武志強(qiáng)課題組

Wu Zhiqiang Lab

[email protected]

13530406763

　　課題組長

武志強(qiáng),，研究員，博士生導(dǎo)師,。

2012年博士畢業(yè)于中國科學(xué)院植物研究所,，2012-2019年之間在瑞典,、美國進(jìn)行博士后研究,，2019年11月加入基因組所,。主要研究領(lǐng)域：以植物細(xì)胞器為研究對(duì)象,，利用組學(xué)大數(shù)據(jù)探索細(xì)胞器基因組的變異和突變機(jī)理,，以及細(xì)胞核質(zhì)互作的分子機(jī)制,，并挖掘以細(xì)胞器為基礎(chǔ)的光合作用系統(tǒng)轉(zhuǎn)化以提高作物產(chǎn)量。目前,，主持包括國家自然科學(xué)基金面上項(xiàng)目,、深圳市優(yōu)秀青年項(xiàng)目、農(nóng)科院青年英才項(xiàng)目,、中國農(nóng)科院南繁育種等多個(gè)項(xiàng)目,。以第一作者或通訊作者在PNAS（2）、MBE,、PBJ,、BIB、MPE,、TPJ,、Genetics等國際知名期刊發(fā)表論文40余篇，總被引達(dá)3200余次,，H 因子達(dá)25,。擔(dān)任多個(gè)國際期刊的審稿人，先后對(duì)70多種SCI期刊雜志進(jìn)行200余次審稿,，使其在植物進(jìn)化生物學(xué)領(lǐng)域得到國際同行的認(rèn)可,。

　　工作經(jīng)歷

　　2019.11–至今             中國農(nóng)業(yè)科學(xué)院（深圳）農(nóng)業(yè)基因組研究所       Principle Investigator 

　　2018.1-2019.12          美國科羅拉多州立大學(xué)                                     Postdoctoral Fellow                                  

　　2016.5-2017.12          美國愛荷華州立大學(xué)                                        Postdoctoral Fellow                                   

　　2014.5-2016.4            美國科羅拉多州立大學(xué)                                     Postdoctoral Fellow                                   

　　2013.2-2014.4            美國德州理工大學(xué)                                            Postdoctoral Fellow                                  

　　2012.2-2013.2            瑞典于默奧大學(xué)                                               Doctoral Fellow                        

　　

　　教育經(jīng)歷

　　2006.9–2012.1           中國科學(xué)院植物研究所         博士            

　　2002.9–2006.7           云南大學(xué)                             學(xué)士    

 

　　研究方向

1. 進(jìn)化生物學(xué)：以植物細(xì)胞器為研究對(duì)象，利用組學(xué)大數(shù)據(jù)探索細(xì)胞器基因組的變異和突變機(jī)理,，以及細(xì)胞核質(zhì)互作的分子機(jī)制，并挖掘以細(xì)胞器為基礎(chǔ)的基因編輯系統(tǒng)研究光合作用和呼吸作用系統(tǒng)轉(zhuǎn)化以提高作物產(chǎn)量,。

2. 園藝物種基因組學(xué)：開展嶺南特色花卉如百合科,、姜科、石竹目,、薔薇科等多物種的全基因組以及花卉功能性狀基礎(chǔ)和分子育種的研究,，從而為嶺南花卉物種的分子育種提供理論基礎(chǔ),。

　　研究進(jìn)展

　　1. 闡述復(fù)雜植物線粒體基因組在種內(nèi)變異的進(jìn)化模式

　　線粒體是植物細(xì)胞的能量和動(dòng)力工廠，研究其起源和進(jìn)化對(duì)生命的認(rèn)識(shí)具有重要的生物學(xué)意義,。我們首次報(bào)道的被子植物物種具有復(fù)雜的線粒體基因組構(gòu)造,；也深入分析其線粒體基因組在RNA 轉(zhuǎn)錄水平的表達(dá)差異和基因編輯的分布；同時(shí)系統(tǒng)研究了線粒體基因組的拷貝數(shù)變化,。這一系列的研究成果已經(jīng)分別發(fā)表在美國科學(xué)院院刊PNAS,、 BMC Genomics、 Heredity和G3: Genes, Genomes, Genetics等期刊雜志,。對(duì)豐富多樣的植物進(jìn)行該研究,，可以幫助我們解析復(fù)雜細(xì)胞器基因組的進(jìn)化。我們將繼續(xù)以不同類群的植物為代表,，深入這一課題的研究,。

　　2. 對(duì)植物線粒體基因的轉(zhuǎn)移和基因轉(zhuǎn)換機(jī)制進(jìn)行系統(tǒng)鑒定和分析

　　在進(jìn)化的歷程中，細(xì)胞器和細(xì)胞核的基因組之間都經(jīng)歷了基因組結(jié)構(gòu)重塑和功能基因轉(zhuǎn)移/丟失的過程,，但是關(guān)于細(xì)胞器基因功能性轉(zhuǎn)移至細(xì)胞核機(jī)制的假說一直缺乏有效的實(shí)驗(yàn)證據(jù),。前期選取經(jīng)濟(jì)作物禾本科內(nèi)90個(gè)物種及其外類群為研究體系，以植物線粒體rpl5基因?yàn)檠芯繉?duì)象,，對(duì)該基因在線粒體和細(xì)胞核基因中的拷貝及轉(zhuǎn)移機(jī)制進(jìn)行詳盡的研究,。這一研究成果發(fā)表在Molecular Biology and Evolution上。我們將繼續(xù)以細(xì)胞器之間基因信息轉(zhuǎn)移為對(duì)象,，從生命之樹的角度解讀基因轉(zhuǎn)移的多樣性和復(fù)雜性的機(jī)制,。

　　3. 細(xì)胞核質(zhì)互作研究

　　在多倍體物種形成中，單親遺傳的細(xì)胞器基因組和雙親遺傳的細(xì)胞核基因組之間在進(jìn)化上存在核質(zhì)互作的不平衡,。使用基因組學(xué)和轉(zhuǎn)錄組學(xué)的數(shù)據(jù),，可以解析不同進(jìn)化時(shí)間尺度內(nèi)的各種多倍體在形成過程中該機(jī)制的變異。

　　

代表論文

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一區(qū))

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一區(qū))

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一區(qū))

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一區(qū))

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一區(qū))

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一區(qū))

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二區(qū))

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一區(qū))

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一區(qū))

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一區(qū))

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二區(qū))

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一區(qū))

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一區(qū))

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, 林學(xué)JCR一區(qū))

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二區(qū))

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二區(qū))

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一區(qū))

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二區(qū))

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二區(qū))

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二區(qū))

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二區(qū))

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一區(qū))

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二區(qū))

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二區(qū))

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三區(qū))

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二區(qū))

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二區(qū))

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三區(qū))

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二區(qū))

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一區(qū))

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三區(qū))

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三區(qū))

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雜志對(duì)本文進(jìn)行了報(bào)道). (IF=12.779, JCR一區(qū))

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三區(qū))

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二區(qū))

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一區(qū))

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三區(qū))

　　武志強(qiáng)課題組更新于2023年3月