Single-Cell Transcriptomics in Plant Systems

Single-cell transcriptomics in plant systems has emerged as a transformative approach to dissect cellular heterogeneity, developmental dynamics and environmental responses with unprecedented resolution. By isolating individual cells or nuclei and profiling their RNA content, researchers can reconstruct cell lineage trajectories, identify rare or transient cell states and infer the regulatory networks that orchestrate organogenesis and tissue function. Advances in microfluidics, protoplast or nucleus isolation and strand-specific library preparation have overcome plant-specific challenges such as rigid cell walls and high endogenous RNase activity. Integration of transcriptome data with chromatin accessibility maps further refines our understanding of how transcription factors and epigenetic landscapes guide cell identity. Applications span model species such as Arabidopsis, staple crops like rice and woody perennials such as poplar, revealing both conserved programmes and lineage-specific innovations. This high-resolution atlas framework holds promise for enhancing crop resilience, informing synthetic circuit design and refining genome-editing strategies by linking genotype to cell-type function.

Research from Nature Portfolio

Engineered serine integrases have been deployed in root tissues to create irreversible lineage-tracing circuits, enabling permanent fluorescent marking of cell descendants following promoter-driven activation. By tuning integrase expression thresholds with degradation tags and split-intein systems, this toolkit decodes the temporal order of gene expression during lateral root initiation and offers a modular platform for recording signalling events in diverse developmental contexts.

A combined single-cell RNA sequencing and chromatin accessibility survey of rice radicles reconstructed continuous developmental trajectories of epidermal and ground tissue lineages. Temporal profiling revealed conserved transcriptional modules between monocots and dicots, while spatiotemporal modelling pinpointed a meristem mutant, illustrating the power of integrated omics for functional gene discovery in crop root systems.

Single-cell ATAC sequencing of Arabidopsis root cells uncovered thousands of cell-type-specific accessible chromatin regions, sufficient to resolve all major root cell identities. Integration with transcriptome profiles characterised developmental progression, endoreduplication and cell division, and linked transcription factor motif enrichments to dynamic accessibility changes, providing a blueprint for inferring plant gene regulatory networks.

Single-Cell Transcriptomics in Plant Systems publication trend

The graph below shows the total number of articles in single-cell transcriptomics in plant systems across all publications each year (not limited to Nature Index journals).

Technical terms

Single-cell RNA sequencing (scRNA-seq): A method to measure the transcriptome of individual cells, revealing cell-type composition and transcriptional heterogeneity within complex tissues.

Single-cell ATAC sequencing (scATAC-seq): A technique for profiling chromatin accessibility at single-cell resolution, identifying regulatory elements that govern gene expression in specific cell types.

Pseudotime analysis: A computational approach that orders single-cell expression profiles along a continuous timeline to infer developmental or differentiation trajectories.

Orthogonal serine integrases: Engineered recombinase enzymes that mediate unidirectional DNA recombination events, used as molecular recorders for cell lineage tracing.

Gene regulatory network: A system of interactions between transcription factors, chromatin regulators and target genes that controls dynamic changes in gene expression.

References

1. An integrase toolbox to record gene-expression during plant development. Nature Communications (2023).
2. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root. Nature Communications (2021).
3. The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nature Communications (2021).
4. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. The Plant Cell (2019).
5. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental Cell (2022).
6. Transcriptional landscape of highly lignified poplar stems at single-cell resolution. Genome Biology (2021).