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Cassava genome from a wild ancestor to cultivated varieties

Author

Listed:
  • Wenquan Wang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Binxiao Feng

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS)
    Tropical Crop Genetic Resources Institute, CATAS)

  • Jingfa Xiao

    (Beijing Institute of Genomics, Chinese Academy of Sciences (CAS))

  • Zhiqiang Xia

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Xincheng Zhou

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Pinghua Li

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Weixiong Zhang

    (Washington University
    Institute for Systems Biology, Jianghan University)

  • Ying Wang

    (South China Botanical Garden, CAS)

  • Birger Lindberg Møller

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Peng Zhang

    (Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS)

  • Ming-Cheng Luo

    (University of California)

  • Gong Xiao

    (South China Botanical Garden, CAS)

  • Jingxing Liu

    (Beijing Institute of Genomics, Chinese Academy of Sciences (CAS))

  • Jun Yang

    (Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS)

  • Songbi Chen

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Pablo D. Rabinowicz

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Xin Chen

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Hong-Bin Zhang

    (Texas A&M University, College Station)

  • Henan Ceballos

    (International Center for Tropical Agriculture (CIAT))

  • Qunfeng Lou

    (State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University)

  • Meiling Zou

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Luiz J.C.B. Carvalho

    (Brazilian Enterprise for Agricultural Research (EMBRAPA), Genetic Resources and Biotechnology)

  • Changying Zeng

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Jing Xia

    (Washington University
    Institute for Systems Biology, Jianghan University)

  • Shixiang Sun

    (Beijing Institute of Genomics, Chinese Academy of Sciences (CAS))

  • Yuhua Fu

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Haiyan Wang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Cheng Lu

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Mengbin Ruan

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Shuigeng Zhou

    (Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University)

  • Zhicheng Wu

    (Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University)

  • Hui Liu

    (Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University)

  • Rubini Maya Kannangara

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Kirsten Jørgensen

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Rebecca Louise Neale

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Maya Bonde

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Nanna Heinz

    (Plant Biochemistry Laboratory, University of Copenhagen)

  • Wenli Zhu

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Shujuan Wang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Yang Zhang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Kun Pan

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Mingfu Wen

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Ping-An Ma

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Zhengxu Li

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Meizhen Hu

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Wenbin Liao

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Wenbin Hu

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Shengkui Zhang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Jinli Pei

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Anping Guo

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Jianchun Guo

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Jiaming Zhang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Zhengwen Zhang

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Jianqiu Ye

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Wenjun Ou

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Yaqin Ma

    (University of California)

  • Xinyue Liu

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Luke J. Tallon

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Kevin Galens

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Sandra Ott

    (Institute for Genome Sciences, University of Maryland School of Medicine)

  • Jie Huang

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Jingjing Xue

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Feifei An

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Qingqun Yao

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Xiaojing Lu

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Martin Fregene

    (International Center for Tropical Agriculture (CIAT)
    Present address: Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA)

  • L. Augusto Becerra López-Lavalle

    (International Center for Tropical Agriculture (CIAT))

  • Jiajie Wu

    (University of California)

  • Frank M. You

    (University of California)

  • Meili Chen

    (Beijing Institute of Genomics, Chinese Academy of Sciences (CAS))

  • Songnian Hu

    (Beijing Institute of Genomics, Chinese Academy of Sciences (CAS))

  • Guojiang Wu

    (South China Botanical Garden, CAS)

  • Silin Zhong

    (State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong)

  • Peng Ling

    (Citrus Research and Education Center (CREC), University of Florida)

  • Yeyuan Chen

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Qinghuang Wang

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

  • Guodao Liu

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Bin Liu

    (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)

  • Kaimian Li

    (Tropical Crop Genetic Resources Institute, CATAS)

  • Ming Peng

    (Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS))

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.

Suggested Citation

  • Wenquan Wang & Binxiao Feng & Jingfa Xiao & Zhiqiang Xia & Xincheng Zhou & Pinghua Li & Weixiong Zhang & Ying Wang & Birger Lindberg Møller & Peng Zhang & Ming-Cheng Luo & Gong Xiao & Jingxing Liu & J, 2014. "Cassava genome from a wild ancestor to cultivated varieties," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6110
    DOI: 10.1038/ncomms6110
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