作物分子育种细胞生物学实验室
2024-11-29
实验室、课题组名称：作物分子育种细胞生物学实验室
实验室、课题组负责人：
实验室、课题组介绍：
1、研究方向：
作物的细胞再生和重要农艺性状相关器官的分化发育。
2、主要研究内容：
基于单细胞测序、空间转录组、纳米孔测序和宏基因组等多组学技术，研究作物细胞干性，转基因效率和性状改良。
3、主要研究成果：
文章：
1、Song et al., Bosheng Li* 2023.Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. PNAS.
2、Chen, X., Liu, Y., Lv, K., Wang, M., Liu, X. and Li, B*., 2023. FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing. Bioinformatics Advances.
3、Mohammad Saidur Rhaman†, Muhammad Ali†, Wenxiu Ye*, Bosheng Li* 2024.Opportunities and Challenges in Advancing Plant Research with Single-Cell Omics. Genomics, Proteomics & Bioinformatics.
4、Li Feng, et al., Bosheng Li* 2024. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis.Communications Biology.
5、Lu D, et al., Li B*. 2024. Nanopore ultra-long sequencing and adaptive sampling spur plant complete telomere-to-telomere genome assembly. Mol Plant.
6、Kaiwen Lv, Bosheng Li* 2024. Spatial transcriptome analysis reveals de novo regeneration of poplar roots. Hortic Res.
专利：
鹿东东, 李博生, 李珊珊, 刘彩娟, 刘艳霞. 植物超长基因组DNA的提取方法, 2024-06-14, CN 116732022 B (专利)
团队成员：
主要成员介绍：
姓名：岳智亮
职务：副研究员
邮箱：zhiliang.yue@pku-iaas.edu.cn
教育背景：
2012.09至2019.06，河北师范大学，细胞生物学，博士；
2009.09至2012.06，河北农业大学，生物化学与分子生物学，硕士；
2005.09至2009.06，河北农业大学，生物技术，学士；
工作经历：
2019.07至2022.02，河北省农林科学院园艺学，博士后；
2022.10至今，北京大学现代农业研究院，副研究员；
研究方向：
空间转录组学与植物嫁接
文章：
1. Yue, Z.L., Liu, N., Deng, Z.P., Zhang, Y., Wu, Z.M., Zhao, J.L., Sun, Y., Wang,Z.Y.,Zhang, S.W. (2022) The receptor kinase OsWAK11 monitors cell wall pectin changes to fine-tune brassinosteroid signaling and regulate cell elongation in rice. Current Biology. 32, 1-13, 2022.
2. Yue, Z.L., Tian, Z.J., Zhang, J.W., Zhang, S.W., Li, Y.D., Wu, Z.M. (2022) Overexpression of Lectin Receptor-Like Kinase 1 in Tomato Confers Resistanceto Fusarium oxysporum f. sp. Radicis-Lycopersici. Front Plant Sci. 2022 Feb3;13:836269.
3. Lv K, Liu N, Niu Y, Song X, Liu Y, Yue Z, Ali M, Guo Q, Lv C, Lu D, Zhang S, Zhou Y, Li B. (2024). Spatial transcriptome analysis reveals de novo regeneration of poplar roots. Horticulture Research, 11(11), uhae237.
4. Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2310163120.
5. Ai, L.F., Yue, Z.L.*, Ma, Y.S., Wang, J.C., Zhang, S.W.*, and Sun, Y. (2015). Simple and rapid determination of N(6)-(Delta(2)-isopentenyl)adenine, zeatin,and dihydrozeatin in plants using on-line cleanup liquid chromatography coupled with hybrid quadrupole-Orbitrap high-resolution mass spectrometry. J Sep Sci38, 1858-1865.
6. Wang, J., Yan, L.L., Yue, Z.L., Li, H.Y., Ji, X.J., Pu, C.X., and Sun, Y. (2020). Receptor-like kinase OsCR4 controls leaf morphogenesis and embryogenesis by fixing the distribution of auxin in rice. J Genet Genomics 47, 577-589.
7. Zhao JL, Zhang LQ, Liu N, Xu SL, Yue ZL, Zhang LL, Deng ZP, Burlingame AL, Sun DY, Wang ZY, Sun Y, Zhang SW. (2019). Mutual Regulation of Receptor-Like Kinase SIT1 and B'kappa-PP2A Shapes the Early Response of Rice to Salt Stress. Plant Cell 31, 2131-2151.
