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

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.

Supplementary information: The online version of this article (10.1007/s12298-020-00922-y) contains supplementary material, which is available to authorized users.

Keywords: Endophytic fungus; Lipid and ion transport; Low temperature; Metabolic pathways; Phytohormone signaling; Piriformospora indica; Transcriptome analysis.

Fig. 1

Freezing phenotypes (a, b showed recovery for 1 and 7 days, respectively), water-soaked area rate, ion leakage and survival rates (c, d and e) of Col Arabidopsis seedlings co-cultivated (or not) with P. indica for 2 weeks. Chlamydospores inside the root cells, bars = 100 μm (f). Data are means of three independent experiments ± SD. Asterisks indicate significant differences compared with the non-inoculated plants (*p < 0.05, ** p < 0.01, t-test). Grey (black) bars: P. indica- (un-) colonized plants

Fig. 2

Statistics of differentially expressed genes (a) and Venn diagram of differentially expressed genes (b) (p < 0.01, FC = 1.5)

Fig. 3

GO classification results of differentially expressed genes

Fig. 4

COG diagram of differentially expressed genes

Fig. 5

KEGG classification of differentially expressed genes

Fig. 6

Cluster diagram of differentially expressed genes. a Signal transduction mechanisms. b Transcription factors. c Lipid transport and metabolism. d Inorganic ion transport and metabolism

Fig. 7

Validation of the RNA-Seq results by qRT-PCR of 28 selected genes under freezing stress. Data are means of three independent experiments ± SD