多倍化与基因复制

甲基化与基因调控

基因组染色体演化

水生开花植物

   

071001-植物学

植物基因组进化

2007-09--2012-06   中国科学院武汉植物园   博士

   

[1] Gao, Zhiyan, Yang, Xingyu, Chen, Jinming, Rausher, Mark D, Shi, Tao. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. PLANT PHYSIOLOGY[J]. 2023, 191(3): 1662-1683, http://dx.doi.org/10.1093/plphys/kiac522.
[2] Shi, Tao, Huneau, Cecile, Zhang, Yue, Li, Yan, Chen, Jinming, Salse, Jerome, Wang, Qingfeng. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. NATURE PLANTS[J]. 2022, 8(7): 764-+, [3] Gao, Zhiyan, Liang, Yuting, Wang, Yuhan, Xiao, Yingjie, Chen, Jinming, Yang, Xingyu, Shi, Tao. Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. FRONTIERS IN PLANT SCIENCE[J]. 2022, 13: http://dx.doi.org/10.3389/fpls.2022.973347.
[4] Zhang, Yue, Yang, Xingyu, Van de Peer, Yves, Chen, Jinming, Marchal, Kathleen, Shi, Tao. Evolution of isoform-level gene expression patterns across tissues during lotus species divergence. PLANT JOURNAL[J]. 2022, 112(3): 830-846, http://dx.doi.org/10.1111/tpj.15984.
[5] Gao, Zhiyan, Li, Hui, Yang, Xingyu, Yang, Pingfang, Chen, Jinming, Shi, Tao. Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera). PLANT MOLECULAR BIOLOGY[J]. 2021, 106(1-2): 207-220, http://dx.doi.org/10.1007/s11103-021-01138-8.
[6] Li, Hui, Yang, Xingyu, Wang, Qingfeng, Chen, Jinming, Shi, Tao. Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus). MOLECULAR ECOLOGY[J]. 2021, 30(12): 2831-2845, http://dx.doi.org/10.1111/mec.15933.
[7] Hui Li, Xingyu Yang, Yue Zhang, Zhiyan Gao, Yuting Liang, Jinming Chen, Tao Shi. Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. SCIENTIFIC DATA[J]. 2021, 8(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000616393500004.
[8] Seyed Rahmani, Razgar, Shi, Tao, Zhang, Dongzhi, Gou, Xiaoping, Yi, Jing, Miclotte, Giles, Marchal, Kathleen, Li, Jia. Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. BMCGENOMICS[J]. 2021, 22(1): http://dx.doi.org/10.1186/s12864-021-07778-w.
[9] Shi, Tao, Chen, Jinming. A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication. GENOME BIOLOGY[J]. 2020, 21(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7722308/.
[10] Huang, Lifang, Wang, Xiaoyang, Dong, Yunping, Long, Yuzhou, Hao, Chaoyun, Yan, Lin, Shi, Tao. Resequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence. PLANT MOLECULAR BIOLOGY[J]. 2020, 103(1-2): 51-61, http://dx.doi.org/10.1007/s11103-020-00974-4.
[11] Shi, Tao, Rahmani, Razgar Seyed, Gugger, Paul F, Wang, Muhua, Li, Hui, Zhang, Yue, Li, Zhizhong, Wang, Qingfeng, Van de Peer, Yves, Marchal, Kathleen, Chen, Jinming. Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants. MOLECULAR BIOLOGY AND EVOLUTION[J]. 2020, 37(8): 2394-2413, http://dx.doi.org/10.1093/molbev/msaa105.
[12] Mekbib, Yeshitila, Huang, ShiXu, Ngarega, Boniface K, Li, ZhiZhong, Shi, Tao, Ou, KeFang, Liang, YuTing, Chen, JinMing, Yang, XingYu. The level of genetic diversity and differentiation of tropical lotus, Nelumbo nucifera Gaertn. (Nelumbonaceae) from Australia, India, and Thailand. BOTANICAL STUDIES[J]. 2020, 61(1): http://dx.doi.org/10.1186/s40529-020-00293-3.
[13] Zhang, Yue, Rahmani, Razgar Seyed, Yang, Xingyu, Chen, Jinming, Shi, Tao. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC GENOMICS[J]. 2020, 21(1): https://doaj.org/article/e507f43ac4054a429fe78460e3991545.
[14] Li, Hui, Yang, Xingyu, Lu, Mengxue, Chen, Jinming, Shi, Tao. Gene expression and evolution of Family-1 UDP-glycosyltransferases-insights from an aquatic flowering plant (sacred lotus). AQUATIC BOTANY[J]. 2020, 166: http://dx.doi.org/10.1016/j.aquabot.2020.103270.
