Homepage of Dongya
See ResearchGate to get more information.
Email: wudongya@zju.edu.cn
Location: Life Sciences Research Interdisciplinary Center, Zhejiang University, China
Bachlor: Horticulture @ Zhejiang University
PhD: Crop genetic breeding @ Zhejiang University
Supervisor: Longjiang Fan (Bioinplant Lab)
Long-read sequencing technology makes it possible to completely decipher the sequences of highly repetitive regions, previously “dark” regions, including tandem genes and non-coding elements (e.g. VNTR/STR). By leveraging multi-omics long-read sequencing technologies and artificial intelligence, we aim to study (1) High-order architecture: deciphering the hierarchical folding and spatial organization of TRs that dictate chromosome integrity; (2) Evolutionary dynamics: quantifying the “Birth-and-Death” processes and evolutionary constraints to identify functional motifs that resist neutral homogenization; (3) Regulatory heterogeneity: mapping the epigenetic polarity within TR arrays to understand their role as “transcriptional rheostats”; (4) Adaptive innovation: Linking TR-mediated structural variation to trait innovation and rapid adaptation across eukaryotic lineages.
The centromere represents one of the most repetitive genomic regions in eukaryotes and what we know is quite limited, despite its essential role in cell division. Our team aims to study (1) the mechanism underlying the centromere paradox, the co-evolutionary arms race between rapidly diversifying centromeric DNA (e.g., satellite arrays) and conserved kinetochore proteins (e.g., CENP-A); (2) Centromere drive, by testing the selection pressure on and “selfish” expansion of centromeres in asymmetric meiosis, identifying how these sequences “cheat” to ensure transmission; (3) Effects on reproduction and speciation, by evaluating how centromeric variation and protein-DNA incompatibility trigger meiotic drive suppression, hybrid sterility, and the formation of reproductive barriers.
Despite the completion of the human genome, over 20% of its regions, primarily complex repeats and structural variants, remain “dark”. We are constructing Platinum-level Human Pan-genomes using T2T gapless assemblies to illuminate these regions and their roles in health and disease. We aim to study the dark regions in the human genome from (1) High-resolution architecture, by deciphering the assembly of complex loci and the mutational mechanisms that drive their formation; (2) Adaptive selection, by mapping the evolutionary signatures within these dark regions to identify novel loci involved in human-specific traits and environmental adaptation; (3) Pathogenic variation, by identifying cryptic variants within dark regions through screening large-scale health and disease panels to solve missing heritability.
#14. Yujie Huang et al., Longjiang Fan*, Dongya Wu*, RIFinder reveals widespread adaptive remote introgression in grass genomes. Plant Communications. (2025).
#13. Lingjuan Xie#, Yujie Huang#, Wei Huang#, Lianguang Shang#, et al., Longjiang Fan*, Dongya Wu*, Genetic diversity and evolution of rice centromeres. Nature Genetics. (2025).
#12. Baohua Chen, Dongya Wu*, Guojie Zhang*, GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction. GigaScience. (2025).
#11. Quanyu Chen, Chentao Yang, Guojie Zhang*, Dongya Wu*, GCI: a continuity inspector for complete genome assembly. *Bioinformatics. (2024).
#10. Dongya Wu et al., A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biology. (2023).
#9. Chentao Yang, Yang Zhou, Yanni Song, Dongya Wu, Yan Zeng et al., The complete and fully-phased diploid genome of a male Han Chinese. Cell Research. (2023).
#8. Dongya Wu et al., Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. The Plant Journal.doi: https://doi.org/10.1111/tpj.15893 (2022).
#7. Dongya Wu et al., Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoid in plants. Plant Communications. doi:https://doi.org/10.1016/j.xplc.2022.100320 (2022).
#6. Dongya Wu et al., Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nature Communications. doi: https://doi.org/10.1038/s41467-022-28359-9 (2022).
#5. Dongya Wu et al., Weedy rice, a hidden gold mine in the paddy field. Molecular Plant. doi: https://doi.org/10.1016/j.molp.2022.01.008 (2022).
