武志强课题组

Wu Zhiqiang Lab

wuzhiqiang@caas.cn

13530406763

　　课题组长

武志强，研究员，博士生导师。

2012年博士毕业于中国科学院植物研究所，2012-2019年之间在瑞典、美国进行博士后研究，2019年11月加入基因组所。主要研究领域：以植物细胞器为研究对象，利用组学大数据探索细胞器基因组的变异和突变机理，以及细胞核质互作的分子机制，并挖掘以细胞器为基础的光合作用系统转化以提高作物产量。目前，主持包括国家自然科学基金面上项目、深圳市优秀青年项目、农科院青年英才项目、中国农科院南繁育种等多个项目。以第一作者或通讯作者在PNAS（2）、MBE、PBJ、BIB、MPE、TPJ、Genetics等国际知名期刊发表论文40余篇，总被引达3200余次，H 因子达25。担任多个国际期刊的审稿人，先后对70多种SCI期刊杂志进行200余次审稿，使其在植物进化生物学领域得到国际同行的认可。

　　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

1. 进化生物学：以植物细胞器为研究对象，利用组学大数据探索细胞器基因组的变异和突变机理，以及细胞核质互作的分子机制，并挖掘以细胞器为基础的基因编辑系统研究光合作用和呼吸作用系统转化以提高作物产量。

2. 园艺物种基因组学：开展岭南特色花卉如百合科、姜科、石竹目、蔷薇科等多物种的全基因组以及花卉功能性状基础和分子育种的研究，从而为岭南花卉物种的分子育种提供理论基础。

　　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、 Heredity和G3: 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。

　　

代表论文

2023年

1. Shuo Zhang, Jie Wang, Wenchuang He, Shenglong Kan, Xuezhu Liao, David R Jordan, Emma S Mace, Yongfu Tao, Alan W Cruickshank, Robert Klein, Daojun Yuan, Luke R Tembrock*, Zhiqiang Wu*. Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution. BMC Plant Biology. 2023. 23(1):91. (IF=5.260, JCR一区)

2. Wenchuang He, Kunli Xiang, Caijin Chen, Jie Wang, Zhiqiang Wu*. Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework. Briefings in Bioinformatics. 2023. 24(1):bbac522. (IF=13.994, JCR一区)

2022年

3. Xiaoni Zhang, Shengnan Lin, Dan Peng, Quanshu Wu, Xuezhu Liao, Kunli Xiang, Zehao Wang, Luke R. Tembrock, Mohammed Bendahmane, Manzhu. Bao, Zhiqiang Wu*, Xiaopeng Fu*. Integrated multi-omic data and analyses reveal the pathways underlying key ornamental traits in carnation flowers. Plant Biotechnology Journal. 2022. 20:1182–1196 (IF=13.263, JCR一区)

4. Zhiqiang Wu*, Xuezhu Liao, Xiaoni Zhang, Luke R. Tembrock, Amanda Broz. Genomic architectural variation of plant mitochondria—A review of multichromosomal structuring. Journal of Systematics and Evolution. 2022. 60(1):160–168. (IF=3.544, JCR一区)

5. Chanjuan Lai, Jie Wang, Shenglong Kan, Shuo Zhang, Pan Li, Wayne Gerald Reeve, Zhiqiang Wu*, Yonghua Zhang. Comparative analysis of mitochondrial genomes of Broussonetia spp. (Moraceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing. Frontiers in Plant Science. 2022. 13:1052151 (IF=6.627, JCR一区)

6. Yi Zou, Weidong Zhu, Daniel B. Sloan, Zhiqiang Wu*. Long-read sequencing characterizes detailed patterns of mitochondrial and plastid genome variants in Arabidopsis msh1 mutants. The Plant Journal. 2022. 112(3):738-755 (IF=7.091, JCR一区)

7. Xuezhu Liao#, Yuanjun Ye#, Xiaoni Zhang#, Dan Peng, Mengmeng Hou, Gaofei Fu, Jianjun Tan, Jianli Zhao, Rihong Jiang, Yechun Xu, Jinmei Liu, Jinliang Yang, Wusheng Liu, Luke R. Tembrock, Genfa Zhu*, Zhiqiang Wu*. The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation. aBIOTECH. 2022. 3(3):178-196.

