Bioinplant Lab

Bioinplant Group of Zhejiang University

生物信息与植物基因组学（bioinformatics and plant genomics）团队（Bioinplant）为浙江大学作物科学研究所、生物信息学研究所、IBM生物计算实验室、中美作物分子育种联合实验室、中美植物与医学健康联合研究中心、海南研究院、新农村发展研究院等重要组成部分。利用生物信息学和基因组等组学技术优势，我们主要开展 (1) 植物基因组及其演化和育种利用技术；(2) 组学大数据分析、数据库与方法工具；(3) 单细胞组学技术及其应用；(4) 植物转化医学与健康。团队承担了《生物信息学》、《植物基因组学》、《单细胞组学》和《组学与大数据分析》等课程教学任务，本网站提供了有关教学相关资源。

团队研究组（PI）：樊龙江教授；叶楚玉教授；褚琴洁研究员；陈露研究员

The Bioinplant (bioinformatics and plant genomics) group is a part of Institute of Crop Sciences, Institute of Bioinformatics, IBM Biocomputing Laboratory, Sino-US Molecular Breeding Joint Lab, Sino-US Plant and Health Medicine Joint Reasearch Center, Hainan Institute, Zhejiang University. Our purpose is to further knowledge of genomes for crop breeding and complex traits/diseases, particularly through approaches of bioinformatics and omics. Our current research interests focus on (1) genomes of crops and their relatives and approaches to bridge the gap between genomics and crop improvement, such as genome-based breeding techniques; (2) Algorithms, databases, bioinformatic tools and analysis of multiple omic data, including single-cell omic data; (3) plant translational medicine and health. Our group undertakes the teaching tasks for courses such as "Bioinformatics," "Plant Genomics," "Single-cell Omics," and "Genomic Data Analysis." This website provides teaching-related resources.

Ø Mol Plant | 植物细胞类型本体（POCT）国际合作联盟发布第一版分类系统及其标记基因（2025-12-27）

Ø Plant Com | 浙江大学樊龙江/吴东亚团队开发远缘遗传渐渗分析工具并揭示其环境适应性重要功能（2025-12-10）

Ø Trends Plant Sci | 中美学者系统总结植物空间多组学研究趋势及其数据分析策略（2025-10-30）

Ø 博士生黄毓杰和Babatunde Kehinde第9届国际杂草科学大会作口头报告（2025-10-24）

Ø Nature Genetics | 浙江大学樊龙江/吴东亚团队揭示水稻基因组着丝粒遗传多样性与演化规律（2025-10-21）

Ø 喜报！博士生许继伟获得2024-2025学年先正达齐尔顿研究生奖学金 (2025-10-18)

Ø 喜讯！博士生黄毓杰荣获袁隆平追梦奖学金博士生科研创新青年奖 (2025-10-14)

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教学材料（Courses）

Ø 《生物信息学》（Bioinformatics）（第二版），樊龙江主编，2021; 致敬经典：《生物信息学》（第二版）出版！ [后记] 《生物信息学实验指导》（2022）

Ø 《植物基因组学》(Plant Genomics)（第二版），樊龙江主编，2025；基因组学研究新标杆|《植物基因组学（第二版）》焕新出版

Ø 《单细胞组学基础》（Single-Cell Omics），樊龙江主编，2024；解锁细胞、洞见微观 | 《单细胞组学基础》重磅发布！

Ø 组学与大数据分析相关经典教材

Ø 《生物信息学札记》（樊龙江，2001，2005，2010）

Ø 生信大讲堂公众号

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数据库与生物信息学工具（Databases and Tools）

BreedingAIDB: A database integrating crop genome-to-phenotype paired data with machine learning tools applicable in breeding

The database of N3: plants,genomes,technologies

POCT: the plant ontology of cell types

PlantscRNAdb: A database for plant single-cell RNA analysis

PlantcircBase: A database for plant circular RNAs

RiceRelativesGD: A database of rice relatives for rice research

PscLncRNA: A database for plant single-cell lncRNA analysis

planTrichome: A database of glandular trichome cells in plants

VarietyFace: A platform for crop variety genomes and breeding

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近期发表论文（Recent Publications）

PlantscRNAdb 4.0: More comprehensive and precise markers under a cell type uniformity for plants. Dihuai Zheng, Xiaolin Lu, Yaqian Lu, Pu Liang, Nianmin Shang, Jiwei Xu, Jie Yao, Fangyu Mo, Qinjie Chu, Longjiang Fan*, Hongyu Chen*. Molecular Plant, 2025. doi:https://doi.org/10.1016/j.molp.2025.12.026

