Liuyang; Wang, Qian; Li, Lina figshare https://doi.org/10.6084/m9.figshare.14069285	dataset	January 2021
Additional file 1 of Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations Zhang, Xingguo; Pandey, Manish K.; Wang, Jianping figshare https://doi.org/10.6084/m9.figshare.17030597.v1	dataset	January 2021
Additional file 6 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner Duan, Zhenquan; Zhang, Yongli; Zhang, Tian figshare https://doi.org/10.6084/m9.figshare.18393503.v1	dataset	January 2022
Additional file 7 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner Duan, Zhenquan; Zhang, Yongli; Zhang, Tian figshare https://doi.org/10.6084/m9.figshare.18393506.v1	dataset	January 2022
Additional file 8 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner Duan, Zhenquan; Zhang, Yongli; Zhang, Tian figshare https://doi.org/10.6084/m9.figshare.18393509	dataset	January 2022
Additional file 9 of Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner Duan, Zhenquan; Zhang, Yongli; Zhang, Tian figshare https://doi.org/10.6084/m9.figshare.18393512.v1	dataset	January 2022
Additional file 2 of Comprehensive evaluation of Chinese peanut mini-mini core collection and QTL mapping for aflatoxin resistance Ding, Yingbin; Qiu, Xike; Luo, Huaiyong figshare https://doi.org/10.6084/m9.figshare.19633800	dataset	January 2022
Additional file 10 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356548.v1	image	January 2022
Additional file 11 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356551	image	January 2022
Additional file 12 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356554.v1	dataset	January 2022
Additional file 13 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356557	dataset	January 2022
Additional file 14 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356560.v1	dataset	January 2022
Additional file 15 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356566	dataset	January 2022
Additional file 16 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356569	dataset	January 2022
Additional file 17 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356572	dataset	January 2022
Additional file 18 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356575	dataset	January 2022
Additional file 19 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356578.v1	image	January 2022
Additional file 1 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356581	dataset	January 2022
Additional file 20 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356584.v1	dataset	January 2022
Additional file 21 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356587.v1	image	January 2022
Additional file 22 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356590.v1	dataset	January 2022
Additional file 23 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356593.v1	dataset	January 2022
Additional file 2 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356599	image	January 2022
Additional file 3 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356602.v1	image	January 2022
Additional file 4 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356605.v1	dataset	January 2022
Additional file 5 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356608.v1	dataset	January 2022
Additional file 6 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356614	dataset	January 2022
Additional file 7 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356617	dataset	January 2022
Additional file 8 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356620	dataset	January 2022
Additional file 9 of Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses Wang, Wei; Shao, An; Xu, Xiao figshare https://doi.org/10.6084/m9.figshare.20356623.v1	dataset	January 2022
Additional file 1 of Comparison of ONT and CCS sequencing technologies on the polyploid genome of a medicinal plant showed that high error rate of ONT reads are not suitable for self-correction Zeng, Peng; Tian, Zunzhe; Han, Yuwei figshare https://doi.org/10.6084/m9.figshare.20462287	dataset	January 2022
Additional file 1 of Genome-wide identification of SWEET genes reveals their roles during seed development in peanuts Li, Yang; Fu, Mengjia; Li, Jiaming figshare https://doi.org/10.6084/m9.figshare.25367362.v1	dataset	January 2024
Additional file 1 of High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut Pandey, Manish K.; Gangurde, Sunil S.; Shasidhar, Yaduru figshare https://doi.org/10.6084/m9.figshare.25572524.v1	dataset	January 2024
Additional file 1 of Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut Wang, Feifei; Miao, Huarong; Zhang, Shengzhong figshare https://doi.org/10.6084/m9.figshare.25865055	dataset	January 2024
Additional file 1 of WRKY transcription factors modulate flowering time in four Arachis species: a bioinformatics analysis Fang, Xiao; Liu, Lubin; Li, Meiran figshare https://doi.org/10.6084/m9.figshare.26129743.v1	dataset	January 2024