Gene expression atlas of embryo development in Arabidopsis

Abstract

Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping patterns of gene expression, as well as temporal shifts in gene activity across embryogenesis. Network analysis revealed stage-specific and multi-stage gene expression clusters and biological functions associated with key stages of embryo development. Methylation-related gene expression was associated with early- and middle-stage embryos, initiation of photosynthesis components with the late embryogenesis stage, and storage/energy-related protein activation with late and mature embryos. These results provide a comprehensive understanding of transcriptome programming in Arabidopsis embryogenesis and identify modules of gene expression corresponding to key stages of embryo development. This dataset and analysis are a unique resource to advance functional genetic analysis of embryo development in plants.

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Acknowledgements

This work was funded by the Aquatic and Crop Resource Development Research Division of the National Research Council of Canada (ACRD manuscript #56424). We thank Dr. Wentao Zhang for reviewing the manuscript and providing suggestions for its improvement.

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Correspondence to Raju Datla.

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A contribution to the special issue ‘Cellular Omics Methods in Plant Reproduction Research’.

RNA sequencing raw data can be found in the Gene Expression Omnibus (GEO) under the accession number “GSE123010.”

Communicated by Dolf Weijers.

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Gao, P., Xiang, D., Quilichini, T.D. et al. Gene expression atlas of embryo development in Arabidopsis. Plant Reprod 32, 93–104 (2019). https://doi.org/10.1007/s00497-019-00364-x

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Keywords

  • Embryogenesis
  • Embryo isolation
  • RNA-seq
  • Transcriptome
  • Bioinformatics
  • Arabidopsis