[15] Razgar Seyed Rahmani, Giles Miclotte, Kathleen Marchal, Tao Shi, Jia Li, Dongzhi Zhang, Xiaoping Gou, Jing Yi. Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. BMC GENOMICS. 202, http://oa.las.ac.cn/oainone/service/browseall/read1?ptype=JA&workid=JA202107227573910ZK.
[16] Zhang, Yue, NyongA, Tonny Maraga, Shi, Tao, Yang, Pingfang. 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[J]. 2019, 26(4): 301-311, [17] Lin, Zhongyuan, Damaris, Rebecca Njeri, Shi, Tao, Li, Juanjuan, Yang, Pingfang. Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera). BMC GENOMICS[J]. 2018, 19(1): http://202.127.146.157/handle/2RYDP1HH/1467.
[18] Huang, Longyu, Yang, Mei, Li, Ling, Li, Hui, Yang, Dong, Shi, Tao, Yang, Pingfang. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera). JOURNAL OF INTEGRATIVE PLANT BIOLOGY[J]. 2018, 60(1): 2-15, http://lib.cqvip.com/Qikan/Article/Detail?id=674662936.
[19] Shi Tao. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus ( Nelumbo nucifera ): microevolution of sacred lotus. Journal of Integrative Plant Biology. 2018, [20] Longyu Huang, Mei Yang, Ling Li, Hui Li, Dong Yang, Tao Shi, Pingfang Yang. Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera). 植物学报：英文版[J]. 2018, 60(1): 2-15, http://lib.cqvip.com/Qikan/Article/Detail?id=674662936.
[21] Li, Juanjuan, Shi, Tao, Huang, Longyu, He, Dongli, NyongA, Tonny Maraga, Yang, Pingfang. Systematic transcriptomic analysis provides insights into lotus (Nelumbo nucifera) seed development. PLANT GROWTH REGULATION[J]. 2018, 86(3): 339-350, http://202.127.146.157/handle/2RYDP1HH/6108.
[22] Li, Juanjuan, Shi, Tao, Huang, Longyu, He, Dongli, NyongA, Tonny Maraga, Yang, Pingfang. Systematic transcriptomic analysis provides insights into lotus (Nelumbo nucifera) seed development. PLANT GROWTH REGULATION[J]. 2018, 86(3): 339-350, http://dx.doi.org/10.1007/s10725-018-0433-1.
[23] Wang, Kun, Wang, Xin, Li, Ming, Shi, Tao, Yang, Pingfang. Low genetic diversity and functional constraint of miRNA genes participating pollen-pistil interaction in rice. PLANT MOLECULAR BIOLOGY[J]. 2017, 95(1-2): 89-98, http://202.127.146.157/handle/2RYDP1HH/1316.
[24] Shi, Tao, Wang, Kun, Yang, Pingfang. The evolution of plant microRNAs: insights from a basal eudicot sacred lotus. PLANT JOURNAL[J]. 2017, 89(3): 442-457, http://dx.doi.org/10.1111/tpj.13394.
[25] Shi, Tao, Wang, Kun, Yang, Pingfang. Ancient microRNA families that regulate transcription factors are preferentially preserved during plant radiation. PLANT SIGNALING & BEHAVIOR[J]. 2016, 11(12): https://www.webofscience.com/wos/woscc/full-record/WOS:000392385400003.
[26] Shi, Tao. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony. MOLECULAR PHYLOGENETICS AND EVOLUTION[J]. 2016, 96: 9-16, http://dx.doi.org/10.1016/j.ympev.2015.12.002.
[27] Shi, Tao, Huang, Hongwen, Barker, Michael S. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. ANNALS OF BOTANY[J]. 2010, 106(3): 497-504, http://dx.doi.org/10.1093/aob/mcq129.

（1） Advances and Prospects in Genomic and Functional Studies of the Aquatic Crop, Sacred Lotus, Springer, 2022-11, 第 1 作者

   

（ 1 ） 温带莲与热带莲杂交F1代的等位基因特异性表达研究, 负责人, 国家任务, 2018-01--2020-12
（ 2 ） 中国科学院青年创新促进会2019年度会员, 负责人, 中国科学院计划, 2019-01--2023-12
（ 3 ） 全球野生莲属植物的遗传与表型多样性评价, 负责人, 地方任务, 2020-01--2021-12
（ 4 ） 水生植物生物地理学学科组, 负责人, 地方任务, 2019-08--2020-08
（ 5 ） 转座子微进化与基因组结构变异对莲两生态型适应性作用机制研究, 负责人, 国家任务, 2022-01--2025-12

现指导学生

周仁慧  硕士研究生  071001-植物学