Agronomy and Horticulture, Department of


Document Type


Date of this Version



Amini S, Doyle JJ and Libault M (2023) The evolving definition of plant cell type. Front. Plant Sci. 14:1271070. doi: 10.3389/fpls.2023.1271070


Open access.


In 1665 Robert Hooke, looking at cork through his microscope, discovered that plants are composed of elementary structures he named “cells”. Variation in the expression of a single genome in a complex eukaryotic organism guides the initiation, maturation, physiology, and biochemistry of cells with different shapes and sizes, playing different structural and functional roles in space and time. How many kinds of cells—”cell types”— an organism possesses of course depends on the organism’s cellular complexity, but the plasticity within a cell type fuels the emergence of the concept of cell state (Figure 1). The transition between cell states is driven by the developmental processes of multicellular organisms (e.g., cell determination and differentiation) and their response to environmental stresses (Wang et al., 2018). In the last decade, single cell/nucleus (sc/sn) omics, especially scRNA-seq, and spatial transcriptomics have enabled high-resolution mapping of molecular profiles of each cell, as well as mirroring cell trajectories through different states. Furthermore, unsupervised clustering of cells based on their transcriptomic (and/or epigenomic) signatures has proven effective in discovering previously unidentified cell types and cell states and providing new insight into cellular heterogeneity within a cell type (Schaum et al., 2018; Liu et al., 2021; Schumacher et al., 2021; Elmentaite et al., 2022). Classifying cells is necessary to conceptualize the biological complexity of some organs like the human brain or the plant root. But how should this be done? What criteria should be used, or, if several criteria are used, how should they be prioritized?