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

Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD

Published: 11 May 2023 in Nature
Keywords: No keywords in Pubmed
Pubmed ID: 37165193
DOI: 10.1038/s41586-023-06053-0

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. 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.

Human Frontiers of Science LT000972/2018-L
National Institutes of Health R01 LM012736
National Institutes of Health R01 MH113005
National Institutes of Health R35GM136362 (primary)
National Science Foundation IOS-1934388 (primary)