Zhichao Xu

Zhichao Xu — Visiting Postdoc
Joined the group in 2019

Education
09, 2013–07, 2016 Peking Union of Medical College & Chinese Academy of Medical Sciences
Ph.D. Major: Pharmacognosy
Topic: Herbgenomics
09, 2009–07, 2012 Jilin Agricultural University
M.S. Major: Fermentation engineering
Topic: Plant molecular biology
09, 2005–07, 2009 Qilu University of Technology
B.S. Major: Biotechonology

Work Experience
09, 2019-present Ghent University
Title: Visiting Scholar
11, 2018-present Peking Union of Medical College & Chinese Academy of Medical Sciences
Institute of Medicinal Plant Development
Title: Associate Professor
08, 2016–11, 2018 Peking Union of Medical College & Chinese Academy of Medical Sciences
Institute of Medicinal Plant Development
Title: Assistant Professor

Publications

No publications to display.

Other publications

  1. Zhichao Xu, Tianyi Xin, Dorothea Bartels, Ying Li, Wei Gu, Hui Yao, Sai Liu, Haoying Yu, Xiangdong Pu, Jianguo Zhou, Jiang Xu, Caicai Xi, Hetian Lei, Jingyuan Song* and Shilin Chen*. Genome analysis of the ancient tracheophyte Selaginella tamariscina reveals evolutionary features relevant to the acquisition of desiccation tolerance. Molecular Plant, 2018, 11: 983-994.

  2. Zhichao Xu#, Reuben J. Peters#, Jason Weirather, Hongmei Luo, Baosheng Liao, Xin Zhang, Yingjie Zhu, Aijia Ji, Bing Zhang, Songnian Hu, Kin Fai Au, Jingyuan Song*, Shilin Chen*. Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis. Plant Journal, 2015, 82:951-961.

  3. Zhichao Xu and Jingyuan Song*. The 2-oxoglutarate-dependent dioxygenase superfamily participates in tanshinone production of Salvia miltiorrhiza. Journal of Experimental Botany, 2017, 68 (9): 2299-2308.

  4. Tianyi Xin, Yu Zhang, Xiangdong Pu, Ranran Gao, Zhichao Xu* and Jingyuan Song*. Trends in Herbgenomics. SCIENCE CHINA Life Sciences, 2019, 62(3): 288-308.

  5. Tianyi Xin, Chang Su, Yulin Lin, Shuhong Wang, Zhichao Xu*, Jingyuan Song*. Precise species detection of traditional Chinese patent medicine by shotgun metagenomic sequencing. Phytomedicine, 2018, 47: 40-47.

  6. Xu, Z., Luo, H., Ji, A., Zhang, X., Song, J., Chen, S. (2016) Global identification of the full-length transcripts and alternative splicing related to salvianolic acid biosynthetic genes in Salvia miltiorrhiza. Frontiers in Plant Science 7:100. doi: 10.3389/fpls.2016.00100.

  7. Hongmei Luo#, Jun Qian#, Zhichao Xu, Wanjing Liu, Lei Xu, Ying Li, Jiang Xu, Jianhong Zhang, Xiaolan Xu, Chang Liu, Liu He, Jianqin Li, Chao Sun, Francis Martin*, Jingyuan Song* and Shilin Chen*. The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of its Edible and Medicinal Sclerotium. Genomics, Proteomics & Bioinformatics, 2019

  8. Wei Sun#, Liang Leng#, Qinggang Yin#, Meimei Xu#, Mingkun Huang, Zhichao Xu, Yujun Zhang, Hui Yao, Caixia Wang, Chao Xiong, Sha Chen, Chunhong Jiang, Ning Xie, Xilong Zheng, Ying Wang, Chi Song*, Reuben J. Peters* and Shilin Chen*, The genome of the medicinal plant Andrographis paniculate provides insight into the biosynthesis of the bioactive diterpenoid neoandrographolide. The Plant Journal, 2019, 97(5): 841-857.

  9. Xu, H., Song, J., Luo, H., …Xu, Z., et al., (2016) Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza. Molecular Plant 9(6): 949-952.

  10. Shuhua Fu, Yingke Ma, Hui Yao, Zhichao Xu, Shilin Chen, Jingyuan Song and Kin Fai Au*. IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing. Bioinformatics, 2018, 34(13): 2168-2176.

  11. Yu Zhang, Zhichao Xu, Aijia Ji, Hongmei Luo, Jingyuan Song*. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza. Acta Pharmaceutica Sinica B, 2018, 8(2): 295-305.

  12. Tianyi Xin, Zhichao Xu, Jing Jia, Christine Leon, Songnian Hu, Yulin Lin, Subramanyam Ragupathy, Jingyuan Song*, Steven G. Newmaster*. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta Pharmaceutica Sinica B, 2018, 8(3): 488-497.

  13. Han Gao#, Fuhuang Li#, Zhichao Xu, Chenhao Huang, Chao Xiong, Chunhong Jiang, Ning Xie, Liang Leng, Yi Zhang, Zubaida Yousaf, Xia Liu*, Wei Sun*. Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata. Industrial Crops and Products, 2019, 135: 39-48.

  14. Ting Gao, Zhichao Xu, Xiaojun Song, Kai Huang, Ying Li, Jianhe Wei, Xunzhi Zhu, Hongwei Ren and Chao Sun*. Hybrid Sequencing of Full-Length cDNA Transcripts of the Medicinal Plant Scutellaria baicalensis. International Journal of Molecular Sciences, 2019, 20(18): 4426.

