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...

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Published inNature (London) Vol. 617; no. 7962; pp. 785 - 791
Main Authors Guillotin, Bruno, Rahni, Ramin, Passalacqua, Michael, Mohammed, Mohammed Ateequr, Xu, Xiaosa, Raju, Sunil Kenchanmane, Ramírez, Carlos Ortiz, Jackson, David, Groen, Simon C, Gillis, Jesse, Birnbaum, Kenneth D
Format Journal Article
LanguageEnglish
Published England Nature Publishing Group 25.05.2023
Subjects
Base Sequence
Cells
Cluster analysis
Comparative analysis
Corn
Crops
Crops, Agricultural - cytology
Crops, Agricultural - genetics
Divergence
Domestication
Evolution
Evolution, Molecular
Gene expression
Gene Expression Regulation, Plant - genetics
Gene sequencing
Genomes
Grasses
Modules
Plant Roots - cytology
Plant species
Sequence Analysis, RNA
Setaria Plant - cytology
Setaria Plant - genetics
Single-Cell Gene Expression Analysis
Sorghum
Sorghum - cytology
Sorghum - genetics
Transcription factors
Transcriptome - genetics
Transcriptomes
Zea mays - cytology
Zea mays - genetics
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Summary: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, 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.
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B.G. and K.D.B designed the research. B.G. generated all single-cell and single-nucleus RNA-seq data, with early profiles performed by C.O.R. M.A.M. and B.G. designed the single-nucleus RNA-seq protocol. R.R. and B.G. performed the whole mount in-situ hybridization analysis. R.R., X.X., and D.J. performed the tissue preparation and histology for the spatial transcriptomics analysis. S.C.G. and B.G. conceived the analysis strategy and performed the tests for dosage compensation. S.K.R. performed the non-WGD duplication identification. M.P and, J.G. performed the MetaNeighbor, MINI-EX, CoCoCoNet, and validation analysis. B.G. analyzed all the data. K.D.B., B.G., and R.R. wrote the manuscript.
Current Address: UGA-LANGEBIO Cinvestav, Guanajuato, México
Contributions
ISSN:0028-0836
1476-4687
1476-4687
DOI:10.1038/s41586-023-06053-0