Genome-wide expression analysis of immune responses in wild type and gtl1df1 mutant plants
Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and gtl1df1 mutant plants in response to different strains of Pseudomonas syringae pv tomato (Pst) bacterium.Methods: Four-week-old Arabidopsis plant leaves were syringe infiltrated with mock (sterile water) or different Pst DC3000 strains at OD600=0.04, and then collected at indicated time points (D28E for 2 h, DC3000 and DC3000(avrRpt2) for 4 h) for RNA extraction and deep sequencing by Illumina. Raw data were cleaned up and trimmed and reads were mapped to Arabidopsis genome. Gene expression levels were calculated using the TPM method (Transcripts per Kb of exon model per Million mapped reads).Results and Conclusions: This study showed that thousands of genes were differentially expressed between WT and gtl1df1 plants, with the largest number of DEGs observed after Pst DC3000(avrRpt2) inoculation. We found that in the gtl1df1 mutant, the expression of many immune response genes was significantly downregulated compared to that in the wild-type, suggesting an impaired immune response in the mutant.