Recently, a research team led by Dr. Xu Xun, Executive Director of BGI Group and Director of BGI-Research, was invited to publish a review article in the Plant Journal, offering an in-depth analysis of the recent progress and challenges faced by spatial transcriptomics (ST) technology for the plant research field. The review covers the technology’s development, unique advantages, practical applications, and its promising potential.
The review “Spatial transcriptomics drives a new era in plant research” was published in the Plant Journal
The Current Status of ST Technology
In recent years, single-cell technology has found widespread application in animal and human-related research. However, due to technical limitations and challenges associated with plant tissue dissection, its application in the plant kingdom lags far behind.
Understanding the physical interactions between cells, which play a pivotal role in tissue development and physiological functions, relies heavily on having spatial information about cell locations. The essential connection between gene expression and cellular positioning, which single-cell technology has failed to provide, has driven the advancement of spatial transcriptomic (ST) technologies.
The emergence of ST technology provides a whole new perspective for the global science community to analyze and understand the dynamic processes of life. This technology has already been successfully applied to identify cell types, reconstruct cell-fate lineages, and reveal cell-to-cell interactions in plant research. With the latest advancements in this technology, it has become possible to study single cells from plant tissues from a spatial perspective.
Based on how spatial information is obtained, ST technology can be categorized into three types:
1. Laser capture microscopy-based methods: This technique can achieve single-cell and even sub-cellular resolution, but it has limitations in the number of genes detected.
2. Imaging-based methods: This approach can mostly achieve single-cell resolution, but it is constrained by the time-consuming image capture process and the need for complex equipment.
3. In-situ capture sequencing methods: The resolution of this method is typically limited by the diameter of the capture spot.
One of the in-situ capture sequencing ST technologies with single-cell resolution is BGI's spatio-temporal omics technology, Stereo-seq (SpaTial Enhanced REsolution Omics-sequencing). With the sequencing chip sizes up to 13 cm x 13 cm, Stereo-seq provides a large field of view at the scale of centimeters. It can sequence a large section, showing cells next to each other in big tissues, giving us useful insights into how tissues are structured and where cells are located.
ST Technologies in Plant Research
ST technology allows the study of the single-cell characteristics of plant tissues from a spatial perspective, covering the following aspects:
1. Identification of Cell Types: Biologists have been analyzing the cellular dynamics of multicellular organisms and deciphering the cellular composition of complex tissues. ST technology can distinguish cell subtypes with similar transcriptomes by utilizing spatial information and classifying them. For example, it can differentiate between the upper and lower epidermis of the Arabidopsis leaf and provide new leaf cell marker genes.
2. Establishing Developmental Lineages of Cell Fate: During plant development, cells can differentiate and develop into various cell types. ST technology can simultaneously record transcriptional heterogeneity and the spatial coordinates of cells, enabling the spatial reconstruction of developmental lineages of cell fate.
3. Cell-to-Cell Communication and Interaction: Intercellular interaction in multicellular organisms regulates their activities and guarantees their ordered and efficient operation. ST technology has evolved into an effective approach to capture the complete morphology of individual cells, examine the cellular microenvironment, and understand the interactions between individual cells. For instance, ST technology can be used to study the interaction between soybeans and rhizobia, a group of soil bacteria that infect the roots of legumes to form root nodules.
The latest applications of ST technology in plant research.
Looking into the Future
In recent years, ST technology has made significant advancements, offering a valuable tool for plant research and allowing scientists to delve deeply into tissue growth and produce spatial images. Potential applications of ST technology in botany science include plant developmental biology, plant-microbe interactions, and the analysis of plant metabolic pathways.
The future of ST technologies for plant research. Innovations and developments in ST technology will regard sample processing, spatial resolution, multi-omics data integration, and applications to various plant species.
However, due to the complexity and diversity of plant samples, ST technology requires further improvements, including sampling, data processing, customizing single-cell segmentation algorithms, and constructing a reference database for plants.
The single-cell resolution and the large-scale field of view offered by ST technologies are ushering in a new era in plant research. This is leading to novel discoveries in plant biology, as it reveals specific transcriptome traits tied to spatial positioning and unravels the interactions between cells.
As ST becomes more widely used, specialized analytical tools, algorithms, and experimental methods will undoubtedly advance and improve. Ultimately, merging ST with other spatial omics techniques will amplify our comprehension of plant development, metabolism, and interactions with microbiota.
At present, based on the great advantages of Stereo-seq, Dr. Xun Xu’s team is collaborating with leading laboratories worldwide and has launched a series of plant spatial transcriptome research, to further promote the development of spatial transcriptome technologies and drive the novel discoveries of plant research.
Read the review article: https://doi.org/10.1111/tpj.16437