PT  - JOURNAL ARTICLE
AU  - Daniel Conde
AU  - Paolo M. Triozzi
AU  - Wendell J. Pereira
AU  - Henry W. Schmidt
AU  - Kelly M. Balmant
AU  - Sara A. Knaack
AU  - Sushmita Roy
AU  - Christopher Dervinis
AU  - Matias Kirst
TI  - Single-cell analysis resolves the genetic program of primary vascular system formation in hybrid poplar
AID  - 10.1101/2021.12.28.474348
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.12.28.474348
4099  - http://biorxiv.org/content/early/2021/12/28/2021.12.28.474348.short
4100  - http://biorxiv.org/content/early/2021/12/28/2021.12.28.474348.full
AB  - Despite the enormous potential of novel approaches to explore gene expression at a single-cell level, we lack a high-resolution and cell type-specific gene expression map of the shoot apex in woody perennials. We use single-nuclei RNA sequencing to determine the cell type-specific transcriptome of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of epidermal cells, leaf mesophyll, and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we created and applied a pipeline for interspecific single-cell expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of primary vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the basic principles underlying cell division and differentiation conserved between herbaceous and perennial species, which also allows the evaluation of the divergencies at single-cell resolution.One Sentence Summary Single-cell RNA-seq of the vegetative shoot apex resolved the genetic program of primary vascular development in hybrid poplar.Competing Interest StatementThe authors have declared no competing interest.