姓名：鹿东东
职务：助理研究员
邮箱：dongdong.lu@pku-iaas.edu.cn
教育背景：
2018-09至2022-06, 南京林业大学，南方科技大学（访学）, 细胞生物学, 博士；
2013-09至2016-06, 中国计量大学, 生物化学与分子生物学, 硕士；
2009-09至2013-06, 山东农业大学, 制药工程（农药方向）, 学士；
工作经历：
2022-07 至今, 北京大学现代农业研究院,助理研究员；
2016-11 至 2018-09, 南方科技大学, 生物系, 实验员；
研究方向：
纳米孔测序与植物基因组组装
文章：
1. Dongdong Lu, Caijuan Liu, Wenjun Ji, Ruiyan Xia, Shanshan Li, Yanxia Liu, Naixu Liu, Yongqi Liu, Xing Wang Deng and Bosheng Li. Nanopore Ultra-long Sequencing and Adaptive Sampling Spur Plant Complete Telomere-to-Telomere Genome Assembly. Molecular Plant，17: 1773-1786. (期刊论文)
2. Dongdong Lu, Li Feng, Jixian Zhai, Bosheng Li, Mengli Xi , Safeguard DCL2-Dependent 22-nt siRNA generation by DCL1. Biochemical and Biophysical Research Communications, 2022, 605(0): 97- 103. (期刊论文)
3. Dongdong Lu, Jixian Zhai, Mengli Xi , Regulation of DNA methylation during plant endosperm development. Frontiers in Genetics, 2022, 13. (期刊论文)
4. Dongdong Lu, Hanwu Shang. Advances in the Study of the Biological Effects of Different Plant Species and Cotton Varieties on the Hibiscus Mealybug. Journal of Environmental Entomology, 2016, 38(4): 669-679. (期刊论文)
5. Yilin Zhang, Mingxia Zhao, Jingsheng Tan, Minghan Huang, Xiao Chu, Yan Li, Xue Han, Taohong Fang, Yao Tian, Robert Jarret, Dongdong Lu, Yijun Chen, Lifang Xue, Xiaoni Li, Guochen Qin, Bosheng Li, Yudong Sun, Xing Wang Deng, Yun Deng, Xingping Zhang and Hang He, Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics, 2024, 56:1750-1761.(期刊论文)
6. Li Feng, Wei Yan, Xianli Tang, Huihui Wu, Yajie Pan, Dongdong Lu, Qianyan Ling-hu, Yuelin Liu, Yongqi Liu, Xiehai Song, Muhammad Ali, Liang Fang, Hongwei Guo and Bosheng Li. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis, Communications Biology 2024, 7: 474. (期刊论文)
7. Kaiwen Lv, Naixu Liu, Yani Niu, Xiehai Song, Yongqi Liu, Zhiliang Yue, Muhammad Ali, Qiuyue Guo, Chunyu Lv, Dongdong Lu, Shaoman Zhang, Yangyan Zhou, Bosheng Li. Spatial transcriptome analysis reveals de novo regeneration of poplar roots. Horticulture Research, 2024, uhae237. (期刊论文)
8. Yanping Long, Liu Zhijian, Jinbu Jia, Weipeng Mo, Liang Fang, Dongdong Lu, Bo Liu, Hong Zhang, Wei Chen, Jixian Zhai , FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants, Genome Biology, 2021, 22(1). (期刊论文)
9. Weipeng Mo, Bo Liu, Hong Zhang, Xianhao Jin, Dongdong Lu, Yiming Yu, Yuelin Liu, Jinbu Jia, Yanping Long, Xian Deng, Xiaofeng Cao, Hongwei Guo and Jixian Zhai Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biology. 2021, 22(1):322.
