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

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…

• NS
  National Science Foundation

  Awards: IOS-2010686, 2010686, DE-AC02-05CH11231
• UD
  U.S. Department of Energy

  Awards: -AC02-05CH11231, 05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
• UD
  U.S. Department of Agriculture

  Award: DE-AC02-05CH11231
• JG
  Joint Genome Institute

  Awards: DE-AC02-05CH11231, AC02-05CH11231
• DF
  Deutsche Forschungsgemeinschaft

  Award: DE-AC02-05CH11231
• NI
  National Institutes of Health

  Awards: 1F32GM136030-01, MIRA 1R35GM131725, DE-AC02-05CH11231, 1F32GM136030, 1R35GM131725
• NI
  National Institute of Food and Agriculture

  Award: 2021-67034-35139
• OO
  Office of Science

  Awards: AC02-05CH11231, -AC02-05CH11231, DE-AC02
• CI
  Canadian Institutes of Health Research

  Award: DE-AC02-05CH11231
• NS
  Natural Sciences and Engineering Research Council of Canada

  Award: DE-AC02-05CH11231