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A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.

Publication ,  Journal Article
Shahan, R; Hsu, C-W; Nolan, TM; Cole, BJ; Taylor, IW; Greenstreet, L; Zhang, S; Afanassiev, A; Vlot, AHC; Schiebinger, G; Benfey, PN; Ohler, U
Published in: Developmental cell
February 2022

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.

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Published In

Developmental cell

DOI

EISSN

1878-1551

ISSN

1534-5807

Publication Date

February 2022

Volume

57

Issue

4

Start / End Page

543 / 560.e9

Related Subject Headings

  • Transcriptome
  • Transcription Factors
  • Single-Cell Analysis
  • Plant Roots
  • Mutation
  • Gene Regulatory Networks
  • Gene Expression Regulation, Plant
  • Developmental Biology
  • Arabidopsis Proteins
  • Arabidopsis
 

Citation

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Chicago
ICMJE
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Shahan, R., Hsu, C.-W., Nolan, T. M., Cole, B. J., Taylor, I. W., Greenstreet, L., … Ohler, U. (2022). A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental Cell, 57(4), 543-560.e9. https://doi.org/10.1016/j.devcel.2022.01.008
Shahan, Rachel, Che-Wei Hsu, Trevor M. Nolan, Benjamin J. Cole, Isaiah W. Taylor, Laura Greenstreet, Stephen Zhang, et al. “A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.Developmental Cell 57, no. 4 (February 2022): 543-560.e9. https://doi.org/10.1016/j.devcel.2022.01.008.
Shahan R, Hsu C-W, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, et al. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental cell. 2022 Feb;57(4):543-560.e9.
Shahan, Rachel, et al. “A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.Developmental Cell, vol. 57, no. 4, Feb. 2022, pp. 543-560.e9. Epmc, doi:10.1016/j.devcel.2022.01.008.
Shahan R, Hsu C-W, Nolan TM, Cole BJ, Taylor IW, Greenstreet L, Zhang S, Afanassiev A, Vlot AHC, Schiebinger G, Benfey PN, Ohler U. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental cell. 2022 Feb;57(4):543-560.e9.
Journal cover image

Published In

Developmental cell

DOI

EISSN

1878-1551

ISSN

1534-5807

Publication Date

February 2022

Volume

57

Issue

4

Start / End Page

543 / 560.e9

Related Subject Headings

  • Transcriptome
  • Transcription Factors
  • Single-Cell Analysis
  • Plant Roots
  • Mutation
  • Gene Regulatory Networks
  • Gene Expression Regulation, Plant
  • Developmental Biology
  • Arabidopsis Proteins
  • Arabidopsis