https://doi.org/10.1016/j.molp.2018.01.002
Basic Information:
Name: Ji Qi
Title: Professor
Position:
Email: qij@fudan.edu.cn
Office Location: School of Life Sciences, E401
Office Phone: 021-31246533
Personal webpage/lab homepage:
Research intrested:
Development: Studying the construction process of plant floral organs based on spatial transcriptomics.
We use the spatial transcriptome technology to study the development of floral organs in model plants of monocots, eudicots and basal angiosperms. Through the analysis of high-resolution spatial expression patterns of thousands of key genes involved in flower development, various cell types in early orchid development were identified, including floral primordia, floral organ primordia, and various meristematic tissues. The meristematic cells at the base of floral organs were found to play a continuous role in multiple developmental stages after organ initiation. The study revealed detailed differentiation trajectories constructed by early organ primordia and various cell types during subsequent development, providing molecular-level information for understanding floral organogenesis and genomic and genetic studies of specific cell types.
Evolution: Plant genome variation and functional differentiation of repetitive genes.
By developing new bioinformatics methods and combining high-throughput sequencing of genomes and transcriptomes of various plants, it was discovered that genome duplication is widespread in different branches of angiosperms, and the retention of repetitive genes follows a consistent exponential decay pattern. The study found that these repetitive genes provide more materials for functional differentiation and the generation of new functions, contributing to increased environmental adaptability in plants.
Algorithms: Machine learning methods for spatial transcriptomics and molecular evolution.
We developed new methods for spatial transcriptomic analysis with single-cell precision, effectively identifying different cell types from sequencing data such as 10X Visium and Slide-seq, with higher accuracy than similar methods. By applying the method to the previously completed spatial transcriptomic analysis of Phalaenopsis orchid floral organs, the results showed high accuracy in predicting floral primordia, four types of floral organ primordia, and tissues undergoing morphogenesis. This is beneficial for precise analysis of key gene expression in different organs and further research into the complexity of cell type differentiation.
Personal Profile:
Ji Qi is a professor at the School of Life Sciences, Fudan University. Currently, his research focuses on plant development, molecular evolution, and bioinformatics methods. He holds a position as a faculty member and mentors doctoral students.He has published research papers in high-impact journals in the field of biology, including Nature Communications, PNAS, Nucleic Acids Research, Molecular Plant, and Molecular Biology and Evolution. His publications have collectively been cited over 10,000 times, with an h-index of 40 (source: Google Scholar).
Teaching: Ji Qi teaches the course Bioinformatics for undergraduate students.
Research Projects: Ji Qi has secured funding for multiple research projects from the National Natural Science Foundation of China (NSFC)
Selected publications:
1. Yamao Chen†, Shengyu Zhou†, Ming Li, Fangqing Zhao* and Ji Qi* (2023) STEEL enables high-resolution delineation of spatiotemporal transcriptomic data. Briefings in Bioinformatics. DOI:10.1093/bib/bbad068
2. Jingting Shen1†, Shengyu Zhou1†, Yamao Chen and Ji Qi* (2023) TransMCL enables the assembly of full-length coding genes for collecting complete hierarchical orthogroups. Methods in Ecology & Evolution.DOI:10.1111/2041-210X.14179
3. Chang Liu, Jing Leng, Yonglong Li, Tingting Ge, Jinglong Li, Yamao Chen, Chunce Guo* and Ji Qi* (2022) A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Research. 50(17):9724-9737
4. Jinglong Li, Jingting Shen, Rui Wang, Yamao Chen, Taikui Zhang, Haifeng Wang, Chunce Guo, Ji Qi* (2022) The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. Plant Communications. 4(1):100422
5. Duoyuan Chen#, Taikui Zhang#, Yamao Chen, Hong Ma and Ji Qi* (2022) Tree2GD: a phylogenomic method to detect large-scale gene duplication events. Bioinformatics. 38(23):5317-5321
6. Ying Zhao#, Duoyuan Chen#, Jianping Tang, Yufang Zheng*, Ji Qi*, Hongyan Wang* (2022) Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations. Cell Discovery. 8:18
7. Chengpeng He#; Zhiyu Chen#; Yiyong Zhao; Yue Yu; Hongkuan Wang; Cong Wang; Gregory P. Cop enhaver; Ji Qi*; Yingxiang Wang* (2022) Histone demethylase IBM1-mediated meiocyte gene expression ensur es meiotic chromosome synapsis and recombination. PLoS Genetics. 18(2):e1010041
8. Q. Lian, Y. Chen, F. Chang, Y. Fu and J. Qi* (2021) inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities. Genomics, Protoemics & Bioinformatics https://doi.org/10.1016/j.gpb.2019.11.014.
9. Caifei Zhang#, Taikui Zhang#, Federico Luebert# Yezi Xiang, Chien-Hsun Huang, Yi Hu, Mathew Rees, Michael W. Frohlich, Ji Qi*, Maximilian Weigend*, Hong Ma*. (2020) Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications. Mol. Biol. Evol. 37:3188-3210
10. S. Zhou, Y. Chen, C. Guo*, J. Qi* (2020) PhyloMCL: accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events. Methods in Ecology & Evolution. 11: 943-954 https://doi.org/10.1111/2041-210X.13401
11. H. Wang, C. Guo, H. Ma, J. Qi* (2019) Meeting the Challenges of Detecting Polyploidy Events from Transcriptomic Data. Mol. Plant 12(2):137-140
12. J. Liu, Q. Lian, Y. Chen, J. Qi* (2019) Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads. Nucleic Acids Res. 47: e30
doi: 10.1093/nar/gkz017.
13. Ren Ren#, Haifeng Wang#, Chunce Guo#, Ning Zhang, Liping Zeng, Yamao Chen, Hong Ma*, Ji Qi* (2018) Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol. Plant 11: 414-428. DOI: https://doi.org/10.1016/j.molp.2018.01.002