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Transcriptome analysis of Arabidopsis reveals freezing-tolerance related genes induced by root endophytic fungus Piriformospora indica

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Abstract

Freezing stress is a serious environmental factor that obstructs plant development. The root endophytic fungus Piriformospora indica has proved to be effective to confer abiotic stress tolerance to host plants. To investigate how P. indica improves freezing tolerance, we compared the expression profiles of P. indica-colonized and uncolonized Arabidopsis seedlings either exposed to freezing stress or not. Nearly 24 million (93.5%) reads were aligned on the Arabidopsis genome. 634 genes were differentially expressed between colonized and uncolonized Arabidopsis exposed to freezing stress. Interestingly, 193 Arabidopsis genes did not respond to freezing stress but were up-regulated by P. indica under freezing stress. Freezing stress-responsive genes encoded various members of the WRKY, ERF, bHLH, HSF, MYB and NAC transcription factor families. The qRT-PCR analyses confirmed the high-throughput sequencing results for 28 genes. Functional enrichment analysis indicated that the fungus mainly controls genes for freezing-stress related proteins involved in lipid and ion transport, metabolism pathways and phytohormone signaling. Our findings identified novel target genes of P. indica in freezing-stress exposed plants and highlight the benefits of the endophyte for plants exposed to a less investigated environmental threat.

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Acknowledgements

We acknowledge Rong Zeng, Guang Chen, Banda Milca Medison, and Hongyu Xia for their discussion on the original draft, and two anonymous reviewers for their critical reading and invaluable comments and suggestions on the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (No. 31870378).

Author information

Author notes

  1. Wei Jiang and Rui Pan have contribute equally to this work.

Authors and Affiliations

  1. Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, China

    Wei Jiang, Rui Pan, Sebastian Buitrago & Wenying Zhang

  2. College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China

    Chu Wu

  3. Faculty of Agriculture, Cairo University, Giza, 12613, Egypt

    Mohamad E. Abdelaziz

  4. Matthias-Schleiden-Institute, Plant Physiology, Friedrich-Schiller-University Jena, 07737, Jena, Germany

    Ralf Oelmüller

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  1. Wei Jiang
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  2. Rui Pan
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  4. Chu Wu
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  5. Mohamad E. Abdelaziz
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Correspondence to Wenying Zhang.

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Table S1

List of primer sequences used in this study, Table S2 Sequencing data statistics, Table S3 Alignment results of each sample.

Supplementary material 1 (DOCX 17 kb)

Table S4

DEGs involved in signal transduction.

Supplementary material 1 (XLXS 61 kb)

Table S5

Information of the 154 predicted TFs.

Supplementary material 1 (XLXS 95 kb)

Table S6

DEGs involved in lipid transport and metabolism.

Supplementary material 1 (XLXS 34 kb)

Table S7

Information of the 35 predicted inorganic ion transport and metabolism.

Supplementary material 1 (XLXS 33 kb)

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Jiang, W., Pan, R., Buitrago, S. et al. Transcriptome analysis of Arabidopsis reveals freezing-tolerance related genes induced by root endophytic fungus Piriformospora indica. Physiol Mol Biol Plants 27, 189–201 (2021). https://doi.org/10.1007/s12298-020-00922-y

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