RNAseq analysis of the transcriptome of an Arabidopsis mutant, ahl13, elicitated by pstDC3000 or flg22

Purpose: The experiment is to compare the NGS-derived seedling and leaf transcriptome profiling (RNAseq) of an Arabidopsis mutant ahl13 with that of wild type upon bacterial pathogen (pst DC3000) and flagellin elicitation. Method： The mRNA profiles of 10-day-old wild-type (WT) and AHL13 knockout (ahl13, SALK_014014) Arabidopsis were generated by RNAseq using Illumina NovaSeq6000. The sequence reads were passed through quality filters and mapped to Arabidopsis genome by TopHat2 followed by transcript splicing and quantitation by Cufflinks. DESeq was done to analyze differential gene expressions. qRT–PCR validation was performed using SYBR Green assays Result: We mapped about 20 million sequencing reads per sample to the Arabidopsis genome and identified approximately 28,000 transcripts in the Arabidopsis Col-0 and ahl13 mutant using TopHat2. Differentially expressed genes were identified using DESeq2 and about 166 genes show up-regulation in ahl13 upon DC3000 infection (FC>2, FDR<0.01) Conclusions: The ahl13 mutant exhibit differential transcription profile from that of Col-0 upon DC3000 treatment but similar upon flg22 treatment. The mRNA profiles of wild type (WT, Col-0) and ahl13-/- Arabidopsis elicitated by a bacterial pathogen (DC3000) or flg22