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Zhang Xingtan Lab


  张兴坦,研究员、博士生导师。2009年于哈尔滨工业大学本科毕业,2015年于重庆大学获得植物学博士学位。张兴坦研究员长期致力于植物功能基因组学研究,研究领域包括复杂基因组的组装和分型、生物信息分析技术的开发、基于组学大数据挖掘重要功能基因等。研究成果以第一或通讯作者(含共同)在Cell, Nature, Nature Genetics, Nature Plants, Nature Communications等高水平期刊发表。



  2020.10-至今           中国农业科学院农业基因组所,研究员

  2015.07-2020.10     福建农林大学,讲师/副教授



  2009.09 - 2015.06     重庆大学 植物学,  理学博士

  2013.10 - 2014.10     J. Craig Venter Institute ,  访问博士生

  2005.09 - 2009.06     哈尔滨工业大学 生物工程 ,  工学学士



  1. 复杂多倍体/高杂合二倍体基因组组装和分型方法的开发

  2. 基于NGS或单分子测序技术开发生物信息分析算法和工具

  3. 基于组学大数据挖掘植物重要功能基因并解析其生物学机制



  开发ALLHiC算法解决同源多倍体染色体分型难题,并破译第一个同源多倍体甘蔗基因组 (Zhang, et., al. Nature Genetics, 2018; Zhang, et., al. Nature Plants, 2019);破译多个榕树基因组,组装和分型X和Y性染色体,揭示榕属性别决定因子、气生根形成机制、榕蜂协同演化、杂交渐渗对其物种快速形成的机制等科学问题 (Zhang, et., al. Cell, 2020, Wang, et., al. Nature Communications, 2021).



  Dr. Xingtan Zhang joined the AGIS as a research professor in October, 2020. He received the bachelor degree from Harbin Institute of Technology in 2009 and his Ph.D. degree in Plant Science from Chongqing University in 2015. Xingtan has been working on plant functional genomics since 2009 and his research interest involves in 1) assembly and phasing of complex genomes, 2) development of bioinformatics tools and 3) mining of functional genes related to agronomic traits in crops. During the past decade, his researches have been published in a series of high-impact SCI journals, such as Cell, Nature, Nature Genetics, Nature Plants and Nature Communications.


  Working Experience

  2020.10 - present,     Agricultural Genomics Institute at Shenzhen-CAAS,   Research Professor

  2015.07 - 2020.10,   Fujian Agriculture and Forestry University,   research associate/associated professor



  2009.09 - 2015.06  Chongqing University, Ph.D in Plant Science

  2013.10 - 2014.10  J. Craig Venter Institute, Visiting Ph.D student

  2005.09 - 2009.06  Harbin Institute of Technology, Bachelor in Bio-engineering


  Research Interest

  1. Assembly and phasing of complex genomes, including polyploid and highly heterozygous diploid genomes.

  2. Development of novel bioinformatics tools based on NGS and/or single-molecular sequencing technologies.

  3. Data mining of functional genes underlying important roles in plant development and crop domestication


  Major Achievement

  Our team has developed the ALLHiC pipeline that can be used to solve the phasing problem of autoploid genomes based on Hi-C data, and this method has been successfully applied to chromosomal-scale assembly of an auto-tetraploid sugarcane genome (Zhang, et., al. Nature Genetics, 2018; Zhang, et., al. Nature Plants, 2019). By analyzing the genomes of two Ficus speices with distinct features, we revealed a couple of biological questions in the Ficus genus, including evolutionary history of X and Y chromosomes, sex determination, development of aerial roots and fig-wasp co-evolution and extensive introgression in this strict mutualism system (Zhang, et., al. Cell, 2020, cover story; Wang, et., al. Nature Communications, 2021).


  Selected Publications

  1. Zhang, Xingtan#, Gang Wang#, Shengcheng Zhang, Shuai Chen et al., 2020. “Genomes of banyan fig and pollinator wasp provide insights into fig-wasp coevolution.” Cell 183 (4): 875-889.

  2. Zhang, Xingtan, Shengcheng Zhang, Qian Zhao, Ray Ming, and Haibao Tang*. 2019. “Assembly of Allele-Aware, Chromosomal-Scale Autopolyploid Genomes Based on Hi-C Data.” Nature Plants 5 (8): 833–45.

  3. Zhang, Liangsheng#, Fei Chen#, Xingtan Zhang#, Zhen Li#, Yiyong Zhao#, Rolf Lohaus, Xiaojun Chang, et al. 2020. “The Water Lily Genome and the Early Evolution of Flowering Plants.” Nature 577 (7788): 79–84. (#co-first author)

  4. Zhang, J.#. Zhang X.#, Tang H#., et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, doi:10.1038/s41588-018-0237-2 (2018). (co-first author)

  5. Wang, G.#, Zhang, X.#, Herre, E., McKey, D., Machado, D., Yu, W., Canno, C., Arnold, M., Pereira., R., Ming, R., Liu, Y., Wang, Y., Ma, D., Chen, J. (2021) Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism. Nature Communications. (Accept; #co-first author)

  6. Zhang, Liwu, Yi Xu, Xingtan Zhang#, Xiaokai Ma, Lilan Zhang, Zhenyang Liao, Qing Zhang, et al. 2020. “The Genome of Kenaf (Hibiscus Cannabinus L.) Provides Insights into Bast Fibre and Leaf Shape Biogenesis.” Plant Biotechnology Journal, January, 10.1111/pbi.13341. (#co-first author)

  7. Zhang, Xingtan, Ruoxi Wu, Yibin Wang, Jiaxin Yu, and Haibao Tang. 2019. “Unzipping Haplotypes in Diploid and Polyploid Genomes.” Computational and Structural Biotechnology Journal 18 (December): 66–72.

  8. Zhang, Xingtan, Xuequn Chen, Pingping Liang, and Haibao Tang. 2018. “Cataloging Plant Genome Structural Variations.” Current Issues in Molecular Biology 27: 181–94.

  9. Zhang, Xingtan, Genhong Wang, Junping Gao, Mengyun Nie, Wenshan Liu, and Qingyou Xia. 2016. “Functional Analysis of NtMPK2 Uncovers Its Positive Role in Response to Pseudomonas Syringae Pv. Tomato DC3000 in Tobacco.” Plant Molecular Biology 90 (1–2): 19–31.

  10. Zhang, Xingtan, Mengyun Nie, Qian Zhao, Yuqian Wu, Genhong Wang, and Qingyou Xia. 2015. “Genome-Wide Patterns of Genetic Variation among Silkworms.” Molecular Genetics and Genomics : MGG 290 (4): 1575–87.

  11. Zhang, Xingtan, Benjamin D Rosen, Haibao Tang, Vivek Krishnakumar, and Christopher D Town. 2015. “Polyribosomal RNA-Seq Reveals the Decreased Complexity and Diversity of the Arabidopsis Translatome.” PloS One 10 (2): e0117699–e0117699.

  12. Zhang, Xingtan, Tingcai Cheng, Genhong Wang, Yafei Yan, and Qingyou Xia. 2013. “Cloning and Evolutionary Analysis of Tobacco MAPK Gene Family.” Molecular Biology Reports 40 (2): 1407–15.