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- Title
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data.
- Authors
Neumann, Manuel; Xu, Xiaocai; Smaczniak, Cezary; Schumacher, Julia; Yan, Wenhao; Blüthgen, Nils; Greb, Thomas; Jönsson, Henrik; Traas, Jan; Kaufmann, Kerstin; Muino, Jose M.
- Abstract
Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com. Single-cell transcriptomics allows gene expression heterogeneity to be assessed at cellular resolution but the original location of each cell is unknown. Here the authors combine single nuclei RNA-seq with 3D spatial reconstruction of floral meristems to link gene activities with morphology.
- Subjects
GENE expression; RNA sequencing; MERISTEMS; CELL growth; CELL physiology
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-30177-y