RNA-seq analysis of in planta condition-dependent genes in Xanthomonas oryzae pv. oryzae KACC10331

Xanthomonas oryzae pv. oryzae (Xoo) causes the bacterial leaf blight of rice, which leads to as much as 50% yield losses. To understand the landscape of virulence mechanisms, we constructed in planta transcriptional profiling of Xoo KACC10331 using RNA-seq. Three in planta transcriptome of Xoo KACC10331 derived from infected rice leafs were compared to three in vitro data from rich media. To obtain differentially expressed genes, we used the DEGseq package with MA-plot-based method in the R statistical environment and identified 2,094 transcripts that were significantly altered. Overall design: Six libraries constructed: three in planta RNA-seq data from rice leafs infected by Xoo KACC10331 and three in vitro RNA-seq data from PSA media.