title: Cassava genome from a wild ancestor to cultivated varieties.
abstract: Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Wenquan
authors.initials: W
authors.lastname: Wang
authors.affiliation: 1] Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China [2] Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Binxiao
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authors.lastname: Feng
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Xia
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Xincheng
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Pinghua
authors.initials: P
authors.lastname: Li
authors.affiliation: 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China.
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
authors.affiliation: South China Botanical Garden, CAS, Guangzhou 510650, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Birger Lindberg
authors.initials: BL
authors.lastname: Møller
authors.affiliation: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.affiliation: South China Botanical Garden, CAS, Guangzhou 510650, China.
authors.forename: Gong
authors.initials: G
authors.lastname: Xiao
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Jingxing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Songbi
authors.initials: S
authors.lastname: Chen
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Hong-Bin
authors.initials: HB
authors.lastname: Zhang
authors.affiliation: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
authors.forename: Henan
authors.initials: H
authors.lastname: Ceballos
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Qunfeng
authors.initials: Q
authors.lastname: Lou
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Meiling
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authors.affiliation: Brazilian Enterprise for Agricultural Research (EMBRAPA), Genetic Resources and Biotechnology, Brasilia 70770, Brazil.
authors.forename: Luiz J C B
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authors.lastname: Carvalho
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Changying
authors.initials: C
authors.lastname: Zeng
authors.affiliation: 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Xia
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Shixiang
authors.initials: S
authors.lastname: Sun
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Lu
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Mengbin
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authors.lastname: Ruan
authors.affiliation: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
authors.forename: Shuigeng
authors.initials: S
authors.lastname: Zhou
authors.affiliation: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
authors.forename: Zhicheng
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authors.lastname: Wu
authors.affiliation: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
authors.forename: Hui
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authors.lastname: Liu
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Rubini Maya
authors.initials: RM
authors.lastname: Kannangara
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Jørgensen
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Rebecca Louise
authors.initials: RL
authors.lastname: Neale
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Maya
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authors.lastname: Bonde
authors.affiliation: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
authors.forename: Nanna
authors.initials: N
authors.lastname: Heinz
authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Wenli
authors.initials: W
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authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Shujuan
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authors.lastname: Wang
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Yang
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authors.lastname: Zhang
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Kun
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authors.lastname: Pan
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Mingfu
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authors.lastname: Wen
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Ping-An
authors.initials: PA
authors.lastname: Ma
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Zhengxu
authors.initials: Z
authors.lastname: Li
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Meizhen
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authors.lastname: Hu
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Wenbin
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authors.lastname: Liao
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Hu
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Shengkui
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authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Jinli
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authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
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authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Jianchun
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authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Wenjun
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authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
authors.forename: Sandra
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
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authors.affiliation: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
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authors.lastname: Fregene
authors.affiliation: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
authors.forename: L Augusto Becerra
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authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
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authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616, USA.
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authors.initials: FM
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authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Meili
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authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
authors.forename: Songnian
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authors.lastname: Hu
authors.affiliation: South China Botanical Garden, CAS, Guangzhou 510650, China.
authors.forename: Guojiang
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authors.lastname: Wu
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Silin
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authors.lastname: Zhong
authors.affiliation: Citrus Research and Education Center (CREC), University of Florida, Gainesville, Florida 32611, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Ling
authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Yeyuan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Qinghuang
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Guodao
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authors.lastname: Liu
authors.affiliation: State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Biogeography and Bioresources in Arid Land, Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
authors.forename: Kaimian
authors.initials: K
authors.lastname: Li
authors.affiliation: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
authors.forename: Ming
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authors.lastname: Peng
mesh_terms: D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D002365:Manihot / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010788:Photosynthesis; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012641:Selection, Genetic; D013213:Starch / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D013213:Starch