石涛 - 中国科学院武汉植物园 -

个人简介

石涛，博士，副研究员。主要从事水生植物基因组学与进化生物学研究。研究方向包括植物基因组古多倍化、基因组表观遗传修饰与进化、基因调控网络构建和群体基因组。近年来，主持国家自然科学基金青年项目、中科院青促会项目、湖北省自然科学基金等项目，在Genome Biology, Molecular Biology and Evolution, The Plant Journal, Scientific Data等杂志上发表SCI论文21篇，构建莲的基因组遗传变异与表达数据库（http://nelumbo.biocloud.net/home） 2018.9至今，中国科学院武汉植物园，副研究员 2015.11-2018.8，中国科学院武汉植物园，助理研究员 2013.9-2015.10，兰州大学，博士后 2007.9-2012.6，中国科学院大学/中国科学院武汉植物园，植物学专业，博士研究生 2004.9-2007.6，华中科技大学，（英语双学位） 2003.9-2007.6，华中农业大学，本科获奖及荣誉： 2020中国科学院武汉植物园明星员工 2019中国科学院青年创新促进会会员 2017中国科学院武汉植物园明星员工 2016第三十界全国荷花展优秀论文奖 2014全国植物生物学大会墙报优秀奖 2010中科院武汉分院“昌华奖学金优秀奖”

研究领域

植物基因组进化，表观组学，基因调控网络，群体基因组学

近期论文

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1.Hui Li, Xingyu Yang, Yue Zhang, Zhiyan Gao, Yuting Liang, Jinming Chen* & Tao Shi* (2021). Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. Scientific Data. 8, 38. 2.Tao Shi, Jinming Chen (2020). A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. Genome Biology. 21, 295. 3.Tao Shi, Razgar Seyed Rahmani, Paul F Gugger, Muhua Wang, Hui Li, Yue Zhang, Zhizhong Li, Qingfeng Wang, Yves Van de Peer, Kathleen Marchal, Jinming Chen (2020). Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Molecular Biology and Evolution.37(8): 2394-2413 4.Tao Shi, Kun Wang, Pingfang Yang . The evolution of plant microRNAs-insights from a basal eudicot sacred lotus. The Plant Journal, 2017, 89(3): 442-457. 5.Yue Zhang, Razgar Seyed Rahmani, Xingyu Yang, Jinming Chen* & Tao Shi*. (2020). Integrative expression network analysis of microrna and gene isoforms in sacred lotus. BMC Genomics, 21(1): 429 6.Hui Li, Xingyu Yang, Mengxue Lu, Jinming Chen*, Tao Shi*. (2020). Gene expression and evolution of family-1 udp-glycosyltransferases-insights from an aquatic flowering plant (sacred lotus). Aquatic Botany, 166:103270. 7.Tao Shi*. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony. Molecular Phylogenetics and Evolution. 2016, 96: 9-16. 8.Tao Shi, Kun Wang, Pingfang Yang. Ancient microRNA families that regulate transcription factors are preferentially preserved during plant radiation. Plant signaling & behavior, 2016,11(12), e1261233. 9.Lifang Huang, Xiaoyang Wang, Yunping Dong, Yuzhou Long, Chaoyun Hao, Lin Yan*, Tao Shi* (2020). Resequencing 93 accessions of coffee unveils independent and parallel selection during coffea species divergence. Plant Molecular Biology, 103(1), 51-61. 10.Yue Zhang, Tonny Maraga Nyong'A , Tao Shi* , Pingfang Yang*. (2019) The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing. DNA Research, 26(4), 301-311. 11.Kun Wang, Xin Wang, Ming Li, Tao Shi*, Yang Pingfang*.(2017). Low genetic diversity and functional constraint of miRNA genes participating pollen-pistil interaction in rice. Plant Molecular Biology, (5):1-10. 12.Longyu Huang, Mei Yang, Ling Li, Hui Li, Tao Shi*, Pingfang Yang*. (2018). Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (nelumbo nucifera). Journal of Integrative Plant Biology, 60(1). 13.Tao Shi, Ivan Dimitrov, Yinling Zhang, Frans E Tax, Jing,Yi , Xiaoping,Gou, Jia,Li (2015). Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. Plant Molecular Biology. 89(3): 253-261. 14.Tao Shi, Hongwen Huang, Michael J. Sanderson, Frans E Tax (2014). Evolutionary dynamics of leucine-rich repeat receptor-like kinases and related genes in plants: A phylogenomic approach. Journal of Integrative Plant Biology. (7): 648-662. 15.Tao Shi, Hongwen Huang, Michael S Barker (2010). Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Annals of Botany. 106 (3): 497-504. 16.Chao Sun, Kan Yan, Jian-Ting Han, Liang Tao Ming-Hui Lv, Tao Shi, Yong-Xing He, Michael Wierzba , Frans E. Tax , Jia Li (2017). Scanning for new BRI1 receptor mutations via TILLING analysis. Plant Physiology, pp-00118. 17.Yunzhe Wu, Qingqing Xun, Yi Guo, Jinghua Zhang, Kaili Cheng, Tao Shi, Kai He, Suiwen Hou, Xiaoping Gou, Jia Li (2016) Genome-Wide Expression Pattern Analyses of the Arabidopsis Leucine-Rich Repeat Receptor-Like Kinases. Molecular Plant, 9 (2): 289-300. 18.Jinghua Zhang , Tong Yuan , Xiaomeng Duan , Xiaoping Wei ,Tao Shi, Jia Li, Scott D. Russell , Xiaoping Gou. Cis-regulatory elements determine germline specificity and expression level of an isopentenyl transferase gene in sperm cells of Arabidopsis. Plant Physiology. 2016, 15: 01510-02015. 19.Yeshitila Mekbib, Shi-Xu Huang, Boniface K. Ngarega, Zhi-Zhong Li, Tao Shi, Ke-Fang Ou, Yu-Ting Liang, Jin-Ming Chen & Xing-Yu Yang. (2020). The level of genetic diversity and differentiation of tropical lotus, nelumbo nucifera gaertn. (nelumbonaceae) from australia, india, and thailand. Botanical Studies, 61:15. 20.Zhongyuan Lin, Rebecca Njeri Damaris, Tao Shi, Juanjuan Li, Pingfang Yang. (2018). Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (nelumbo nucifera). BMC Genomics, 19(1), 554. 21.Juanjuan Li, Tao Shi, Longyu Huang ,Dongli He,Tonny Maraga Nyong’A ,Pingfang Yang. (2018). Systematic transcriptomic analysis provides insights into lotus (nelumbo nucifera) seed development. Plant Growth Regulation, 86: 339-350.