PMID- 35134336 OWN - NLM STAT- MEDLINE VI - 57 IP - 4 TI - A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. PG - 543-560.e9 CI - Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Dev Cell JT - Developmental cell JID - 101120028 IS - 1878-1551 (Electronic) LID - S1534-5807(22)00033-8 [pii] LID - 10.1016/j.devcel.2022.01.008 [doi] FAU - Shahan, Rachel AU - Shahan R AD - Department of Biology, Duke University, Durham, NC 27708, USA. FAU - Hsu, Che-Wei AU - Hsu CW AD - Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany. FAU - Nolan, Trevor M AU - Nolan TM AD - Department of Biology, Duke University, Durham, NC 27708, USA. FAU - Cole, Benjamin J AU - Cole BJ AD - Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. FAU - Taylor, Isaiah W AU - Taylor IW AD - Department of Biology, Duke University, Durham, NC 27708, USA. FAU - Greenstreet, Laura AU - Greenstreet L AD - Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada. FAU - Zhang, Stephen AU - Zhang S AD - Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada. FAU - Afanassiev, Anton AU - Afanassiev A AD - Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada. FAU - Vlot, Anna Hendrika Cornelia AU - Vlot AHC AD - The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany. FAU - Schiebinger, Geoffrey AU - Schiebinger G AD - Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada. FAU - Benfey, Philip N AU - Benfey PN AD - Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA. Electronic address: philip.benfey@duke.edu. FAU - Ohler, Uwe AU - Ohler U AD - Department of Biology, Humboldt Universität zu Berlin, 10117 Berlin, Germany; The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany; Department of Computer Science, Humboldt Universität zu Berlin, 10117 Berlin, Germany. Electronic address: uwe.ohler@mdc-berlin.de. IS - 1534-5807 (Linking) RN - 0 (Arabidopsis Proteins) RN - 0 (Transcription Factors) SB - IM MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Gene Expression Regulation, Plant/*genetics/physiology MH - Gene Regulatory Networks/*genetics/physiology MH - Mutation/genetics MH - Plant Roots/*genetics/metabolism MH - Single-Cell Analysis/methods MH - Transcription Factors/genetics/metabolism MH - Transcriptome/physiology OTO - NOTNLM OT - *Arabidopsis OT - *SCARECROW OT - *SHORTROOT OT - *cell fate OT - *development OT - *root OT - *scRNA-seq OT - *transcriptomics PMC - PMC9014886 DCOM- 20220311 LR - 20220716 DP - 20220228 DEP - 20220207 AB - 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.