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(1). Key traits that distinguish these species are mediated by specialized cell types(2). Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in 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 those of 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 favour 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 provide insight on the evolution of cells that mediate key functions in crops.

Automated summary

Comparative analysis of root cell transcriptomes in three grass species reveals that some cell types diverged more rapidly, driven by recruitment of gene modules from other cell types. The recent whole-genome duplication provides new, highly localized gene expression domains that favour fast-evolving cell types. Cell-by-cell comparative analysis can extract conserved modules and provide insight on the evolution of cells mediating key functions in crops.