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Single-cell RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

ABSTRACT: Plant somatic cells can be reprogrammed to form a pluripotent cell mass, known as callus, which can be used to regenerate organs or an entire plant via de novo organogenesis. Exogenous treatment of tissue explants with a high auxin-to-cytokinin ratio stimulates callus formation. Here, we found that the pluripotency acquisition in the callus is transient during callus formation, independent of explant origin. Using single-cell transcriptome analysis of pluripotent and nonpluripotent calli, obtained at 7 and 12 days after incubation on callus-inducing medium (CIM), respectively, we found that root stem cell activity conferred by the WUSCHEL-RELATED HOMEOBOX5 (WOX5)-TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) module is diminished by the prolonged incubation of callus on CIM. The reduced root stem cell activity led to the differentiation mainly into mature lateral root cap (LRC)-like cells in callus. Concomitant with differentiation into LRC-like cells, epidermis-like cells accumulating very long chain fatty acids (VLCFAs) that promote cellular pluripotency are sloughed off. Additionally, stress responses that induce the loss of pluripotency are activated in the mature LRC-like cells and a sub-cluster of xylem pole pericycle cells. Taken together, our data indicate that callus formation is likely a continuous developmental program, in which stem cell activity is acquired then lost, resulting in the transient nature of cellular pluripotency in callus.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE234192 | GEO | 2026/04/15

REPOSITORIES: GEO

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Bulk RNA-sequencing of calli harvested 7 and 12 days after incubation on callus-inducing medium

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