Dongya Wu
Homepage of Dongya
Welcome to EvoComX WU Lab’s Homepage
We are a genomics research group dedicated to illuminating the ‘dark matter’ of genomes. Our research focuses on resolving complex genomic regions through advanced long-read sequencing technologies.
Contact
Email: wudongya@zju.edu.cn
Phone: 0571-88208707
Affiliation: Centre for Evolutionary & Organismal Biology, ZJU; School of Basic Medical Sciences, ZJU
Location: Life Sciences Research Interdisciplinary Center, Zhejiang University, China
Events
🔍Details
Mingyu Suo attended the Human Genome Meeting 2026 (HGM2026) in Greece, held under the theme “Bringing our Genomes to Medicine.” The conference provided a dynamic forum for advances in genome-stratified medicine, population genomics, and therapeutic interventions, drawing global experts from academia, clinical practice, and industry. During the meeting, Mingyu delivered an oral presentation titled “Deciphering complete archaic introgression sequences in modern human genomes.” The talk introduced ASMaid (Assembly-based archaic introgression detector), a novel Hidden Markov Model-based framework that leverages haplotype-resolved pangenome assemblies to identify introgressed sequences from Neanderthals and Denisovans with unprecedented completeness.
Researches
Genomic complexity of tandem repeats (TRs)
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.
Centromere genomics and biology
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.
Human genomics and disease
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.
Members
Bioinformatics Tools
| Tools | Type | Description | Ref |
| SynPan | Pangenome | a pipeline for syntelog-based pangenome construction | Wu et al., 2022 |
| GCI | T2T assembly | a continuity inspector for complete genome assembly | Chen et al., 2024 |
| GFFx | Annotation | a high-performance, Rust-based toolkit for extracting and querying annotations from GFF3 files | Chen et al., 2025 |
Publications
(#, Co-first author; *, Corresponding author)
2025
#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).
2024
#11. Quanyu Chen, Chentao Yang, Guojie Zhang*, Dongya Wu*, GCI: a continuity inspector for complete genome assembly. *Bioinformatics. (2024).
2023
#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).
2022
#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).
Before 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
See ResearchGate to get more information.