10. Daoheng Hu, Yiming Yu, Kejian Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, Jixian Zhai , Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions, The Plant Cell, 2021, 33: 2950-2964. (期刊论文)
11. Jinbu Jia, Yanping Long, Hong Zhang, Zhuowen Li, Zhijian Liu, Yan Zhao, Dongdong Lu, Xianhao Jin, Xian Deng, Rui Xia, Xiaofeng Cao, Jixian Zhai, Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants, Nature Plants, 2020, 6(7): 780-+. (期刊论文)
12. Ye Tan, Mufei Zhu, Wenyan Xu, Wenwu Zhou, Dongdong Lu, Hanwu Shang, Zengrong Zhu. Influence of water-stressed rice on feeding behavior of brown planthopper, Nilaparvata lugens (Stål), Journal of Asia-Pacific Entomology, 2017, 20(2): 665-670. (期刊论文)
专利：
1. 鹿东东, 李博生, 李珊珊, 刘彩娟, 刘艳霞. 植物超长基因组DNA的提取方法, 2024-06-14, CN 116732022 B (专利)
2. 席梦利, 赵乙琏, 辛昊阳, 鹿东东, 刘光欣, 尚大鑫, 宁仪杭. 一种基于石蜡切片的杨树根尖3D荧光 原位杂交方法, 2020-12-22, 中国, CN202010090059.X (专利)
3. 席梦利, 尚大鑫, 刘光欣, 辛昊阳, 赵乙琏, 鹿东东, 宁仪杭. 一种基于冰冻切片的杨树根尖3D荧光 原位杂交方法, 2021-01-26, 中国, CN202010106601.6 (专利)
4. 翟继先, 龙艳萍, 肖丽丹, 张飞, 鹿东东, 刘智剑. 单细胞基因组测序用的DNA文库的构建方法, 2019-12-18, 中国, CN201911311804.2 (专利)
姓名：宋协海
职务：副研究员
邮箱：xiehai.song@pku-iaas.edu.cn
教育背景：
2015-09 至 2021-06, 北京林业大学, 森林培育, 博士 ；
2011-09 至 2015-06, 东北林业大学, 林学, 学士；
工作经历：
2023-11 至 今, 北京大学现代农业研究院, 作物分子育种细胞生物学实验室, 副研究员 ；
2021-10 至 2023-10, 北京大学现代农业研究院, 作物分子育种细胞生物学实验室, 助理研究员；
研究方向：
单细胞空间转录组和植物再生。
文章：
1. Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2310163120. doi: 10.1073/pnas.2310163120.
2. Feng L, Yan W, Tang X, Wu H, Pan Y, Lu D, Ling-Hu Q, Liu Y, Liu Y, Song X, Ali M, Fang L, Guo H, Li B. Multiple factors and features dictate the selective production of ct-siRNA in Arabidopsis. Commun Biol. 2024 Apr 18;7(1):474. doi: 10.1038/s42003-024-06142-4.
3. Lv K, Liu N, Niu Y, Song X, Liu Y, Yue Z, Ali M, Guo Q, Lv C, Lu D, Zhang S, Zhou Y, Li B. Spatial transcriptome analysis reveals de novo regeneration of poplar roots. Horticulture Research. 2024 Aug. doi: 10.1093/hr/uhae237
姓名：张春雷
职务：副研究员
邮箱：chunlei.zhang@pku-iaas.edu.cn
教育背景：
2005年9月至2009年6月，枣庄学院，生物技术，学士；
2009年9月至2012年6月，兰州大学，植物学，硕士；
2012年9月至2018年1月，中科院遗传与发育生物学研究所，遗传学，博士；
工作经历：
2018年5月至2021年12月，山东大学，植物学，博士后；
2021年12月至今，北京大学现代农业研究院李博生课题组，副研究员；
研究方向：
植物向性运动
文章：
1. Zhang, C., Zhang, Y., Ding, Z., and Bai, Y. (2019).
Contribution of Microbial Inter-kingdom Balance to Plant Health. Mol Plant 12, 148-149. （JCR 1区， IF = 21.9496）
2. Kong X#, Zhang C#, Zheng H, Sun M, Zhang F, Zhang M, Cui F, Lv D, Liu L, Guo S, Zhang Y, Yuan X, Zhao S, Tian H, Ding Z (2020) Antagonistic Interaction between Auxin and SA Signaling Pathways Regulates Bacterial Infection through Lateral Root in Arabidopsis. Cell Rep 32(8):108060 （JCR 1区， IF = 9.995）
3. Zhang CL#, Zhang MY#, Yan ZW#, Wang FX, Yuan XZ, Zhao S, Zhang L, Tian HY, Ding ZJ (2020) CO2 is a key constituent of the plant growth-promoting volatiles generated by bacteria in a sealed system. Plant Cell Reports （JCR 2区， IF = 4.964）
4. Zhang C#, Yu Z#, Zhang M, Li X, Wang M, Li L, Li X, Ding Z, Tian H (2022 Accept) Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis. Journal of Experimental Botany (JCR 1区，IF = 7.298)