Hidden Transcriptome Complexity in Pseudomonas-Infected Arabidopsis

I will describe the results of an RNA-seq time-course experiment that probes transcription in Arabidopsis thaliana after infection with Pseudomonas syringae pathovar tomato [1]. Our study characterizes the response to infection in both susceptible and resistant hosts. We analyzed more than 500 million read pairs focusing especially on the detection of alternative splicing (AS), and on measuring changes in isoform ratios between treatments. Our results extend previous microarray-based studies and revealed a large number of novel transcripts: we found 165 candidates for novel genes, and more than 44% of the TAIR 10 multi-exon genes showed evidence for novel splice variants. The surprisingly large amount of the detected AS events supports the hypothesis that AS might play an important role in stress adaptation and plant defense [2,3].  This research was performed in collaboration with Brian Howard, Qiwen Hu, Ahmet Can Babaoglu, Manan Chandra, Monica Borghi, Xiaoping Tan, Luyan He, Heike Winter-Sederoff, Walter Gassmann, and Paola Veronese.