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
Language
- eng