Abstract
Key message
A comparative transcriptomic and genomic analysis between Arabidopsis thaliana and Glycine max root hair genes reveals the evolution of the expression of plant genes after speciation and whole genome duplication.
Abstract
Our understanding of the conservation and divergence of the expression patterns of genes between plant species is limited by the quality of the genomic and transcriptomic resources available. Specifically, the transcriptomes generated from plant organs are the reflection of the contribution of the different cell types composing the samples weighted by their relative abundances in the sample. These contributions can vary between plant species leading to the generation of datasets which are difficult to compare. To gain a deeper understanding of the evolution of gene transcription in and between plant species, we performed a comparative transcriptomic and genomic analysis at the level of one single plant cell type, the root hair cell, and between two model plants: Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max). These two species, which diverged 90 million years ago, were selected as models based on the large amount of genomic and root hair transcriptomic information currently available. Our analysis revealed in detail the transcriptional divergence and conservation between soybean paralogs (i.e., the soybean genome is the product of two successive whole genome duplications) and between Arabidopsis and soybean orthologs in this single plant cell type. Taking advantage of this evolutionary study, we combined bioinformatics, molecular, cellular and microscopic tools to characterize plant promoter sequences and the discovery of two root hair regulatory elements (RHE1 and RHE2) consistently and specifically active in plant root hair cells.
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Acknowledgements
This work was funded by the U.S. National Science Foundation (#IOS-1339194 and 1453613), the Oklahoma Center for the Advancement of Science and Technology (OCAST) Plant Science Research Program (PS14-025) and by the Office of the Vice President for Research at the University of Oklahoma. We thank Michelle Wood and Spencer Huynh for technical support. We also thank Daniel Jones for critical reading of the manuscript.
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ML designed research. ZQ and ML performed cloning. LP and AF performed the bioinformatics analysis. ZQ, PZ, ML and NR transformed and observed promoter activity in planta. ZQ, LP and ML wrote the article.
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Qiao, Z., Pingault, L., Zogli, P. et al. A comparative genomic and transcriptomic analysis at the level of isolated root hair cells reveals new conserved root hair regulatory elements. Plant Mol Biol 94, 641–655 (2017). https://doi.org/10.1007/s11103-017-0630-8
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DOI: https://doi.org/10.1007/s11103-017-0630-8