Single-cell RNA-sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent

New Phytol. 2022 Apr;234(2):527-544. doi: 10.1111/nph.17992. Epub 2022 Feb 15.


High-throughput single-cell RNA sequencing (scRNA-Seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of the density of gene expression profiles, we can observe the metabolic features of each cell population. Here, we employ the scRNA-Seq technique to reveal the entire biosynthetic pathway of a flower volatile. The corolla of the wild tobacco Nicotiana attenuata emits a bouquet of scents that are composed mainly of benzylacetone (BA). Protoplasts from the N. attenuata corolla limbs and throat cups were isolated at three different time points, and the transcript levels of > 16 000 genes were analyzed in 3756 single cells. We performed unsupervised clustering analysis to determine which cell clusters were involved in BA biosynthesis. The biosynthetic pathway of BA was uncovered by analyzing gene co-expression in scRNA-Seq datasets and by silencing candidate genes in the corolla. In conclusion, the high-resolution spatiotemporal atlas of gene expression provided by scRNA-Seq reveals the molecular features underlying cell-type-specific metabolism in a plant.

Keywords: Nicotiana attenuata; 10x genomics; benzylacetone; corolla; floral scents; scRNA-Seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosynthetic Pathways / genetics
  • Flowers / genetics
  • Flowers / metabolism
  • Gene Expression Profiling
  • Odorants*
  • RNA / metabolism
  • Sequence Analysis, RNA
  • Tobacco* / genetics
  • Tobacco* / metabolism


  • RNA