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

Bruno Guillotin, Ramin Rahni, Michael Passalacqua, Mohammed Ateequr Mohammed, Xiaosa Xu, Sunil Kenchanmane Raju, Carlos Ortiz Ramírez, David Jackson, Simon C. Groen, Jesse Gillis and Kenneth D. Birnbaum ()
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Bruno Guillotin: New York University
Ramin Rahni: New York University
Michael Passalacqua: Cold Spring Harbor Laboratory
Mohammed Ateequr Mohammed: New York University Abu Dhabi
Xiaosa Xu: Cold Spring Harbor Laboratory
Sunil Kenchanmane Raju: New York University
Carlos Ortiz Ramírez: New York University
David Jackson: Cold Spring Harbor Laboratory
Simon C. Groen: University of California
Jesse Gillis: University of Toronto
Kenneth D. Birnbaum: New York University

Nature, 2023, vol. 617, issue 7962, 785-791

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41586-023-06053-0

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