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Nature communications
Oct 10, 2014;5 5110.

Cassava genome from a wild ancestor to cultivated varieties.

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, Jun Yang, Songbi Chen, Pablo D Rabinowicz, Xin Chen, Hong-Bin Zhang, Henan Ceballos, Qunfeng Lou, Meiling Zou, Luiz J C B Carvalho, Changying Zeng, Jing Xia, Shixiang Sun, Yuhua Fu, Haiyan Wang, Cheng Lu, Mengbin Ruan, Shuigeng Zhou, Zhicheng Wu, Hui Liu, Rubini Maya Kannangara, Kirsten Jørgensen, Rebecca Louise Neale, Maya Bonde, Nanna Heinz, Wenli Zhu, Shujuan Wang, Yang Zhang, Kun Pan, Mingfu Wen, Ping-An Ma, Zhengxu Li, Meizhen Hu, Wenbin Liao, Wenbin Hu, Shengkui Zhang, Jinli Pei, Anping Guo, Jianchun Guo, Jiaming Zhang, Zhengwen Zhang, Jianqiu Ye, Wenjun Ou, Yaqin Ma, Xinyue Liu, Luke J Tallon, Kevin Galens, Sandra Ott, Jie Huang, Jingjing Xue, Feifei An, Qingqun Yao, Xiaojing Lu, Martin Fregene, L Augusto Becerra López-Lavalle, Jiajie Wu, Frank M You, Meili Chen, Songnian Hu, Guojiang Wu, Silin Zhong, Peng Ling, Yeyuan Chen, Qinghuang Wang, Guodao Liu, Bin Liu, Kaimian Li, Ming Peng
Author Information
  1. Wenquan Wang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  2. Binxiao Feng: 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.
  3. Jingfa Xiao: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
  4. Zhiqiang Xia: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  5. Xincheng Zhou: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  6. Pinghua Li: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  7. Weixiong Zhang: 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.
  8. Ying Wang: South China Botanical Garden, CAS, Guangzhou 510650, China.
  9. Birger Lindberg Møller: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  10. Peng Zhang: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China.
  11. Ming-Cheng Luo: Department of Plant Sciences, University of California, Davis, California 95616, USA.
  12. Gong Xiao: South China Botanical Garden, CAS, Guangzhou 510650, China.
  13. Jingxing Liu: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
  14. Jun Yang: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China.
  15. Songbi Chen: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  16. Pablo D Rabinowicz: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
  17. Xin Chen: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  18. Hong-Bin Zhang: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA.
  19. Henan Ceballos: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
  20. Qunfeng Lou: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
  21. Meiling Zou: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  22. Luiz J C B Carvalho: Brazilian Enterprise for Agricultural Research (EMBRAPA), Genetic Resources and Biotechnology, Brasilia 70770, Brazil.
  23. Changying Zeng: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  24. Jing Xia: 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.
  25. Shixiang Sun: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
  26. Yuhua Fu: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  27. Haiyan Wang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  28. Cheng Lu: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  29. Mengbin Ruan: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  30. Shuigeng Zhou: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
  31. Zhicheng Wu: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
  32. Hui Liu: Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China.
  33. Rubini Maya Kannangara: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  34. Kirsten Jørgensen: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  35. Rebecca Louise Neale: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  36. Maya Bonde: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  37. Nanna Heinz: Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark.
  38. Wenli Zhu: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  39. Shujuan Wang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  40. Yang Zhang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  41. Kun Pan: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  42. Mingfu Wen: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  43. Ping-An Ma: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  44. Zhengxu Li: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  45. Meizhen Hu: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  46. Wenbin Liao: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  47. Wenbin Hu: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  48. Shengkui Zhang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  49. Jinli Pei: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  50. Anping Guo: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  51. Jianchun Guo: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  52. Jiaming Zhang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  53. Zhengwen Zhang: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  54. Jianqiu Ye: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  55. Wenjun Ou: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  56. Yaqin Ma: Department of Plant Sciences, University of California, Davis, California 95616, USA.
  57. Xinyue Liu: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
  58. Luke J Tallon: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
  59. Kevin Galens: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
  60. Sandra Ott: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
  61. Jie Huang: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  62. Jingjing Xue: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  63. Feifei An: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  64. Qingqun Yao: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  65. Xiaojing Lu: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  66. Martin Fregene: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
  67. L Augusto Becerra López-Lavalle: International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia.
  68. Jiajie Wu: Department of Plant Sciences, University of California, Davis, California 95616, USA.
  69. Frank M You: Department of Plant Sciences, University of California, Davis, California 95616, USA.
  70. Meili Chen: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
  71. Songnian Hu: Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China.
  72. Guojiang Wu: South China Botanical Garden, CAS, Guangzhou 510650, China.
  73. Silin Zhong: State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China.
  74. Peng Ling: Citrus Research and Education Center (CREC), University of Florida, Gainesville, Florida 32611, USA.
  75. Yeyuan Chen: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  76. Qinghuang Wang: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
  77. Guodao Liu: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  78. 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, Urumqi 830011, China.
  79. Kaimian Li: Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China.
  80. Ming Peng: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
PMID: 25300236 DOI: 10.1038/ncomms6110

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.

Associated Data

GENBANK | JPQE00000000; JPQF00000000
SRA | SRX551093; SRX553797; SRX553798; SRX553799; SRX553800; SRX553801; SRX553802; SRX553803; SRX553804; SRX553805; SRX553806; SRX553807

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Grants

  1. R01 GM100364/NIGMS NIH HHS

MeSH Term

Evolution, Molecular
Genetic Variation
Genome, Plant
Manihot
Molecular Sequence Data
Photosynthesis
Phylogeny
Plant Proteins
Selection, Genetic
Starch

Chemicals

Plant Proteins
Starch
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 22

Word Cloud

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