Elucidating post-translational interference of phytopathogen Pseudomonas sp effector HopA1 on defense-associated transcripts

The goals of this study are to compare NGS-derived Arabidopsis transcriptome profiling (RNA-seq) in susceptible background (eds1-2) to elucidate post-translational interference of phytopathogen Pseudomonas sp effector HopA1 on defense-associated transcripts.Arabidopsis mRNA profiles of 3 week old DEX: HopA1pss-myceds1-2 transgenic line post 12 hr with(plus) and without(minus) Dexamethasone treatment were generated by deep sequencing, in duplicate, using Illumina Hiseq4000.The raw reads were filtered using Trimmomatic for Quality scores and adapters. Filtered reads were aligned to Arabidopsis thaliana genome using splice aware aligner like HISAT2 to quantify reads mapped to each transcript. Alignment percentage of reads were in the range of 96 percentage.Total number of unique mapped reads were counted using feature counts. The uniquely mapped reads were subjected to differential gene expression using DESEQ2.Alternate splicing analysis was performed using rMATS using paired replicates T1, T2 (plus) and T1, T2 (minus) samples.Our study represents the first detailed analysis of HopA1 effector triggered immunity transcriptome independent of EDS1 target, with biological replicates, generated by RNA-seq technology. Our data indicate early and independent EDS1 defense response after HopA1 perception in planta. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions of both HopA1 effector and EDS1 protein from plant during effector triggered immunity.