Abstract
Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.
Highlights
Single-cell genomic analysis is the tracking and study of single isolated cells using sequencing technologies such as whole genome sequencing (WGS) and RNA sequencing
In addition to suspension based isolation methods, techniques such as laser microdissection (LMD), laser microdissection and pressure catapulting (LMPC), and laser capture microdissection (LCM) [42] are used to extract single cells in situ based on cellular morphology [50,54]
Zong et al [2] estimated that the value of allelic dropout could reach up to 60% for scDNA sequencing, which leads to inaccurate Single nucleotide polymorphisms (SNPs) calling
Summary
Single-cell genomic analysis is the tracking and study of single isolated cells using sequencing technologies such as whole genome sequencing (WGS) and RNA sequencing. Single-cell genomic analysis has successfully described cancer cell states, for example, of stem cells in leukaemia patients [28] and biological developmental processes such as ageing [29]. Technical issues, such as cell isolation difficulties [30], have delayed the use of single-cell analysis in plants. Single-cell studies in plants have the potential to increase the resolution of previous studies in two major areas: (1) developmental dynamics of plant tissues to identify non-anatomical markers for important cell populations; and (2) plant stress signalling, responses, and adaptation. We review the opportunities provided by plant single-cell analysis and discuss the experimental and analytical challenges that need to be addressed to maximise the scientific impact of this approach
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