Application and Prospect of Spatial Transcriptome Technology in Plant Research

doi:10.7525/j.issn.1673-5102.2025.01.002

Abstract

Abstract:

Spatial transcriptomics（ST） is a technique used to resolve RNA-seq data at the spatial level， thereby resolving all mRNA in a single tissue section. The orderly attachment of spatial barcoding oligo（dT） primers to the surface of microscope slides makes it possible to encode and obtain positional information during mRNA sample processing and subsequent sequencing. Compared with the traditional transcriptome technology， the spatial transcriptome technology can obtain the true gene expression characteristics of cells in the in-situ environment of tissues and the relationship with the microenvironment， and provide high-precision and high-resolution in-situ spatial information for gene expression. In recent years， the development of spatial transcriptome technology has made significant progress. The detected cell flow， the quantity and quality of transcripts are continuously improved， and spatial location information is more accurate and comprehensive. It has been studied in Arabidopsis thaliana， Oryza sativa， and Populus， etc. In this paper， the successful applications of spatial transcriptome technology in the study of plant dynamic development trajectory， the analysis of differences between different tissues and cell types， and decoding of the interaction between plants and microbial communities were described. The problems and challenges of space transcriptome sequencing technology in plant research were discussed， and the great potential of space transcriptome technology in plant research was revealed， which provided a new perspective for further research and application in related fields.

Key words: spatial transcriptome technology, spatial distribution patterns, developmental lineages, cell type identification, cell-to-cell interactions

CLC Number:

Man MEI, Chencan WANG, Hongxia LIN, Yuqian ZHANG, Wenjing DING, Yuanyuan ZHAO. Application and Prospect of Spatial Transcriptome Technology in Plant Research[J]. Bulletin of Botanical Research, 2025, 45(1): 3-14.

Figures/Tables 4

Table 1

Comparison of technical characteristics of different types of spatial transcriptome

技术类型 Technical type	技术名称 Technical name	技术特点 Technical characteristics	优点 Advantage	缺点 Disadvantage
基于激光捕获显微切割	LCM-seq	进行特定区域切割，结合NGS测序获得单细胞转录组数据	为分离的区域提供空间信息	切割步骤繁琐，低通量
基于激光捕获显微切割	GEO-seq	对组织进行染色、LCM切割，Smart2-seq进行建库及测序	比LCM-seq更灵敏	切割步骤繁琐，低通量
基于荧光原位杂交	FISSEQ	双碱基测序技术SOLiD原位测序	非靶标	低检测效率
	MERFISH	原位荧光杂交和成像分析	高度多元化	视野有限，操作复杂
	osmFISH	一种非条形码技术	复用能力较低	能较好地处理较大组织区域
	BaristaSeq	基于缺口填充挂锁探针进行原位测序	读取长度增加到15个碱基	视野有限
	STARmap	基于DNA串联测序技术，利用DNA的互补配对原则和荧光染料标记的核苷酸探针进行序列测定	能够对完整的组织样本进行3D分析，保留细胞方向性	只能应用于100~150 μm厚的切片和较少的目标数量
基于原位捕获测序	Visium	高通量测序结合原位捕获信息，绘制复杂组织样品的空间基因表达图谱	可从组织切片中获取细胞的转录组信息及位置信息	低分辨率，捕获区域包含多个细胞
	Slide-seq	将组织切片贴在带有DNA条形码的玻璃片上进行高通量测序，获得单细胞转录组数据和组织结构信息	高通量，高分辨率	低灵敏度
	HDST	探针杂交	提高空间分辨率	高成本，捕获效率低
	DbiT-seq	在切片组织中共同绘制mRNA和蛋白质定位	高通量，高分辨率	存在微流体扩散
	Stereo-seq	时空捕获芯片，结合原位RNA捕获	实现500 nm的分辨率，基因与影像同时分析	捕获区域不遵循细胞的复杂轮廓
	Seq-Scope	对mRNA catcher扩增，得到组织不同部位的细胞转录组信息	高分辨率	相对较低的检测灵敏度

Table 1

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Table 2

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