Homepage of Dongya
See ResearchGate to get more information.
Email: wudongya@zju.edu.cn
Location: Zhejiang University, China
Bachlor | Horticulture | Zhejiang University
PhD | Crop genetic breeding | Zhejiang University
Supervisor: Longjiang Fan (Bioinplant Lab)
Long-read sequencing makes it not difficult to assemble a high-quality genome assembly, even a telomere-to-telomere gapless assembly. We have the opportunity to explore the variations in complex repetitive regions (e.g. centromere, telemore, rDNA), which have not been visited before.
At individual level, combining genome assemblies, transcriptomics, epi-genomics and other omics data could uncover the mechanism of plant adaptation under stress (e.g. disease resistance). At population level, population genome re-sequencing and GWAS or whole-genome selection scan are powerful ways to exploit key genes regulating plant adaptation (natural population) or agronomic traits (crop).
Horizontal transfer, gene introgression, in-complete lineage sorting would result in the discordance in gene phylogeny inference (e.g. in Poaceae). How frequent they are across species and how they affect species adaptation are interesting questions to explore. (Wu et al., 2022, Plant Commun.; Wu et al., 2022, Plant J.)
#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
#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.
#1.Dongya Wu et al., Horizontal transfers lead to the birth of momilactone biosynthetic gene clusters in grass. bioRxiv. doi:https://doi.org/10.1101/2022.01.11.475971 (2022).