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武志强课题组

来源: 发布者: 时间:2020年02月13日

  武志强课题组

  Wu Zhiqiang Lab

  课题组长

  武志强,研究员,博导,农科院青年英才。2012年博士毕业于中国科学院植物研究所,2012-2019期间先后在瑞典于默奥大学,美国德州理工大学,美国爱荷华州立大学和美国科罗拉多州立大学从事植物细胞器复杂基因组进化及其与细胞核基因组之间相互作用机制的相关研究。在Proc. Natl. Acad. Sci. U.S.A、Molecular Biology and Evolution、Molecular Phylogenetics and Evolution、Heredity等国际权威期刊发表SCI论文20余篇。

 

  工作经历

  2019.11–至今          中国农业科学院(深圳)农业基因组研究所       Principle Investigator 

       2018.1-2019.12       美国科罗拉多州立大学                                    Postdoctoral Fellow                                  

  2016.5-2017.12       美国爱荷华州立大学                                        Postdoctoral Fellow                                   

  2014.5-2016.4         美国科罗拉多州立大学                                    Postdoctoral Fellow                                   

  2013.2-2014.4         美国德州理工大学                                           Postdoctoral Fellow                                  

  2012.2-2013.2         瑞典于默奥大学                                              Doctoral Fellow                                       

  

  教育经历

  2006.9–2012.1         中国科学院植物研究所             博士            

  2002.9–2006.7         云南大学                                 学士           

  

  研究方向

  团队综合运用进化生物学,比较基因组学及功能基因组学等研究手段,以植物细胞器(叶绿体和线粒体)和细胞核为研究对象,致力于基因组变异,细胞器突变机理和细胞核质互作的研究,同时将开展多种物种基因组测定和进化变异的研究。

 

  研究进展

  1. 阐述复杂植物线粒体基因组在种内变异的进化模式

  线粒体是植物细胞的能量和动力工厂,研究其起源和进化对生命的认识具有重要的生物学意义。我们首次报道的被子植物物种具有复杂的线粒体基因组构造;也深入分析其线粒体基因组在RNA 转录水平的表达差异和基因编辑的分布;同时系统研究了线粒体基因组的拷贝数变化。这一系列的研究成果已经分别发表在美国科学院院刊PNAS、 BMC Genomics、 HeredityG3: Genes, Genomes, Genetics等期刊杂志。对丰富多样的植物进行该研究,可以帮助我们解析复杂细胞器基因组的进化。我们将继续以不同类群的植物为代表,深入这一课题的研究。

  2. 对植物线粒体基因的转移和基因转换机制进行系统鉴定和分析

  在进化的历程中,细胞器和细胞核的基因组之间都经历了基因组结构重塑和功能基因转移/丢失的过程,但是关于细胞器基因功能性转移至细胞核机制的假说一直缺乏有效的实验证据。前期选取经济作物禾本科内90个物种及其外类群为研究体系,以植物线粒体rpl5基因为研究对象,对该基因在线粒体和细胞核基因中的拷贝及转移机制进行详尽的研究。这一研究成果发表在Molecular Biology and Evolution上。我们将继续以细胞器之间基因信息转移为对象,从生命之树的角度解读基因转移的多样性和复杂性的机制。

  3. 细胞核质互作研究

  在多倍体物种形成中,单亲遗传的细胞器基因组和双亲遗传的细胞核基因组之间在进化上存在核质互作的不平衡。使用基因组学和转录组学的数据,可以解析不同进化时间尺度内的各种多倍体在形成过程中该机制的变异。

  

  PI

  Zhiqiang Wu, Principle Investigator, Doctoral Advisor,[m1]  “Outstanding Young Talent” of Chinese Academy of Agricultural Science (CAAS). He is mainly engaged in the research of the complex organelle genome evolution and its interaction with their own nuclear genome in different kinds of plant species. He has published more than 20 SCI papers (as the first author or corresponding author) including Proc. Natl. Acad. Sci. U. S. A, Molecular Biology and Evolution, Molecular Phylogenetics and Evolution, Heredity, etc.

 

  Working Experience

  2019.11–Present           Agricultural Genomics Institute at Shenzhen-CAAS           Principle Investigator                                                                       

  2018.1-2019.12            Colorado State University                                                     Postdoctoral Fellow                                     

  2016.5-2017.12            Iowa State University                                                            Postdoctoral Fellow                                   

  2014.5-2016.4              Colorado State University                                                     Postdoctoral Fellow                                   

  2013.2-2014.4              Texas Tech University                                                           Postdoctoral Fellow                                   

  2012.2-2013.2              Umeå universitet                                                                    Doctoral Fellow   

 

  Education Experience

  2006.9–2012.1                        IBCAS                                       Ph.D.          

