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

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

doi:10.1016/j.devcel.2022.01.008

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

Journal Article · 06 February 2022 · Developmental Cell

DOI: https://doi.org/10.1016/j.devcel.2022.01.008 · OSTI ID:1904100

Shahan, Rachel ^[1]; Hsu, Che-Wei ^[2]; Nolan, Trevor M. ^[3]; Cole, Benjamin J. ^[4]; Taylor, Isaiah W. ^[3]; Greenstreet, Laura ^[5]; Zhang, Stephen ^[5]; Afanassiev, Anton ^[5]; Vlot, Anna Hendrika Cornelia ^[6]; Schiebinger, Geoffrey ^[5]; Benfey, Philip N. ^[7]; Ohler, Uwe ^[8]

Duke University, Durham, NC (United States); OSTI
Humboldt University of Berlin (Germany); Max Delbrück Center for Molecular Medicine, Berlin (Germany)
Duke University, Durham, NC (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
University of British Columbia, Vancouver, BC (Canada)
Max Delbrück Center for Molecular Medicine, Berlin (Germany); Humboldt University of Berlin (Germany)
Duke University, Durham, NC (United States); Duke Univ., Durham, NC (United States). Howard Hughes Medical Institute
Humboldt University of Berlin (Germany); Max Delbrück Center for Molecular Medicine, Berlin (Germany); Humboldt University of Berlin (Germany)

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model to investigate 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.

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Research Organization:: USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: Burroughs Wellcome Fund; Canadian Institutes of Health Research (CIHR); German Research Foundation (DFG); Helmholtz Association; Howard Hughes Medical Institute; National Institutes of Health (NIH); National Science Foundation (NSF); Natural Sciences and Engineering Research Council of Canada (NSERC); New Frontiers in Research Fund (NFRF); US Department of Agriculture (USDA); USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904100

Journal Information:: Developmental Cell, Journal Name: Developmental Cell Journal Issue: 4 Vol. 57; ISSN 1534-5807

Publisher:: Cell Press - ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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