Abstract
Insect wing development involves tissue patterning, cell fate transitions, and hormone signaling, yet its spatiotemporal logic remains unclear. The silkworm, with large wing discs and defined stages, provides an ideal model for high resolution analysis. Here, we construct a spatiotemporal single-cell atlas of the silkworm wing disc across 10 timepoints, identifying 12 major cell types and their developmental transitions. Wing morphogenesis (Wm) cells act as central progenitors, differentiating into epithelial and cuticle lineages under lineage-specific transcription factors. Time‑resolved snRNA‑seq reveals hierarchical transcriptional reprogramming, with Wm cells functioning as early signaling hubs. Functional modules and signaling pathways were activated in spatiotemporal controlled manner. 20‑hydroxyecdysone treatment rapidly accelerates fate transitions and gene expression, recapitulating natural development within hours. Integration of morphology, hormone levels, and gene expression supports a five-stage Gene Transition Model describing progressive fate resolution. This work reveals wing development in silkworm and provides insights into hormone-driven organogenesis and potential manipulation of insect development in agriculture.
Data availability
The scRNA-seq, snRNA-seq and Stereo spatial raw sequeneing data have been deposited in Genome Sequence Archive (GSA) under bioproject PRJCA053684. scRNA-seq and snRNA-seq transcriptomics sequencing data and gene expression matrix files have been deposited in the China National GeneBank Sequence Archive (CNGB) under project CNP0005964. Stereo spatial transcriptomics sequencing data and gene expression matrix files have also been deposited in STOmicsDB under project STT0000176. Previously published Drosophila melanogaster wing disc of scRNA-seq data is available in the NCBI GEO database (GSE155543 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155543]). All other data are available in the article or Supplementary files. Source data are provided with this paper. The processed data for all figures are available in the source data file associated with this manuscript. Source data are provided with this paper.
Code availability
The R and Python analysis code, encompassing all steps from preprocessing to visualization, is available on GitHub (https://github.com/meimeihe/Bombyx-mori-wing-disc.git) and archived on Zenodo (https://doi.org/10.5281/zenodo.17973196) with an assigned DOI. A detailed README.md file provides execution instructions.
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Acknowledgements
We thank Yun He, Xiaoman Zhang, Jianxin Song, and Yu Zhang for assistance with tissue collection. This work was supported by the National Natural Science Foundation of China (Grant No. 32030103 to Q.X.) and the National Key Research and Development Program of China (2022YFD1201600 to Q.X. and 2022YFC3400400 to X.X.). Thanks for the support of the academy for advanced interdisciplinary studies device sharing service platform (equipment No.14A00784), Southwest University. We also would like to thank DCS Cloud (https://cloud.stomics.tech/) for providing the computational resources and software support necessary for this study.
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Q.X., M.X., A.C., P.Z. and Q.L. conceived the idea and designed the project. Q.L, H.C. and Y.F.Z. supervised sample preparation and sequencing data generation. Y.L. and L.Y.W. contributed silkworm materials. Q.L., H.C., X.W., H.N.L., Z.T., L.Z., G.L.L., X.C., X.L. and L.J. contributed to the selection of materials. M.H. and L.X.W., X.Z., H.Y.L, D.R., Y.W., X.J.Z, J.H., and G.C.L performed data processing and analysis. Q.L., M.H., H.C., W.L., P.Z, A.C., M.X. and Q.X. interpreted results and synthesized the scientific contents. H.C. performed RNAi experiment and slice staining. Q.L., M.H., H.C, P.Z., A.C., M.X. and Q.X. wrote the first draft of the manuscript. F.X., G.B.L. and X.X. revised the manuscript. Q.L., M.H., H.C, L.X.W., P.Z., A.C., M.X. and Q.X. wrote the final manuscript. All authors approved the final manuscript.
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W.L., G.C.L., and J.H. are employees at MGI Tech. The remaining authors declare no competing interests.
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Liu, Q., He, M., Chen, H. et al. Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69518-6
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DOI: https://doi.org/10.1038/s41467-026-69518-6
