Single-nucleus RNA sequencing of plant tissues using a nanowell-based system

Area of Science:

• Plant biology
• Genomics
• Molecular biology

Background:

• Single-cell genomics offers powerful insights into plant development and responses.
• Current protoplast isolation methods for plant single-cell genomics can be challenging for certain tissues.

Purpose of the Study:

• To introduce a generic, efficient procedure for plant nucleus isolation for single-cell transcriptome analysis.
• To provide an alternative to protoplast isolation for plant single-cell genomics.

Main Methods:

• A generic procedure for plant nucleus isolation was developed.
• Nanowell-based library preparation was combined with nucleus isolation.
• Single-nucleus RNA sequencing was performed on isolated nuclei.

Main Results:

• The method enables transcriptome analysis of thousands of individual plant nuclei.
• Applicability was demonstrated across different plant species and tissues.
• Transcriptome dynamics during early anther development in Arabidopsis thaliana were characterized, identifying stage-specific transcription factors and predicting target genes.

Conclusions:

• The developed nucleus isolation procedure is applicable to diverse plant species and tissues.
• This method expands the toolkit for plant single-cell genomics, facilitating research on plant development and environmental responses.