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A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

Nature Genetics volume 41, pages 258–263 (2009)Cite this article

Abstract

The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cell specificity for individual genes and gene classes. Cell type comparisons uncovered previously unrecognized properties, including cell-specific promoter motifs and coexpressed cognate binding factor candidates, interaction partner candidates and hormone response centers. We inferred developmental regulatory hierarchies of gene expression in specific cell types by comparison of several stages within root, shoot and embryo.

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Figure 1: Global patterns of cellular gene expression.
Figure 2: Cell-specific transcripts and selected metabolic pathways.
Figure 3: Cellular distributions of transcripts from selected hormone-related genes.
Figure 4: Identification of candidate cis and trans transcriptional control cognate partners on the basis of cellular coexpression.

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Acknowledgements

We thank N. Li for valuable database advice and assistance and P. Wu (Zhejiang University) for the rice root micrograph in Figure 3. This work was supported by US National Science Foundation Plant Genome Program grant DBI-0325821 to T.N., X.-W.D. and H.Z. T.L. and M.C. were supported in part by Peking-Yale Monsanto Fellowships.

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Author notes

  1. Yuling Jiao, Tie Liu, Nicole K Clay, Teresa Ceserani, Meiqin Chen, Ligeng Ma & Hui-yong Zhang

    Present address: Present addresses: Division of Biology, California Institute of Technology, Pasadena, California 91125, USA (Y.J.); Biology Department, Stanford University, Stanford, California 94305, USA (T.L.); Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA (N.K.C.); Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada (T.C.); Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China (M.C.); National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China (L.M. and H.-Y.Z.).,

  2. Yuling Jiao, S Lori Tausta, Neeru Gandotra, Ning Sun and Tie Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, 06520, Connecticut, USA

    Yuling Jiao, S Lori Tausta, Neeru Gandotra, Tie Liu, Nicole K Clay, Teresa Ceserani, Meiqin Chen, Ligeng Ma, Hui-yong Zhang, Xing-Wang Deng & Timothy Nelson

  2. Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing, 100871, China

    Yuling Jiao, S Lori Tausta, Neeru Gandotra, Tie Liu, Nicole K Clay, Teresa Ceserani, Meiqin Chen, Ligeng Ma, Hui-yong Zhang, Xing-Wang Deng & Timothy Nelson

  3. Center for Statistical Genomics and Proteomics, Yale University, New Haven, 06520, Connecticut, USA

    Ning Sun, Matthew Holford & Hongyu Zhao

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  1. Yuling Jiao
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Contributions

T.N., X.-W.D. and H.Z. conceived and oversaw the research. S.L.T., N.G. and T.L. performed cell isolations, RNA isolations and informatic analysis. Y.J., H.Z. and L.M. performed microarray hybridizations and informatic analysis. T.C., N.K.C. and M.C. performed cell and RNA isolations. N.S. designed and performed statistical methods for data processing and analysis. M.H. designed and implemented the atlas database and analytical tools. T.N. prepared the manuscript, with assistance from all coauthors.

Note: Supplementary information is available on the Nature Genetics website.

Corresponding author

Correspondence to Timothy Nelson.

Supplementary information

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Supplementary Methods, Supplementary Figures 1–6 and Supplementary Tables 1–4 (PDF 2128 kb)

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Jiao, Y., Lori Tausta, S., Gandotra, N. et al. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41, 258–263 (2009). https://doi.org/10.1038/ng.282

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