HMN 2026: How Arabidopsis meristem map uncovers 18 cell clusters shaping stems and flowers

Researchers have produced the most detailed map yet of how stem cells in the growing tip of a plant begin their journey to form the many cell types that shape flowers and stems. They identified 18 distinct cell type clusters in the inflorescence meristem (the stem cell niche at the tip of the flowering shoot) that generates a plant’s above-ground organs, such as stems and flowers.

The cell groups identified include precursors to the plant cortex (a tissue layer that helps support the plant and store nutrients) and vascular cell tissues, including phloem, xylem and cambium. This indicates that tissue patterning starts much earlier in the meristem than previously thought, with distinct groups of cells diverging during primordia formation.

Published in Science Advances, the research, led through a collaboration among the research groups of Henrik Jönsson, Elliot Meyerowitz and James Locke at the Sainsbury Laboratory Cambridge University (SLCU), provides new insights into how the inflorescence meristem generates the remarkable diversity of cell types that make up a plant’s above-ground organs.

Unlike animals, plants continue producing new organs throughout their lives. This lifelong growth depends on populations of stem cells being maintained within specialized tissues called meristems.

The inflorescence meristem continuously produces cells that will develop into flowers, stems and the vascular tissues that transport water and nutrients around the plant.

Although scientists already know the meristem contains distinct functional regions, it is not clear how stem cells make the transition from an undifferentiated state to specialized cell types.

This is particularly fascinating because cells sitting right next to each other may end up with totally different fates—one cell becomes the water-conducting xylem while its neighbor becomes a petal.

How do cells determine their fates?

Using a relatively new technique called single-nucleus RNA-sequencing (snRNA-seq), the researchers traced these developmental pathways in unprecedented detail in the model plant Arabidopsis thaliana.

The study measured the expression of 19,491 genes in 10,025 individual nuclei extracted from finely dissected meristematic tissue.

By analyzing the activity of genes (gene expression) in thousands of individual nuclei isolated from inflorescence meristems, lead author Dr. Sebastián Moreno-Ramírez linked stem cells to their earliest differentiation states.

Single-nucleus RNA sequencing (snRNA-seq)

Single-nucleus RNA sequencing (snRNA-seq) is emerging as a powerful tool for studying plant development because nuclei can be isolated from frozen tissues.

This is particularly valuable for small and hard-to-isolate tissues, such as the inflorescence meristem, because carefully dissected samples can be frozen and pooled over time. This allows researchers to enrich the data set for cells from a specific tissue of interest.

Instead of analyzing the whole cell like traditional single-cell RNA sequencing, snRNA-seq isolates and sequences genetic material from only the cell’s nucleus. The nuclei are released from tissue while preserving nuclear RNA, then isolated and sequenced.

This approach also reduces the risk that gene expression is affected during sample preparation.

Using marker genes that they know are already more active in specific locations, the researchers were able to infer where different cell states arise in the meristem.

“We wanted to understand how a relatively small population of stem cells can continually generate the many different cell types needed to build a plant,” said Dr. Moreno-Ramírez.

“By looking at gene expression of nuclei, we were able to infer developmental trajectories through big data analysis tools and advanced trajectory software to reconstruct developmental pathways.”

These trajectories revealed gene expression programs associated with the formation of early floral organs and vascular cell types, including cambium, xylem and phloem.

The analysis also captured dynamic changes associated with progression through the cell cycle.

“Our data allowed us to follow the earliest steps of differentiation as stem cells commit to different developmental fates,” Moreno-Ramírez said.

“Understanding these transitions is essential if we want to uncover the regulatory networks that control plant architecture and organ formation.”

By analyzing genes expressed in specific domains, the researchers identified roles for members of the GH3 gene family, which participate in auxin metabolism. They linked these genes to meristem activity and the position of new organs, known as phyllotaxis.

Using GH3 mutant plants, the researchers observed altered growth patterns, confirming predictions generated from the snRNA-seq data set.

These data provide a valuable resource for future studies investigating how stem cells generate the diverse tissues that shape plant form.

“This gives us a framework for identifying the genetic networks that drive cell fate decisions in the meristem,” Moreno-Ramírez said. “The next challenge is to understand how these regulatory programs interact to control growth and to ensure that plants continuously produce organs and their cell types in the right place at the right time.”

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