Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Single-Cell Genomics of Poplar Wood Development


Wendell Pereira1*(, Wilfred Vermerris1, Christopher Dervinis1, Kelly Balmant1, Sushmita Roy2, and Matias Kirst1


1University of Florida; and 2University of Wisconsin


(1) Uncover the cellular developmental program of woody biomass in the perennial bioenergy crop poplar by dissecting the cell lineages that originate in the vascular cambium. (2) Modify the regulatory programs that lead to the formation of the various cell types in poplar wood to achieve less recalcitrant biomass for bioenergy production.


The vascular cambium is responsible for the production of the secondary xylem, which comprises the most abundant form of biomass on Earth, wood. Despite its massive global importance, the genetic networks underlying the production of secondary xylem remain partially ambiguous. Differentiation of stem cells in the plant apex gives rise to aerial tissues and organs. These cells later differentiate to form the vascular cambium, from which secondary xylem is generated. Here the team used single-nuclei RNA sequencing (snRNA-seq) to determine cell-type specific transcriptomes of the Populus trichocarpa vegetative shoot apex and lignified stem to create a cell-type specific atlas of their tissues and uncover the regulators of cell lineage trajectories.

From P. trichocarpa shoot apex, researchers identified highly heterogeneous cell populations that clustered into seven broad groups represented by 18 transcriptionally distinct types (Fig. 1). Next, researchers established the developmental trajectories of the epidermis, leaf mesophyll, and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell populations in the vegetative apex, researchers applied a pipeline for interspecific single-cell gene expression data integration. Researchers contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of vascular development between a model annual herbaceous and a woody perennial plant species. In addition to providing a cell atlas of the shoot apical meristem and its derived lineages, the results offer a valuable resource for investigating the principles underlying cell division and differentiation between herbaceous and perennial species.

In parallel to the Populus shoot apex analysis, researchers performed an snRNA-seq of 11,673 nuclei derived from lignified stem to profile the transcriptome and create a single-cell atlas. Cell-type specific marker genes were utilized to identify 20 transcriptionally distinct cell clusters representing nearly all cell types within the sampled tissue. Reporter gene assays were carried out to confirm the cluster identity of vessel elements, fibers, ray parenchyma, cambial cells, and sub-cell type vessel-associated cells. Finally, the developmental trajectory of cambial cells and their xylem-specific derivates was carried out to identify lineages containing putative regulators related to vascular development and xylogenesis. This trajectory analysis identified putative regulators of the cell lineages that result in the formation of fibers and vessels. The functions of these regulators are being evaluated in knockout experiments, in which researchers will assess if cell lineages can be redirected toward developing specific cell types.


Funding Information

This research is supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0023082.