LA JOLLA (August 19, 2025)—Nearly everything you know about plants was first discovered in a plant you've likely never heard of. Arabidopsis thaliana, also known as thale cress, is a small, flowering weed that has shaped much of plant biology as we know it. Serving as the representative plant species in most plant research across the last half century, Arabidopsis has taught us how plants respond to light, which hormones control plant behavior, and why some plants grow long, deep roots while others grow them shallow and wide. But despite its beloved reputation among plant biologists worldwide, many elements of the Arabidopsis life cycle have remained a mystery.
Salk Institute researchers have now established the first genetic atlas to span the entire Arabidopsis life cycle. The new atlas—created using detailed single-cell and spatial transcriptomics—captures the gene expression patterns of 400,000 cells within multiple developmental stages as Arabidopsis grows from a single seed to a mature plant. The publicly available resource will be hugely informative to future studies of different plant cell types and developmental stages, and how they respond to stress and environmental stimuli.
The findings, published in Nature Plants on August 19, 2025, will help expand research and development in plant biotechnology, agriculture, and environmental sciences.
"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."
How to map a plant
In its many years as a model plant, Arabidopsis has seen its fair share of experiments. Scientists have been working to decode Arabidopsis' genome for decades, mapping which genes are expressed in each cell type across various plant tissues and organs. Using these incremental maps, scientists can start to figure out which genes control the identity and behavior of different parts of the plant.
One effective way to make these maps is by using single-cell RNA sequencing. This genetic sequencing technique looks at the genome's products—strands of RNA—rather than the original DNA code. This makes it easy for scientists to see which genes are actually used in a cell, and how many. Gene expression maps also help researchers characterize the different types of cells within a species. Since every cell in an organism contains the same genetic code, different cell types can be identified by the unique pattern of genes they express.
While single-cell RNA sequencing has allowed scientists to make detailed maps of cell types, these maps are often restricted to select organs or tissues—for example, looking only at the plant's roots and ignoring the stem, flowers, and leaves. To move from small genetic maps to a sophisticated atlas, the Salk researchers paired single-cell RNA sequencing with another technology: spatial transcriptomics.
Better technology, better maps
With single-cell RNA sequencing, researchers are forced to separate tissues of interest and process their cells in isolation. With spatial transcriptomics, researchers can create genomic maps of plants as they exist in the real world, within the tissue context. The structure, shape, and location of cells and tissues across the entire plant can remain intact throughout the sequencing process. The result is an insightful view into the identity of cells within multiple tissues and organs at once.
"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 spans 10 Arabidopsis developmental stages, from seed in the ground to flowering adulthood. More than 400,000 cells were captured across this life cycle, demonstrating the striking diversity of cell types that can be found in just one organism.
Where the new map leads us
By looking at the full life cycle of Arabidopsis rather than at a single snapshot in time, the researchers have already found a surprisingly dynamic and complex cast of characters responsible for regulating plant development. They also learned about many new genes whose expression and function in unique cell types can now be further explored.
"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 new resource— currently available for free online —will enable deeper exploration of plant cell development, help explain how plants respond to genetic and environmental perturbations, and advance the field of plant biology overall.
Other authors include Jiaying Xu, Bruce Jow, and Joseph Nery of Salk, as well as Tatsuya Nobori, formerly of Salk and presently at The Sainsbury Laboratory in the United Kingdom.
The work was supported by the Human Frontiers Science Program (no. LT000661/2020-L), George E. Hewitt Foundation for Medical Research, Weizmann Institute of Science, National Institutes of Health (NIGMS K99GM154136), and Howard Hughes Medical Institute.
About the Salk Institute for Biological Studies:
Unlocking the secrets of life itself is the driving force behind the Salk Institute. Our team of world-class, award-winning scientists pushes the boundaries of knowledge in areas such as neuroscience, cancer research, aging, immunobiology, plant biology, computational biology, and more. Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Learn more at www.salk.edu .
