Single-nucleus full-length RNA profiling in plants incorporates isoform information to facilitate cell type identification

Abstract

The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced. To capture the isoform information, we combined 10x Genomics and Nanopore long-read sequencing to develop a protoplasting-free full-length single-nucleus RNA profiling method in plants. Our results demonstrated using Arabidopsis root that nuclear mRNAs faithfully retain cell identity information, and single-molecule full-length RNA sequencing could further improve cell type identification by revealing splicing status and alternative polyadenylation at single-cell level.

Spatial and Temporal Regulation of Parent-of-Origin Allelic Expression in the Endosperm

“…Nuclear RNA was isolated and cDNA libraries were sequenced yielding 150 bp paired-end reads (SData 1). Although nuclear RNA contains higher levels of pre-RNA and unspliced transcripts (Long et al, 2021), a high correlation between nuclear and total cellular mRNA has previously been demonstrated in plants, also including triploid endosperm tissue (Jacob et al, 2007;Deal and Henikoff, 2010;Del Toro-De León and Köhler, 2019;Picard et al, 2021). An average of 25 million reads per replicate mapped to Col-0 and Tsu-1 reference transcriptomes polished by Pilon (Walker et al, 2014) (SData 1).…”