  2002.9–2006.7                        Yunnan University                     Bachelor   

 

  Research Interest

  Our lab comprehensively employs the evolutionary biology, comparative genomics and functional genomics research to investigate the genome variation mechanism of both plant organelles (chloroplast and mitochondria) and their own nucleus genome, as well as the cytonuclear interaction and organelle mutation. Meanwhile, we also focus on plant genome sequencing and evolutionary variation across the multiple species’ families.

   

        Major Achievements

  1. The evolution pattern of intraspecific variation in complex plant mitochondrial genome

  It is important and meaningful to investigate the origin and evolution of mitochondria, which regarded as the energy factory of cells. We reported that angiosperm species could contain the complex mitochondrial genome structure than certain bacterial genome. Moreover, the expression of mitochondrial genomes at the RNA transcription level and the distribution of gene editing were also diversified. Meanwhile, the copy number changes of mitochondrial genome were systematically studied. The series results had been published in PNAS, BMC Genomics, Heredity and G3: Genes, Genomes and Genetics, etc. In all, the research of complex organelle genomes from various plants will help us to understand the evolution patterns of plant species, and We will continue to research on this topic from the representatives of different clade plants.

  2. The mechanism of mitochondrial gene transfer and gene transition were systematically identified and analyzed in plant

  During the evolution, genome of organelle and their nucleus has undergone the genome structure remodeling and functional gene transfer or loss. But there few effective experimental evidences to verify the hypothesis about how organelle gene functional transfer to nucleus. Here, the rpl5 gene in mitochondria was investigated in 90 species and their outgroup species in grass family, the copy and transfer mechanism within organelle and nucleus have been elucidated. The research results were published in Molecular Biology and Evolution and further study of gene transfer between organelle and nucleus will be conducted to interpret the mechanism of diversity and complexity of gene transfer from the perspective of life tree.

  3. Study on cytonuclear interaction

  As we know, the evolutionary imbalance between the parthenogenetic organelle genome and the biparental inherited nuclear genome had been produced in speciation of polyploids. Therefore, the data from genomics and transcriptome levels will make it possible to analyze the mechanism variation during the formation of polyploids with different evolutionary time scales. It could help us to understand the mechanism of speciation and to generate the new species in crop.

 

  Selected Publication

  1. Zhiqiang Wu, Jocelyn M. Cuthbert, Douglas R. Taylor, Daniel B. Sloan. The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes, Proceedings of the National Academy of Sciences USA. 2015, 112(33): 10185-10191.

  2. Zhiqiang Wu, Daniel B Sloan, Colin W Brown, Mónica Rosenblueth, Jeffrey D Palmer, Han Chuan Ong. Mitochondrial retroprocessing promoted functional transfers of rpl5 to the nucleus in grasses, Molecular Biology and Evolution. 2017, 34(9): 2340-2354.

  3. Zhiqiang Wu and Song Ge. The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts, Molecular Phylogenetics and Evolution. 2012, 62: 573-578.

  4. Zhiqiang Wu, James D. Stone, Helena Štorchová, Daniel B. Sloan. High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora, BMC genomics. 2015, 16(1): 938.

  5. Zhiqiang Wu and Daniel B. Sloan. Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes, Heredity. 2019, 122 (5): 647–659.

  6. Zhiqiang Wu, Gus Waneka, Daniel B. Sloan. The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana. G3: Genes, Genomes, Genetics. (2020, Online)

  7. Gang Zheng, Lingling Wei, Li Ma, Zhiqiang Wu, Cuihua Gu, Kai Chen. Comparative analyses of chloroplast genomes from 13 Lagerstroemia (Lythraceae) species: identification of highly divergent regions and inference of phylogenetic relationships. (2020, accept by Plant Molecular Biology) (并列第一作)

  8. Cuihua Gu, Luke Tembrock, Shaoyu Zheng, Zhiqiang Wu*. The complete chloroplast genome of Catha edulis: A comparative analysis of genome features with related species, International journal of molecular sciences. 2018, 19(2): 525. (通讯作者)

  9. Cuihua Gu, Bin Dong, Liang Xu, Luke R. Tembrock, Shaoyu Zheng, Zhiqiang Wu*. The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales. Molecules. 2018, 23(4): 846. (通讯作者)

  10. Zhiqiang Wu, Cuihua Gu, Luke R Tembrock, Dong Zhang, Song Ge. Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species. Plos One. 2017, 12(5).

  11. Zhiqiang Wu, Luke R Tembrock, Song Ge. Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes. PloS one. 2015, 10(2): e0118019.

  12. Li Wang, Zhiqiang Wu, Nadia Bystriakova, Stephen W Ansell, Qiao-Ping Xiang, Jochen Heinrichs, Harald Schneider, Xian-Chun Zhang. Phylogeography of the Sino-Himalayan fern Lepisorus clathratus on “the roof of the world”. PloS one. 2011, 6(7): e25896. (并列第一作)

 

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