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Shifeng Cheng Lab



  Shifeng CHENG, research Professor, doctoral advisor. He completed his PhD in 2016 at the University of Hong Kong, majoring in Genomics-based Bioinformatics. His main research interest is “how plant acquired new traits along the entire evolutionary innovation journey”, and particularly to pinpoint the underlying molecular mechanisms, either by species-based phylogenomics approach (comparative evolutionary genomics) or via population-based sampling & association study (GWAS and genome-wide selection scanning). In the past a few of years, his team has been focusing on the origin and diversification of Nitrogen-fixing root nodule symbiosis, plant terrestrialization, and population evolution and domestication history for polyploidy crops. Achievements have been made to unravel the genomic novelties and master regulators that were responsible for pre-adaptation and parallel evolution of plant key traits. These results were published in Science, Cell, Nature Biotechnology, and Plant Cell, etc., some of which have been selected to Faculty 1000, highly cited with a global impact in the community, and reported and recommended in top-tiers journal like Science, Nature Plants.


  Working Experience

  2018.10–Present     Agricultural Genomics Institute at Shenzhen-CAAS    Research Professor            

  2011.07–2018.10    BGI-SHENZHEN                                                          Senior Scientist     


  Education Experience

  University of Hong Kong           Ph.D               2013.09–2016.12

  BGI-SHENZHEN                       Master            2008.09–2011.07

  Hubei University                        Bachelor          2004.09–2008.07


  Research Interest

  His team focuses on plant biodiversity and evolutionary genomics, particularly on large-scale phylogenomics both for cereal grains and legume grains, in which two key scientific questions are highlighted: N-fixing root nodule symbiosis and C4 photosynthesis. The vision is: borrow genes from nature, evolution, and biodiversity to ‘real crops’. Current research topics include:

  1)Origin and evolutionary genetic pathway of N-fixing root nodule symbiosis;

  2)large-scale phylogenomics and the underlying molecular mechanism of the parallel evolution of C4 photosynthesis;

  3) G3RP: Global Grain Genomics Research Program, an international consortia

  4) horizontal gene transfer and plant macroevolution.


  Major Achievements

  Through large-scale phylogenomics study, his team explores the genome evolution and diversity of Root Nodule Symbiosis across N-fixing Nodulation Clade, proposed a “multiple independent losses” hypothesis to explain the underlying mechanism of the "deep homology and phylogenetic distribution" for RNS in NFN clade, the results was published in Science (Science 2018, DOI: 10.1126/science.aat1743), a series of follow-up studies are still ongoing. Meanwhile, by collaborating with Michael Melkonian and the 10KP team, they identified two key genes, which were transferred from soil bacterial to the ancestor of land plants at around 550 milliion years ago, playing key role in plant terrestrialization and adaptation process. This result was published in Cell (Cell, 2019, DOI: They are still exploring the molecular mechanism of primary endosymbiosis 1.5 billion years ago, the gradual loss and gains (kleptoplastid) responsible for the horizontal spread of photosynthesis among many ocean algae and protists. Recently, they initiated the G3RP program, to call for global effort to have a systematic study on both cereal grains and legume grain genomes.


  Selected Publication

  1.Shifeng Cheng, Wenfei Xian, et al. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution. Cell, 2019, 179(5): P1057-1067.E14 DOI:

  2.Maximilian Griesmann, et al., Martin Parniske*, Pierre-Marc Delaux*, Shifeng Cheng*. Phylogenomics reveals multiple independent losses of the nitrogen-fixing root nodule symbiosis. 24 May 2018. Science. eaat1743. DOI: 10.1126/science.aat1743

  3.Shifeng Cheng, Michael Melkonian, Stephen A. Smith, Samuel Brockington, John M. Archibald, Pierre-Marc Delaux, Fay-wei Li, Barbara Melkonian, Evgeny V. Mavrodiev, Wenjing Sun, Yuan Fu, Huanming Yang, Douglas E. Soltis, Sean W. Graham, Pamela S. Soltis, Xin Liu, Xun Xu, Gane Ka-Shu Wong. 10KP: A Phylodiverse Genome Sequencing Plan. 2018. GigaScience, giy013,

  4.Shifeng Cheng, Bernard Gutmann, Xiao Zhong, Yongtao Ye, Mark F. Fisher, Fengqi Bai, Ian Castleden, Yue Song, Bo Song, Xin Liu, Xun Xu, Boon Leong Lim, Charles S. Bond, Siu-Ming Yiu, Ian Small. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants. The Plant Journal, (2016), doi: 10.1111/tpj.13121.

  5.Senjie Lin, † Shifeng Cheng, † Bo Song, † Xiao Zhong, † Xin Lin, † Wujiao Li, Ling Li, Yaqun Zhang, Huan Zhang, Zhiliang Ji, Meichun Cai, Yunyun Zhuang, ‡ Xinguo Shi, Lingxiao Lin, Lu Wang, Zhaobao Wang, Xin Liu, Sheng Yu, Peng Zeng, Han Hao, Quan Zou, Chengxuan Chen, Yanjun Li, Ying Wang, Chunyan Xu, Shanshan Meng, Xun Xu, Jun Wang, Huanming Yang, David A. Campbell, Nancy R. Sturm, Steve Dagenais-Bellefeuille, David Morse: The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science 11/2015; 350(6261):691-694. DOI:10.1126/science.aad0408

  6.Shifeng Cheng, Erik van den Bergh, Peng Zeng, Xiao Zhong, Jiajia Xu, Xin Liu, Johannes Hofberger, Suzanne de Bruijn, Amey S Bhide, Canan Kuelahoglu, Chao Bian, Jing Chen, Guangyi Fan, Kerstin Kaufmann, Jocelyn C Hall, Annette Becker, Andrea Bräutigam, Andreas P M Weber, Chengcheng Shi, Zhijun Zheng, Wujiao Li, Mingju Lv, Yimin Tao, Junyi Wang, Hongfeng Zou, Zhiwu Quan, Julian M Hibberd, Gengyun Zhang, Xin-Guang Zhu, Xun Xu, M Eric Schranz: The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers. The Plant Cell 08/2013; 25(8). DOI:10.1105/tpc.113.113480

  7.Gengyun Zhang†, Xin Liu†, Zhiwu Quan†, Shifeng Cheng†, Xun Xu†, Shengkai Pan†, Min Xie, Peng Zeng, Zhen Yue, Wenliang Wang, Ye Tao, et. al, Jian Wang: Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol. Nature Biotechnology 05/2012; 30(6):549-54.