Genome-Wide Identification of Transcriptional Start Sites in the Plant Pathogen Pseudomonas syringae pv. tomato

RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina’s high-throughput sequencing technology, we globally identified 59-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 59-ends obtained by this method were consistent with results obtained using global RNA-Seq and 59RACE. As expected, many 59-ends were positioned a short distance upstream of annotated genes. We also captured 59-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 59-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broa