Woody tissue of plants contains many different cell types with different functions. While there is a relatively good understanding of the cell types that are highly differentiated, such as water-conducting xylem and sugar-conducting phloem, the morphologically similar parenchyma cells are poorly characterized despite their importance in plant physiology. Mähönen lab combined single-cell RNA sequencing, lineage tracing and reporter gene analysis to obtain high resolution gene expression and cell type map of Arabidopsis root woody tissue.
Arabidopsis mature roots provide an excellent model for studying secondary growth (i.e. growth in radial dimension). Stem cells within these roots undergo cell divisions, producing diverse cell types in radial dimension, such as conductive cells, barrier cells, and parenchyma cells. Single-cell RNA sequencing, a powerful tool for comprehensively detecting gene expression patterns in individual cells, is crucial for understanding the distinct identities of these cell types. While cell isolation for single-cell analysis is notoriously challenging in mature roots, making this analysis highly desirable yet previously unachievable, Munan Lyu, a doctoral researcher in Mähönen’s group, successfully overcame this obstacle and obtained high-quality single-cell data for all cell types.
“Our single cell analysis revealed several unexpected findings. Notably, we were surprised to identify distinct identities within the parenchyma — a cell type that appears highly uniform in morphology. Our study showed that these parenchyma cells actively support their neighbors to become water- or nutrient-conducting cells," Lyu says.
Furthermore, Hiroyuki Iida, a post-doctoral researcher of the Mähönen lab, demonstrated that parenchyma cells not only facilitate conductive cell formation but also transform themselves into barrier cells to replenish barrier tissues upon wounding. This revealed that parenchyma as a highly dynamic and functional tissue, far from being just a 'fluffy filler'. In many crops, parenchyma also serves as storage organs, accumulating sugars and nutrients.
“Our research provides a foundation for future studies aiming at enhancing storage capabilities in crops. The single-cell data, along with a user-friendly visualization tool, have been deposited on a public online platform. This resource will benefit researchers studying secondary growth in Arabidopsis and in crops such as cassava and poplar," Iida says.
”This paper was a good example of fluent teamwork – in addition to my own team, we collaborated with colleagues in VIB-Gent, Belgium who are experts in analysis of the single cell data,” Mähönen concluded.
Next, the Mähönen lab is using the single cell RNA sequencing technique to generate high resolution gene expression maps of tree stems.
Original article
Lyu, M., Iida, H., Eekhout, T. et al. The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth. Nat. Plants (2025). https://doi.org/10.1038/s41477-025-01938-6