title: The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut.
abstract: Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
authors.affiliation: Institute of Biological Sciences, University of Brasília, Brasília, Brazil.|Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: David John
authors.identifier: http://orcid.org/0000-0003-0294-7284
authors.initials: DJ
authors.lastname: Bertioli
authors.affiliation: Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, Iowa, USA.
authors.forename: Steven B
authors.identifier: http://orcid.org/0000-0003-2777-8034
authors.initials: SB
authors.lastname: Cannon
authors.affiliation: Genome Center, University of California, Davis, Davis, California, USA.|Department of Plant Sciences, University of California, Davis, Davis, California, USA.
authors.forename: Lutz
authors.initials: L
authors.lastname: Froenicke
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Guodong
authors.initials: G
authors.lastname: Huang
authors.affiliation: National Center for Genome Resources, Santa Fe, New Mexico, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.affiliation: Department of Computer Science, Iowa State University, Ames, Iowa, USA.
authors.forename: Ethalinda K S
authors.initials: EK
authors.lastname: Cannon
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Dongying
authors.initials: D
authors.lastname: Gao
authors.affiliation: Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, Georgia, USA.
authors.forename: Josh
authors.initials: J
authors.lastname: Clevenger
authors.affiliation: National Center for Genome Resources, Santa Fe, New Mexico, USA.
authors.forename: Sudhansu
authors.initials: S
authors.lastname: Dash
authors.affiliation: Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, USA.
authors.forename: Longhui
authors.initials: L
authors.lastname: Ren
authors.affiliation: Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
authors.forename: Márcio C
authors.initials: MC
authors.lastname: Moretzsohn
authors.affiliation: Kazusa DNA Research Institute, Department of Frontier Research, Kisarazu, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.affiliation: Department of Agronomy, Iowa State University, Ames, Iowa, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.affiliation: Institute of Biological Sciences, University of Brasília, Brasília, Brazil.|Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
authors.forename: Bruna
authors.initials: B
authors.lastname: Vidigal
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.affiliation: Department of Horticulture, University of Georgia, Tifton, Georgia, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Chu
authors.affiliation: Department of Genetics, University of Georgia, Athens, Georgia, USA.
authors.forename: Chad E
authors.initials: CE
authors.lastname: Niederhuth
authors.affiliation: National Center for Genome Resources, Santa Fe, New Mexico, USA.
authors.forename: Pooja
authors.initials: P
authors.lastname: Umale
authors.affiliation: Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
authors.forename: Ana Cláudia G
authors.initials: AC
authors.lastname: Araújo
authors.affiliation: Genome Center, University of California, Davis, Davis, California, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kozik
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Kyung Do
authors.initials: KD
authors.lastname: Kim
authors.affiliation: Texas A&M AgriLife Research, Lubbock, Texas, USA.|Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Burow
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Shandong Academy of Agricultural Sciences, Biotechnology Research Center, Jinan, China.
authors.forename: Xingjun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Henan Academy of Agricultural Sciences, Zhengzhou, China.
authors.forename: Xinyou
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Plant Genetic Resources Conservation Unit, US Department of Agriculture-Agricultural Research Service, Griffin, Georgia, USA.|International Potato Center, Lima, Peru.
authors.forename: Noelle
authors.initials: N
authors.lastname: Barkley
authors.affiliation: Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
authors.forename: Patrícia M
authors.initials: PM
authors.lastname: Guimarães
authors.affiliation: Kazusa DNA Research Institute, Department of Frontier Research, Kisarazu, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Isobe
authors.affiliation: Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service, Tifton, Georgia, USA.
authors.forename: Baozhu
authors.initials: B
authors.lastname: Guo
authors.affiliation: Chinese Academy of Agricultural Sciences, Oil Crops Research Institute, Wuhan, China.
authors.forename: Boshou
authors.initials: B
authors.lastname: Liao
authors.affiliation: Department of Crop Science, North Carolina State University, Raleigh, North Carolina, USA.
authors.forename: H Thomas
authors.initials: HT
authors.lastname: Stalker
authors.affiliation: Department of Genetics, University of Georgia, Athens, Georgia, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Middle Southern Area Genomics Laboratory, US Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi, USA.
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.|Embrapa Genetic Resources and Biotechnology, Brasília, Brazil.
authors.forename: Soraya C M
authors.initials: SC
authors.lastname: Leal-Bertioli
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Xun
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Genome Center, University of California, Davis, Davis, California, USA.|Department of Plant Sciences, University of California, Davis, Davis, California, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Michelmore
authors.affiliation: Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, Georgia, USA.|Department of Horticulture, University of Georgia, Tifton, Georgia, USA.
authors.forename: Peggy
authors.initials: P
authors.lastname: Ozias-Akins
mesh_terms: D010367:Arachis / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D019175:DNA Methylation; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D008040:Genetic Linkage; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D011003:Ploidies; D017422:Sequence Analysis, DNA; D026801:Synteny
chemical_list: D004251:DNA Transposable Elements