  15. Jing Jia, Zhichao Xu, Tianyi Xin, Linchun Shi, Jingyuan Song*. Quality control of the traditional patent medicine Yimu Wan based on SMRT sequencing and DNA barcoding. Frontiers in Plant Science, 2017, 8: 926.

  16. Aijia Ji#, Jing Jia#, Zhichao Xu, Ying Li, Wu Bi, Fengming Ren, Chunnian He, Jie Liu, Kaizhi Hu* and Jingyuan Song*. Transcriptome-guided mining of genes involved in crocin biosynthesis. Frontiers in Plant Science, 2017, 8: 518.

  17. Yu Zhang#, Aijia Ji#, Zhichao Xu, Hongmei Luo, Jingyuan Song*. The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza. Plant Molecular Biology, 2019, 100(1-2): 83–93.

  18. Fengming Huang#, Jianchao Du#, Zhu Liang#, Zhichao Xu, Jiantao Xu, Yan Zhao, Yexuan Lin, Song Mei, Quan He, Jindong Zhu, Qiang Liu, Yanxu Zhang, Yuhao Qin, Wei Sun, Jingyuan Song, Shilin Chen and Chengyu Jiang*. Large-scale analysis of small RNAs derived from traditional Chinese herbs in human tissues. SCIENCE CHINA Life Sciences, 2019, 62(3): 321-332.

  19. Qing Li#, Jingxian Feng#, Liang Chen, Zhichao Xu, Yingjie Zhu, Yun Wang, Ying Xiao, Junfeng Chen, Yangyun Zhou, Hexin Tan, Lei Zhang* and Wansheng Chen*. Genome-wide identification and characterization of Salvia miltiorrhiza laccases reveal potential targets for salvianolic acid B biosynthesis. Frontiers in Plant Science, 2019, 10: 435.

  20. Liu He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Li, Kin Fai Au* and Hui Yao*. Hybrid sequencing of full-length cDNA transcripts of stems and leaves in Dendrobium officinale. Genes, 2017, 8(10): 257.

  21. Fengming Ren, Yingwei Wang, Zhichao Xu, Ying Li, Tianyi Xin, Jianguo Zhou, Yaodong Qi, Xueping Wei, Hui Yao, Jingyuan Song*. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecology and Evolution, 2019, 9(4): 1934-1945.

  22. Ying Li#, Jianguo Zhou#, Xinlian Chen, Yingxian Cui, Zhichao Xu, Yonghua Li, Jingyuan Song, Baozhong Liao and Hui Yao*. Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. Scientific reports, 2017, 7(1): 12834.

  23. Jianguo Zhou, Yingxian Cui, Xinlian Chen, Ying Li, Zhichao Xu, Baozhong Duan, Yonghua Li, Jingyuan Song and Hui Yao*. Complete chloroplast genomes of Papaver rhoeas and Papaver orientale: molecular structures, comparative analysis, and phylogenetic analysis. Molecules, 2018, 23(2): 437.

  24. Yingxian Cui, Liping Nie, Wei Sun, Zhichao Xu, Yu Wang, Jingyuan Song and Hui Yao*. Comparative and Phylogenetic Analyses of Ginger (Zingiber officinale) in the Family Zingiberaceae Based on the Complete Chloroplast Genome. Plants, 2019, 8(8): 283.

  25. Xinlian Chen, Yingxian Cui, Liping Nie, Haoyu Hu, Zhichao Xu, Wei Sun, Ting Gao, Jingyuan Song and Hui Yao*. Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine. BioMed research international, 2019: 5921725.

  26. Liping Nie, Yingxian Cui, Xinlian Chen, Zhichao Xu, Wei Sun, Yu Wang, Jingyuan Song and Hui Yao*. Complete chloroplast genome sequence of the medicinal plant Arctium lappa. Genome, 2019, doi: 10.1139/gen-2019-0070.

  27. Xu, Z., Xu, J., Ji, A., Zhu, Y., et al. (2015) Genome-wide selection of superior reference genes for expression studies in Ganoderma lucidum. Gene 574(2):352-8.

  28. Xu, Z., Ji, A., Song, J., Chen, S. (2016) Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza. Biology Open doi:10.1242/bio.017178.

  29. Xu, Z., Ji, A., Zhang, X., Song, J., Chen, S. (2016) Biosynthesis and regulation of active constituents in medicinal model plant, Salvia miltiorrhiza. Chinese Herbal Medicines 2016, 8(1): 3-11.

  30. Zhang, X., Luo, H., Xu, Z., Zhu, Y., Ji, A., Song, J., et al. (2015) Genome-wide characterization and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza. Scientific Reports 5, 11244; doi:10.1038/srep11244.

  31. Ji, A., Luo, H., Xu, Z., Zhang, X., Zhu, Y., Liao, B., Yao, H., Song, J., Chen, S., (2015). Genome-wide identification of the AP2/ERF gene family involved in active constituent biosynthesis in Salvia miltiorrhiza. The Plant Genome doi: 10.3835/plantgenome 2015.08.0077.

  32. Zhang, X., Xu, Z., Xu, J., Ji, A. J., Luo, H. M., & Song, J. Y., et al. (2016). Selection and validation of reference genes for normalization of quantitative real-time reverse transcription pcr analysis in Poria cocos (schw.) wolf (fuling). Chinese Medicine 11(1), 1-17.

  33. Xu, J., Xu, Z., Zhu, Y., Luo, H., Qian, J., Ji, A., et al. (2014) Identification and evaluation of reference genes for qRT-PCR normalization in Ganoderma lucidum. Current microbiology 68(1):120-126.