The plant ontology of cell types. Hongyu Chen, Pu Liang, Xiaolin Lu, Shuai Jiang, Jingjing Jin, Jiaqi Cai, Yaqian Lu, Dihuai Zheng, Jie Yao, Qinjie Chu, Huixia Shou, Chengxin Fu, Tingting Lu, Yi Jing, Yinqi Bai, Ning Yang, Silin Zhong, Jun Xiao, Fang Yang, Xing Guo, Jixian Zhai, Alexandre P. Marand, Zhixi Tian, Fan Chen, Jian Xu, Yuling Jiao, Dijun Chen, Peijian Cao, Xiaofeng Cui, Dave Jackson, Tatsuya Nobori, Xiaofeng Gu, Jiawei Wang, James Whelan, Jianbing Yan, Robert J. Schmitz, Zhang Zhang, Longjiang Fan*, POCT Consortium. Molecular Plant, 2025. doi:https://doi.org/10.1016/j.molp.2025.12.025

Mitochondrial genome of African rice (Oryza glaberrima): comparative analysis and phylogenetic relationships. Babatunde O. Kehinde, Shiyu Zhang, Linfeng Jin, Lingjuan Xie, Longjiang Fan*. Mitochondrial DNA Part B: Resources, 2025. doi:https://doi.org/10.1080/23802359.2025.2603826

Widespread remote introgression in the grass genomes. Yujie Huang, Shiyu Zhang, Hanyang Lin, Chenxu Liu, Zhefu Li, Kun Yang, Yutong Liu1, Linfeng Jin, Chuanlong Lu, Yuan Cheng, Chaoyi Hu, Huifang Zhao, Guoping Zhang, Qian Qian, Longjiang Fan* and Dongya Wu*. Plant Communications, 2025. doi:https://doi.org/10.1016/j.xplc.2025.101658

A transcriptomic profiling across tissues, developmental stages, and types of Nicotiana tabacum. Kun Yang, Zhijun Tong, Xueyi Sui, Xuejun Chen, Zhefu Li, Fei Xu, Yujie Huang, Enhui Shen, Sanling Wu, Longjiang Fan* and Bingguang Xiao*. Scientific Data, 2025. in press.

Genetic diversity and evolution of rice centromeres. Xie Lingjuan, Yujie Huang, Wei Huang, Lianguang Shang, Yanqing Sun, Quanyu Chen, Shuangtian Bi, Mingyu Suo, Shiyu Zhang, Chentao Yang, Xiaoming Zheng, Weiwei Jin, Qian Qian, Longjiang Fan*, Dongya Wu*. Nature Genetics, 2025. doi:https://doi.org/10.1038/s41588-025-02365-1

Weeds provide genomic resources for climate-adapted crops. Babatunde O. Kehinde, Yujie Huang, Qian Qian, Jian Sun*, Longjiang Fan*. Science Bulletin, 2025. doi:https://doi.org/10.1016/j.scib.2025.10.047

Advances in plant spatial multi-omics data analysis. Jie Yao, Alexandre P. Marand, Yinqi Bai, Robert J. Schmitz, Longjiang Fan*. Trends in Plant Science, 2025. doi:https://doi.org/10.1016/j.tplants.2025.10.005

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重要链接（Links）

Important Databases and Bioinformatics Portals

✽ CNCB（中国国家生物信息中心）

✽ NCBI

✽ EMBL

✽ ExPASy

✽ JCVI

✽ CBI-PU

Plant genomes by us

✽ Rice / cultivated red rice [NGDC(Wu)][NGDC(Xie)][RiceRelativesGD]（Wu et al., 2023; Xie et al., 2023; Xie et al., 2025）

✽ Weedy rice (red rice) [RiceRelativesGD] (Qiu et al., 2014;Qiu et al., 2017; Qiu et al., 2020; Wu et al., 2023)