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Summary The plant community has a strong track record of RNA sequencing technology deployment, which combined with the recent advent of spatial platforms (e.g. 10× genomics) has resulted in an explosion of single‐cell and nuclei datasets that can be positioned in anin situcontext within tissues (e.g. a cell atlas). In the genomics era, application of proteomics technologies in the plant sciences has always trailed behind that of RNA sequencing technologies, largely due in part to upfront cost, ease‐of‐use, and access to expertise. Conversely, the use of early analytical tools for characterizing small molecules (metabolites) from plant systems predates nucleic acid sequencing and proteomics analysis, as the search for plant‐based natural products has played a significant role in improving human health throughout history. As the plant sciences field now aims to fully define cell states, cell‐specific regulatory networks, metabolic asymmetry and phenotypes, the measurement of proteins and metabolites at the single‐cell level will be paramount. As a result of these efforts, the plant community will unlock exciting opportunities to accelerate discovery and drive toward meaningful translational outcomes.
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Toward a data infrastructure for the Plant Cell Atlas
Abstract We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.
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- Award ID(s):
- 1916797
- PAR ID:
- 10451337
- Date Published:
- Journal Name:
- Plant Physiology
- Volume:
- 191
- Issue:
- 1
- ISSN:
- 0032-0889
- Page Range / eLocation ID:
- 35 to 46
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/plphys/kiac468