8. Haoqi Wang, Xuezhu Liao, Luke R Tembrock, Zuoren Yang*, Zhiqiang Wu*. Evaluation of intracellular gene transfers from plastome to nuclear genome across progressively improved assemblies for Arabidopsis thaliana and Oryza sativa. Genes. 2022. (IF=4.141, JCR二区)

9. Sidan Hong, Jie Wang, Qun Wang, Guozhe Zhang, Yu Zhao, Qingqing Ma, Zhiqiang Wu*, Jin Ma*, Cuihua Gu*. Decoding the formation of diverse petal colors of Lagerstroemia indica by integrating the data from transcriptome and metabolome. Frontiers in Plant Science. 2022. 13:970023. (IF=6.627, JCR一区)

10. Xiaoni Zhang, Shengnan Lin, Quanshu Wu, Qijian Wang, Chunmei Shi, Manzhu Bao, Mohammed Bendahmane*, Xiaopeng Fu*, Zhiqiang Wu*. Floral primordium morphogenesis in double flower formation and transcriptomes reveal its networks in Dianthus chinensis. Horticultural Plant Journal. 2022. (Accepted). (IF=4.24, JCR一区)

11. Jie Wang, Wenchuang He, Xuezhu Liao, Jin Ma, Wei Gao, Haoqi Wang，Dili Wu, Luke R. Tembrock, Zhiqiang Wu*, Cuihua Gu*. Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia (Lythraceae) using plastome sequences. Horticultural Plant Journal. 2022. (Online). (IF=4.24, JCR一区)

12. Shenglong Kan, Xuezhu Liao, Zhiqiang Wu*. The Roles of Mutation and Selection Acting on Mitochondrial Genomes Inferred from Intraspecific Variation in Seed Plants. Genes. 2022. 13:1036. https://doi.org/10.3390/genes13061036 (IF=4.141, JCR二区)

13. Jie Wang#, Gaofei Fu#, Luke R. Tembrock, Xuezhu Liao, Song Ge, Zhiqiang Wu*. Mutational meltdown or controlled chain reaction: the dynamics of rapid plastome evolution in the hyperdiversity of Poaceae. Journal of Systematics and Evolution. 2022. doi.org/10.1111/jse.12854. (IF=3.544, JCR一区)

14. Kunli Xiang, Wei Mao, Huanwen Peng, Andrey Erst*, Wenchuang He*, Zhiqiang Wu*. Organization, phylogenetic marker exploitation and gene evolution in the plastome of Thalictrum (Ranunculaceae). Frontiers in Plant Science. 2022. 13:897843. (IF=6.627, JCR一区)

15. Zhou Hong, Wenchuang He, Xiaojing Liu, Luke R. Tembrock, Zhiqiang Wu*, Daping Xu*, Xuezhu Liao*. Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood. Forests. 2022. 13(4), 626. (IF=3.282, 林学JCR一区)

16. Liang Tang#, Xuezhu Liao#, Luke R Tembrock, Song Ge, Zhiqiang Wu*. A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae). DNA Research. 2022. 29(2):dsac005. (IF=4.477, JCR二区)

17. Guihua Huang#, Xuezhu Liao#, Qiang Han, Zaizhi Zhou, Kunnan Liang, Guangyou Li, Guang Yang, Luke R Tembrock, Xianbang Wang*, Zhiqiang Wu*. Integrated metabolome and transcriptome analyses reveal dissimilarities in the anthocyanin synthesis pathway between different developmental leaf color transitions in Hopea hainanensis (Dipterocarpaceae). Frontiers in Plant Science. 2022. 13:830413. (IF=6.627, JCR二区)

