A pan-grass transcriptome reveals patterns of cellular divergence in crops

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits. Key traits that distinguish these species are mediated by specialized cell types. Here, we compare the transcriptomes of root cells in three grass species—Zea mays (maize), Sorghum bicolor (sorghum), and Setaria viridis (Setaria). We first show that single-cell and single-nucleus RNA-seq provide complementary readouts of cell identity in both dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than others—driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole genome duplication provides a rich source of new, highly localized gene expression domains that favor fast- evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and shed light on the evolution of cells that mediate key functions in crops. Overall design: Single cell and single nuclei integration of Arabidospsis thaliana, Zea mays, Sorghum bicolor and Setaria viridis root meristems. Arabidopsis 6 cell replicates and 3 nuclei replicates. Maize 4 nuclei replicates and 3 cell replicates from (Ortiz Ramirez et al., 2021, ?10.1126/science.abj2327). Sorghum 1 cell replicate and 3 nuclei replicates. Setaria 3 cell replicates and 2 nuclei replicates