Super-resolution single-cell spatial atlas of plant de novo regeneration

Song, X.; Zhang, S.; Yue, Z.; Liu, Y.; Chen, S.; Niu, Y.; Shi, Y.; Yang, H.; Xu, L.; Liu, N.; Miao, Y.; Lv, M.; Li, J.; Wang, T.; Xu, M.; Sun, B.; Qiu, C.; Xu, R.; Wang, J.; Zhang, H.; Hou, S.; Li, G.; Chen, H.; Deng, X. W.; Li, B.

doi:10.64898/2026.02.20.705279

bioRxiv · 10.64898/2026.02.20.705279

Super-resolution single-cell spatial atlas of plant de novo regeneration

Song, X.·Zhang, S.·Yue, Z.·Liu, Y.·Chen, S.·Niu, Y.·Shi, Y.·Yang, H.·Xu, L.·Liu, N.·Miao, Y.·Lv, M.·Li, J.·Wang, T.·Xu, M.·Sun, B.·Qiu, C.·Xu, R.·Wang, J.·Zhang, H.·Hou, S.·Li, G.·Chen, H.·Deng, X. W.·Li, B.

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Abstract

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com.

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Song, X., Zhang, S., Yue, Z., Liu, Y., Chen, S., Niu, Y., Shi, Y., Yang, H., Xu, L., Liu, N., Miao, Y., Lv, M., Li, J., Wang, T., Xu, M., Sun, B., Qiu, C., Xu, R., Wang, J., Zhang, H., Hou, S., Li, G., Chen, H., Deng, X. W., Li, B.. 2026-02-20. Super-resolution single-cell spatial atlas of plant de novo regeneration. https://doi.org/10.64898/2026.02.20.705279

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