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Advances in plant spatial multi-omics data analysis.

Jie Yao1, Alexandre P Marand2, Yinqi Bai3

  • 1Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA; Department of Genetics, University of Georgia, Athens, GA, USA.

Trends in Plant Science
|October 29, 2025
PubMed
Summary

Plant spatial multi-omics integrates spatial data with single-cell technologies for cellular insights. This review guides researchers on experimental and computational methods for plant spatial multi-omics analysis.

Keywords:
data analysis workflowmulti-omic data integrationplant spatial omicspatial transcriptomics

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Area of Science:

  • Plant biology
  • Genomics
  • Metabolomics

Background:

  • Spatial omics technologies provide cellular-level insights by integrating spatial information.
  • Droplet-based single-cell technologies combined with spatial approaches enhance understanding of biological processes.
  • Plant-specific challenges like rigid cell walls necessitate adaptations of mammalian-derived methods.

Purpose of the Study:

  • To review current strategies for acquiring plant spatial multi-omics data.
  • To focus on accessible commercial platforms for plant spatial multi-omics.
  • To outline analysis workflows and provide a practical tutorial for plant spatial multi-omics.

Main Methods:

  • Summarizing current strategies for plant spatial multi-omics data acquisition.
  • Focusing on widely accessible commercial platforms.
  • Outlining analysis workflows from preprocessing to downstream interpretation.

Main Results:

  • The review covers experimental and computational approaches for plant spatial multi-omics.
  • A practical tutorial using demonstration datasets is provided.
  • The resource offers a concise guide for researchers.

Conclusions:

  • Plant spatial multi-omics is a rapidly advancing field.
  • Adaptation of existing methods is crucial for plant research.
  • This review serves as a valuable guide for researchers entering the field.