Revolutionary Tools for Decoding the Complexity of Forest Trees: The Application of Single-Cell and Spatial Transcriptomics in Woody Plants.

The heterogeneity of cells constitutes the foundation of development, adaptation and evolution, therefore understanding the expression and spatial distribution patterns of genes in different plant tissues has extremely high research value. Traditional transcriptome sequencing can only perform mixed-sequencing analysis on multicellular tissues and fails to detect intercellular heterogeneity. However, the groundbreaking development and integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) are leading forest tree biology into a new era. This review systematically illustrates the developmental history, technical workflows, and integration of these two technologies and elaborates in detail on their cutting-edge applications in woody plants, such as vascular cambium differentiation, abiotic stress response analysis, and the identification and characterization of rare cell types. In addition, we discuss the challenges encountered in applying these technologies to forest tree research and point out the key directions for future research that should be focused on solving the difficulties in upcoming woody plant studies. This paper reveals the enormous potential of scRNA-seq and ST in research on woody plants, providing a new perspective for further research and applications in related fields.