18. Yuanjun Ye#, Xiaoni Zhang#, Xueqing Chen, Yechun Xu, Jinmei Liu, Jianjun Tan, Wei Li, Luke R. Tembrock, Zhiqiang Wu*, Genfa Zhu*. The use of widely targeted metabolomics profiling to quantify differences in medicinally important compounds from five Curcuma (Zingiberaceae) species. Industrial Crops and Products. 2022. 175:114289. (IF=6.449 JCR一区)

2021年

19. Wenchuang He, Caijin Chen, Kunli Xiang, Jie Wang, Ping Zheng, Luke R Tembrock*, Deming Jin*, Zhiqiang Wu*. The history and diversity of rice domestication as resolved from 1464 complete plastid genomes. Frontiers in Plant Science. 2021. 12:781793. (IF=6.627, JCR二区)

20. Zhou Hong#, Xuezhu Liao#, Yuanjun Ye#, Ningnan Zhang, Zengjiang Yang, Weidong Zhu, Wei Gao, Joel Sharbrough, Luke R Tembrock, Daping Xu*, Zhiqiang Wu*. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics. 2021. 22:672. (IF=4.547, JCR二区)

21. Basanta Bista#, Zhiqiang Wu#, Robert Literman, Nicole Valenzuela*. Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Philosophical Transactions of The Royal Society B. 2021. 376(1833):20200101. (IF=6.671, JCR二区)

22. Amanda K Broz#, Gus Waneka#, Zhiqiang Wu#, Matheus Fernandes Gyorfy, Daniel B Sloan*. Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates. Genetics. 2021. 218(1):iyab039. (IF=4.402, JCR二区)

2020年

23. Zhiqiang Wu#, Gus Waneka#, Amanda K Broz#, Connor R King, Daniel B Sloan*. MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proceedings of the National Academy of Sciences USA. 2020. 117(28):16448-16455. (IF=12.779, JCR一区)

24. Zhou Hong#, Zhiqiang Wu#, Kunkun Zhao, Zengjiang Yang, Ningnan Zhang, Junyu Guo, Luke R Tembrock, Daping Xu*. Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). International Journal of Molecular Sciences. 2020. 21(11):3758. (IF=6.208, JCR二区)

25. 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. Plant Molecular Biology. 2020. 102:659–676. (IF=4.335, JCR二区)

26. 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. 10:1077-1086. (IF=3.542, JCR三区)

2019年及之前

27. Zhiqiang Wu*, Daniel B Sloan. Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes. Heredity. 2019. 122 (5), 647–659. (IF=3.832, JCR二区)

28. Cuihua Gu#, Li Ma#, Zhiqiang Wu#, Kai Chen, Yixiang Wang. Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales. BMC Plant Biology. 2019. 19:281. (IF=5.26, JCR二区)

29. 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. (IF=4.927, JCR三区)

30. Cuihua Gu, Luke R 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. (IF=6.208, JCR二区)

31. 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. (IF=8.8, JCR一区)

32. 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): e0177553. (IF=3.752, JCR三区)

33. Cuihua Gu#, Luke R Tembrock#, Nels G Johnson, Mark P Simmons, Zhiqiang Wu*. The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae). PLoS One. 2016. 11(3):e0150752. (IF=3.752, JCR三区)

34. Zhqiang Wu, Cuthbert JM, Taylor DR, Sloan DB. 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 (30): 10185–10191. (Science杂志对本文进行了报道). (IF=12.779, JCR一区)

35. 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. (IF=3.752, JCR三区)

36. Zhiqiang Wu*, Stone JD, ?torchová H, Sloan DB*.  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: 938. (IF=4.547, JCR二区)

37. 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. (IF=5.019, JCR一区)

38. 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(9):e25896. (IF=3.752, JCR三区)

　　武志强课题组更新于2023年3月