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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • 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 Date

  • February 2022

Published In

Volume / Issue

  • 57 / 4

Start / End Page

  • 543 - 560.e9

PubMed ID

  • 35134336

Pubmed Central ID

  • PMC9014886

Electronic International Standard Serial Number (EISSN)

  • 1878-1551

International Standard Serial Number (ISSN)

  • 1534-5807

Digital Object Identifier (DOI)

  • 10.1016/j.devcel.2022.01.008


  • eng