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程时锋课题组

程时锋课题组

Cheng Shifeng Lab

  课题组长

  程时锋,研究员,博士生导师。国家自然科学基金委优秀青年科学基金获得者,中国农业科学院“青年英才”,深圳市重大人才项目获得者。主要从事植物比较进化基因组学、作物群体遗传学、和关键性状起源和表型演化机制的多组学ENCODE研究。

  近年来重点关注trait-basedPhylo-GWAS研究方法、大规模比较进化基因组学、作物群体大数据gene-trait关联和连锁研究方法,如开发多倍体作物(小麦、燕麦等)群体多样性绘制(包括Pan-genome、Pan-SVPan-NLRome)和高效的GWAS关联分析基因发现工具和算法,包括开发kmer-based GWAS,PAV/SV-GWAS,eGWAS,mGWAS等。

  主要项目包括:(1)“谷-豆”国际基因组联盟计划()下的禾本科作物和豆科豆类比较基因组和群体基因组;(2)结瘤生物固氮分支N-fixing Root Nodule Symbiosis祖先新性状起源与多样性演化的基因表达表观调控机制;(3)C4高光合大规模比较进化基因组学,及其起源和平行演化的基因表达表观调控机制。团队先后参与完成了多个重大项目,相关研究成果以第一或通讯作者(含共同)发表在Science(2篇)、CELLNature BiotechnologyPlant Cell等杂志10篇,共发表SCI论文36篇,他引9000多次。多次主持国际学术研讨会并作报告,审稿<Nature Communication>、<Trends in Plant Science>等多篇文章。目前拥有团队成员15名,主要来自计算机科学、基因组学、生物信息学、植物分子生物学、进化与群体遗传学等多个学科。

  

  工作经历

  2018/10-至今               中国农业科学院农业基因组研究所              研究员

  2011/07-2018/10        华大基因研究院                                         资深科学家

  

  教育经历

  2013/09-2016/12          香港大学                         博士研究生

  2008/09-2011/07          深圳华大基因研究院        硕士研究生

  2004/09-2008/07          湖北大学,生物科学        本科

  

  团队研究方向

  课题组关注植物生物多样性基因组,聚焦于禾本科与豆科,以及背后两个关键的科学问题:结瘤共生固氮与C4高光效的分子机制,并致力于从“phylogenomics”、“population genetics”和“trait-based ENCODE”三个维度进行系统研究。愿景是学习大自然与进化的智慧并应用于农业与食品领域。主要研究方向包括:

  1. 结瘤共生固氮演化起源与遗传调控网络构建;

  2. C4/CAM高光效性状平行演化的分子机制;

  3. 禾本科谷物与豆科豆类作物群体基因组及基因发现(G3RP: Global Grain Genomics Research Program);

  4. 水平基因转移在植物(生命)起源与大进化中的关键角色。

  

  研究进展

  运用大规模比较系统发育基因组学技术分析结瘤固氮的祖先起源、分布和多样性形成机制,首次提出“多重独立丢失”学说,为结瘤固氮遗传调控网络构建、结瘤固氮功能基因组学和将以豆科为代表的结瘤固氮性状通过工程化手段移植到非豆科作物中奠定了坚实的理论基础;通过基因组测序和生物信息学分析手段,研究禾本科、豆科等生物多样性丰富的植物科属及其代表性物种,探索其基因组进化历史和祖先重构,关键基因家族演化史,非编码区调控元件及关键遗传代谢通路网络构建;积累大量有关真核生物的起源、陆地植物、植物、微生物symbiosis的起源等关键进化节化点上的基因组数据和发现。文章先后发表在 Science , Cell , Nature , Nature Genetics , Plant Cell , Plant Journal 等知名学术刊物中。

  

  PI

  Shifeng CHENG, professor, doctoral advisor. “Outstanding Young Talent” of CAAS, winner of National Excellent Youth Fund, national leading talent at Shenzhen.

  His main research interest is “how plant acquired new traits, and how crop evolved with phenotypic changes”, either by comparative & evolutionary genomics (phylogenomics) in plant long evolutionary history, or by population genomics in species level. In the past a few of years, his team has been focusing on the molecular mechanism underlying the origin and diversification of Nitrogen-fixing root nodule symbiosis, C4 photosynthesis, plant macroevolution, as well as the domestication history and key trait evolution in the two most important crop clade: cereal and legume. He is leading the “Global Grain Genomics Research Program”: G3RP, , to decode the global grain crop wild relatives from three dimensions: (1) phylogenomics; (2) population genetics; (3) trait-based ENCODE (multi-omics), and utilize genomics-based big data to guide precise agriculture. Achievements have been made to unravel the genomic novelties and master regulators that were responsible for root nodule symbiosis (NIN genes), and plant terrestrialization (GRAS gene family). These results were published as leading author in Science , Cell , Nature Biotechnology , and Plant Cell , etc., mostly were selected to Faculty 1000.

 

  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: https://doi.org/10.1016/j.cell.2019.10.019). 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. Cheng S*, Wong G, Melkonian M. Giant DNA viruses make big strides in eukaryote evolution. Cell Host & Microbe (2021). https://doi.org/10.1016/j.chom.2021.01.008  

  2. Cheng S*, Xian W, Fu Y, et al. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution. Cell , 2019, 179(5): 1057-1067. e14.  

  3. Griesmann M, Chang Y, Liu X, et al. Cheng S†. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science , 2018, 361(6398): eaat1743.  

  4. Cheng S*, Melkonian M, Smith SA, et al. 10KP: A phylodiverse genome sequencing plan.  Gigascience . 2018;7(3):1–9.  

  5. Cheng S*, Gutmann B, Zhong X, et al. Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants.  Plant J . 2016;85(4):532–547.  

  6. Lin S, Cheng S*, Song B, et al. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis.  Science . 2015;350(6261):691–694. 

  7. Cheng S*, van den Bergh E, Zeng P, et al. The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers.  Plant Cell . 2013;25(8):2813–2830.  

  8. Zhang, G., Liu, X., Quan, Z. Cheng S*.  et al.  Genome sequence of foxtail millet ( Setaria italica ) provides insights into grass evolution and biofuel potential. Nat Biotechnol  30, 549–554 (2012).

  程时锋课题组更新于2021年2月

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