We have analyzed the maize leaf transcriptome using Illumina sequencing. We mapped more than 120 million reads to define gene structure and alternative splicing events and to quantify transcript abundance along a leaf developmental gradient and in mature bundle sheath and mesophyll cells. We detected differential mRNA processing events for most maize genes. We found that 64% and 21% of genes were differentially expressed along the developmental gradient and between bundle sheath and mesophyll cells, respectively. We implemented Gbrowse, an electronic fluorescent pictograph browser, and created a two-cell biochemical pathway viewer to visualize datasets. Cluster analysis of the data revealed a dynamic transcriptome, with transcripts for primary cell wall and basic cellular metabolism at the leaf base transitioning to transcripts for secondary cell wall biosynthesis and C4 photosynthetic development toward the tip. This dataset will serve as the foundation for a systems biology approach to the understanding of photosynthetic development.
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This work was supported by grants from the National Science Foundation (IOS-0701736 to R.T., P.L., Q.S., T.N. and T.P.B.). C.R.M. acknowledges support from a grant to the International Rice Research Institute from the Bill and Melinda Gates Foundation and T.P.B. acknowledges support from the iPlant Collaborative for development of the eFP browser.
The authors declare no competing financial interests.
Supplementary Table 1, Supplementary Figures 1–13 and Supplementary Note (PDF 8744 kb)
Verification of RNA-seq results by qRT-PCR. (XLS 35 kb)
List of the K-means clusters. (XLS 4141 kb)
List of genes exhibiting differential expression between bundle sheath and mesophyll cells. (XLS 1078 kb)
Correlation between RNA-seq and proteomics data in the bundle sheath and mesophyll cells. (XLS 268 kb)
List of C4 genes and their expression changes along developmental zones. (XLS 41 kb)
List of differentially expressed transcription factors in the developmental zones and bundle sheath and mesophyll cells. (XLS 725 kb)
List of gene ID?s and RPKM estimates for Supplementary Figs. 8-12. (XLS 52 kb)
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Li, P., Ponnala, L., Gandotra, N. et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet 42, 1060–1067 (2010). https://doi.org/10.1038/ng.703
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