Almost everything we know about plants traces back to one humble species most people have never heard of: Arabidopsis thaliana, or thale cress. This small flowering weed has been the cornerstone of plant biology for the past 50 years, helping scientists understand how plants respond to light, which hormones regulate growth, and why some plants develop deep roots while others spread them shallow and wide. Yet despite its central role in research, many aspects of Arabidopsis’ life cycle have remained poorly understood.
Now, researchers at the Salk Institute have created the first comprehensive genetic atlas covering the entire Arabidopsis life cycle. Using advanced single-cell and spatial transcriptomics, the atlas maps gene expression in 400,000 cells across multiple developmental stages, from a single seed to a fully grown plant. This publicly available resource will be invaluable for studying plant cell types, developmental processes, and responses to stress and environmental changes.
Published in Nature Plants on AuG. 19, 2025, the findings are expected to accelerate progress in plant biotechnology, agriculture, and environmental science, according to a press release.
“We’ve come very far in our understanding of plant biology, but until recently, there has been a technological bottleneck preventing us from comprehensively cataloguing cell types and the genes they express uniformly, across developmental stages,” says senior author Joseph Ecker, professor, Salk International Council Chair in Genetics, and Howard Hughes Medical Institute investigator. “Our study changes that. We created a foundational gene expression dataset of most cell types, tissues, and organs, across the spectrum of the Arabidopsis life cycle.”
From left: Tatsuya Nobori, Natanella Illouz Eliaz, and Travis Lee. Photo: Salk Institute
How to Map a Plant
Over decades of research, Arabidopsis thaliana has been the subject of countless experiments. Scientists have worked to decode its genome, mapping which genes are active in each cell type across different tissues and organs. These incremental maps help researchers understand which genes govern the identity and function of various parts of the plant.
One powerful tool for creating these maps is single-cell RNA sequencing. Unlike DNA sequencing, which reads the genome itself, this technique examines the RNA transcripts a cell produces. This allows scientists to see which genes are actually being used, and in what quantity. By analyzing these gene expression patterns, researchers can distinguish between different cell types, even though every cell contains the same underlying genetic code.
While single-cell RNA sequencing has produced detailed maps, they are often limited to specific organs or tissues — such as roots, leaving stems, leaves, and flowers uncharted. To build a more complete atlas, Salk researchers combined single-cell RNA sequencing with spatial transcriptomics.
Better Technology, Better Maps
Single-cell RNA sequencing requires tissues to be separated and processed in isolation. In contrast, spatial transcriptomics allows researchers to map gene activity while preserving the plant’s natural tissue structure. This method keeps the cells in place, maintaining their location and context within stems, leaves, flowers, and roots. The result is a comprehensive view of cell identity across multiple tissues and organs, providing unprecedented insight into plant development.
“What excites me most about this work is that we can now see things we simply couldn’t see before,” says co-first author Natanella Illouz-Eliaz, a postdoctoral researcher in Ecker’s lab. “Imagine being able to watch where up to a thousand genes are active all at once, in the real tissue and cell context of the plant. It’s not only fascinating on its own, but it’s already led us to discoveries, like finding genes involved in seedpod development that no one knew about before. There’s so much more waiting to be uncovered in this data, and that sense of possibility is what I am truly enthusiastic about.”
The single-cell and spatial transcriptomic atlas covers 10 developmental stages of Arabidopsis, from a seed in the soil to a flowering adult. Over 400,000 cells were analyzed, revealing the remarkable diversity of cell types that exist within a single plant.
Where the New Map Leads
By examining the entire life cycle rather than a single moment in time, researchers have uncovered a dynamic and complex network of cells driving plant development. The study also identified numerous new genes whose activity and roles in specific cell types can now be investigated in greater detail, opening fresh avenues for understanding plant biology.
“This study will be a powerful tool for hypothesis generation across the entire plant biology field,” says co-first author Travis Lee, a postdoctoral researcher in Ecker’s lab. “Our easy-to-use web application makes this life cycle atlas easily accessible to the plant science community through simply navigating to our website, and we can’t wait to learn from the many single-cell genomic studies it will now enable.”
The researchers hope this freely available online resource will enable deeper insights into plant cell development, shed light on how plants respond to genetic and environmental changes, and drive further advances in plant biology.
Other contributors include Jiaying Xu, Bruce Jow, and Joseph Nery of Salk, as well as Tatsuya Nobori, formerly at Salk and now at The Sainsbury Laboratory in the UK.
The work was supported by the Human Frontiers Science Program (LT000661/2020-L), George E. Hewitt Foundation for Medical Research, Weizmann Institute of Science, National Institutes of Health (NIGMS K99GM154136), and the Howard Hughes Medical Institute.