#4. Dongya Wu et al., De-domestication: an extension of crop evolution. Trends in Plant Science. 26, 560-574 (2021).
#3. Chu-Yu Ye#, Dongya Wu# et al., The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Molecular Plant. 13, 1298-1310 (2020). MP Highlight
#2. Jie Qiu#, Lei Jia#, Dongya Wu# et al., Diverse genetic mechanisms underlie worldwide convergent rice feralization. Genome Biology. 21, 70 (2020).
#1. Chu-Yu Ye#, Wei Tang#, Dongya Wu# et al., Genomic evidence of human selection on Vavilovian mimicry. Nature Ecology & Evolution. 3, 1474-1482 (2019). Nature Plants Highlight F1000 Recommendation by Prof. Manyuan Long
#9. Yujie Huang et al., Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance. Nature Communications. (2026).
#8. Zhang et al., Integrated analysis of the complete sequence of a macaque genome. Nature. (2025).
#7. Lingjuan Xie et al., Technology-enabled great leap in deciphering plant genomes. Nature Plants. (2024).
#6.Yanqing Sun#, Enhui Shen#, Yiyu Hu, Dongya Wu, Yu Feng, Sangting Lao, Chenfeng Dong, Tianyu Du, Wei Hua, Chu-Yu Ye, Jinhuan Zhu, Qian-Hao Zhu, Daguang Cai, Lidia Skuza, Jie Qiu and Longjiang Fan* (2022). Population genomic analysis reveals domestication of cultivated rye from weedy rye. Molecular Plant 15:552–561.
#5.Lingfeng Mao, Meihong Chen, Qinjie Chu, Lei Jia, Most. Humaira Sultana, Dongya Wu, Kong X, Jie Qiu, Chu-Yu Ye, Xi Chen*, and Longjiang Fan (2019). RiceRelativesGD: a genomic database of rice relatives for rice research. Database 2019:1–8.
#4.Sultana Most. Humaira, Fangjie Liu, Md. Alamin, Lingfeng Mao, Lei Jia, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chuyu Ye, Qian-hao Zhu, Jie Qiu*, Longjiang Fan (2019). Gene modules co-regulated with biosynthetic gene clusters for allelopathy between rice and barnyardgrass. International Journal of Molecular Science 20:3846.
#3.Bowen Jiang, Sangting Lao, Dongya Wu, Longjiang Fan and Chu-Yu Ye* (2021). The complete chloroplast genome of Echinochloa haploclada. Mitochondrial DNA Part B 6:3105–3106.
#2.Jun Zhou, Lingfeng Mao, Jie Qiu, Meng Wang, Lei Jia, Dongya Wu, Zhesi He, Meihong Chen, Yifei Shen, Enhui Shen, Yongji Huang, Ruiyuan Li, Dandan Hu, Lei Shi, Kai Wang, Qian-Hao Zhu, Chuyu Ye, Ian Bancroft, Graham J King, Jinling Meng, Longjiang Fan* (2019). Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Plant Biotechnology Journal 17:1998–2010.
#1.Longbiao Guo#, Jie Qiu#, Chuyu Ye, Gulei Jin, Lingfeng Mao, Haiqiang Zhang, Xuefang Yang, Qiong Peng, Yingying Wang, Lei Jia, Zhangxiang Lin, Gengmi Li, Fei Fu, Chen Liu, Li Chen, Enhui Shen, Weidi Wang, Qinjie Chu, Dongya Wu, Sanling Wu, Chenyang Xia, Yongfei Zhang, Xiaomao Zhou, Lifeng Wang, Lamei Wu, Weijie Song, Yunfei Wang, Qingyao Shu, Daisuke Aoki, Emi Yumoto, Takao Yokota, Koji Miyamoto, Kazunori Okada, Do-Soon Kim, Daguang Cai, Chulong Zhang, Yonggen Lou, Qian Qian, Hirofumi Yamaguchi, Hisakazu Yamane, Chui-Hua Kong, Michael P. Timko, Lianyang Bai* and Longjiang Fan* (2017). Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nature Commununications 8:1031.