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bioRxiv · 10.1101/2022.10.24.513543

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Cao, S.·He, C.·Zhao, X.·Yu, R.·Li, Y.·Fang, W.·Zhang, C.-Y.·Yan, W.·Chen, D.
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Abstract

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks at a cell-type specific manner. Here we presented a reference single-cell transcriptomic atlas of Arabidopsis seedlings by integration of 40 published scRNA-seq datasets from representative tissues as well as the entire under- and above-ground parts. We identified 34 distinct cell types or states, largely expanding our current view of plant cell compositions. We then mapped the developmental trajectory of root-shoot lineage separation and identified differential gene expression programs that may regulate the cell fate determination of under- and above-ground organs. Lastly, we systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordination manner to control cell-type specific gene expression. Taken together, our study not only offers a valuable resource plant cell atlas exploration but also provides molecular insights into gene-regulatory programs that determines organ specify, particularly the differentiation between root and shoot.

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Cao, S., He, C., Zhao, X., Yu, R., Li, Y., Fang, W., Zhang, C.-Y., Yan, W., Chen, D.. 2022-10-25. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. https://doi.org/10.1101/2022.10.24.513543

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