A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
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IF: 13.417
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Cited by: 67
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Abstract

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.

Keywords

novoSpaRc
ProximID
Omics
Seurat
Gene Expression
Arabidopsis
SCARECROW
SHORTROOT
cell fate
development
root
scRNA-seq
transcriptomics

MeSH terms

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

Authors

Shahan, Rachel
Hsu, Che-Wei
Nolan, Trevor M
Cole, Benjamin J
Taylor, Isaiah W
Greenstreet, Laura
Zhang, Stephen
Afanassiev, Anton
Vlot, Anna Hendrika Cornelia
Schiebinger, Geoffrey
Benfey, Philip N
Ohler, Uwe

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