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 () and Ming Peng ()
Additional contact information
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)
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
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
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)
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)

Nature Communications, 2014, vol. 5, issue 1, 1-9

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms6110

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