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

doi:10.1038/ncomms6110

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 LouMeiling 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

Research output: Contribution to journal › Article › peer-review

197 Scopus citations

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.

Original language	English (US)
Article number	5110
Journal	Nature communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms6110
State	Published - Oct 10 2014
Externally published	Yes

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/ncomms6110

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Wang, W, Feng, B, Xiao, J, Xia, Z, Zhou, X, Li, P, Zhang, W, Wang, Y, Møller, BL, Zhang, P, Luo, MC, Xiao, G, Liu, J, Yang, J, Chen, S, Rabinowicz, PD, Chen, X, Zhang, HB, Ceballos, H, Lou, Q, Zou, M, Carvalho, LJCB, Zeng, C, Xia, J, Sun, S, Fu, Y, Wang, H, Lu, C, Ruan, M, Zhou, S, Wu, Z, Liu, H, Kannangara, RM, Jørgensen, K, Neale, RL, Bonde, M, Heinz, N, Zhu, W, Wang, S, Zhang, Y, Pan, K, Wen, M, Ma, PA, Li, Z, Hu, M, Liao, W, Hu, W, Zhang, S, Pei, J, Guo, A, Guo, J, Zhang, J, Zhang, Z, Ye, J, Ou, W, Ma, Y, Liu, X, Tallon, LJ, Galens, K, Ott, S, Huang, J, Xue, J, An, F, Yao, Q, Lu, X, Fregene, M, López-Lavalle, LAB, Wu, J, You, FM, Chen, M, Hu, S, Wu, G, Zhong, S, Ling, P, Chen, Y, Wang, Q, Liu, G, Liu, B, Li, K & Peng, M 2014, 'Cassava genome from a wild ancestor to cultivated varieties', Nature communications, vol. 5, 5110. https://doi.org/10.1038/ncomms6110

@article{3e42ec6350d242ea867c086aea94b1e6,

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.",

author = "Wenquan Wang and Binxiao Feng and Jingfa Xiao and Zhiqiang Xia and Xincheng Zhou and Pinghua Li and Weixiong Zhang and Ying Wang and M{\o}ller, {Birger Lindberg} and Peng Zhang and Luo, {Ming Cheng} and Gong Xiao and Jingxing Liu and Jun Yang and Songbi Chen and Rabinowicz, {Pablo D.} and Xin Chen and Zhang, {Hong Bin} and Henan Ceballos and Qunfeng Lou and Meiling Zou and Carvalho, {Luiz J.C.B.} and Changying Zeng and Jing Xia and Shixiang Sun and Yuhua Fu and Haiyan Wang and Cheng Lu and Mengbin Ruan and Shuigeng Zhou and Zhicheng Wu and Hui Liu and Kannangara, {Rubini Maya} and Kirsten J{\o}rgensen and Neale, {Rebecca Louise} and Maya Bonde and Nanna Heinz and Wenli Zhu and Shujuan Wang and Yang Zhang and Kun Pan and Mingfu Wen and Ma, {Ping An} and Zhengxu Li and Meizhen Hu and Wenbin Liao and Wenbin Hu and Shengkui Zhang and Jinli Pei and Anping Guo and Jianchun Guo and Jiaming Zhang and Zhengwen Zhang and Jianqiu Ye and Wenjun Ou and Yaqin Ma and Xinyue Liu and Tallon, {Luke J.} and Kevin Galens and Sandra Ott and Jie Huang and Jingjing Xue and Feifei An and Qingqun Yao and Xiaojing Lu and Martin Fregene and L{\'o}pez-Lavalle, {L. Augusto Becerra} and Jiajie Wu and You, {Frank M.} and Meili Chen and Songnian Hu and Guojiang Wu and Silin Zhong and Peng Ling and Yeyuan Chen and Qinghuang Wang and Guodao Liu and Bin Liu and Kaimian Li and Ming Peng",

year = "2014",

month = oct,

day = "10",

doi = "10.1038/ncomms6110",

language = "English (US)",

volume = "5",

journal = "Nature communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Cassava genome from a wild ancestor to cultivated varieties

AU - Wang, Wenquan

AU - Feng, Binxiao

AU - Xiao, Jingfa

AU - Xia, Zhiqiang

AU - Zhou, Xincheng

AU - Li, Pinghua

AU - Zhang, Weixiong

AU - Wang, Ying

AU - Møller, Birger Lindberg

AU - Zhang, Peng

AU - Luo, Ming Cheng

AU - Xiao, Gong

AU - Liu, Jingxing

AU - Yang, Jun

AU - Chen, Songbi

AU - Rabinowicz, Pablo D.

AU - Chen, Xin

AU - Zhang, Hong Bin

AU - Ceballos, Henan

AU - Lou, Qunfeng

AU - Zou, Meiling

AU - Carvalho, Luiz J.C.B.

AU - Zeng, Changying

AU - Xia, Jing

AU - Sun, Shixiang

AU - Fu, Yuhua

AU - Wang, Haiyan

AU - Lu, Cheng

AU - Ruan, Mengbin

AU - Zhou, Shuigeng

AU - Wu, Zhicheng

AU - Liu, Hui

AU - Kannangara, Rubini Maya

AU - Jørgensen, Kirsten

AU - Neale, Rebecca Louise

AU - Bonde, Maya

AU - Heinz, Nanna

AU - Zhu, Wenli

AU - Wang, Shujuan

AU - Zhang, Yang

AU - Pan, Kun

AU - Wen, Mingfu

AU - Ma, Ping An

AU - Li, Zhengxu

AU - Hu, Meizhen

AU - Liao, Wenbin

AU - Hu, Wenbin

AU - Zhang, Shengkui

AU - Pei, Jinli

AU - Guo, Anping

AU - Guo, Jianchun

AU - Zhang, Jiaming

AU - Zhang, Zhengwen

AU - Ye, Jianqiu

AU - Ou, Wenjun

AU - Ma, Yaqin

AU - Liu, Xinyue

AU - Tallon, Luke J.

AU - Galens, Kevin

AU - Ott, Sandra

AU - Huang, Jie

AU - Xue, Jingjing

AU - An, Feifei

AU - Yao, Qingqun

AU - Lu, Xiaojing

AU - Fregene, Martin

AU - López-Lavalle, L. Augusto Becerra

AU - Wu, Jiajie

AU - You, Frank M.

AU - Chen, Meili

AU - Hu, Songnian

AU - Wu, Guojiang

AU - Zhong, Silin

AU - Ling, Peng

AU - Chen, Yeyuan

AU - Wang, Qinghuang

AU - Liu, Guodao

AU - Liu, Bin

AU - Li, Kaimian

AU - Peng, Ming

PY - 2014/10/10

Y1 - 2014/10/10

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=84923046944&partnerID=8YFLogxK

U2 - 10.1038/ncomms6110

DO - 10.1038/ncomms6110

M3 - Article

C2 - 25300236

AN - SCOPUS:84923046944

SN - 2041-1723

VL - 5

JO - Nature communications

JF - Nature communications

M1 - 5110

ER -

Cassava genome from a wild ancestor to cultivated varieties

Abstract

ASJC Scopus subject areas

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