Gene

Biology

Operating system

Computer science

Computational biology

Genetics

Transcriptome

Arabidopsis

Genome

RNA splicing

Mutant

Alternative splicing

Endosperm

RNA-Seq

Genomics

Polyadenylation

Cell

Single-cell analysis

Gene expression

Gene isoform

Profiling (computer programming)

Genome biology

The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq, for large-scale full-length RNA profiling at a single-nucleus level in plants using isolated nuclei. Combined with 10x Genomics and Nanopore long-read sequencing, we validate the robustness of this approach in Arabidopsis root cells and the developing endosperm. Sequencing results demonstrate that it allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, which facilitates characterizing cell identities.

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants