[ODP-091] The complex landscape of Vibrio parahaemolyticus transcriptome
Conventional bacterial genome annotation detects coding genes by looking for open reading frames. However, untranslated regions and operon maps are ignored. Annotation has improved using RNA-seq data. But given the compact nature of bacterial genomes, many challenges still cannot be resolved through short reads generated by classical RNA-seq because losing the original transcript structure. Direct RNA sequencing is a technology that sequences RNA directly and keep transcript structure intact. Here we employed it to annotate the Vibrio parahaemolyticus transcriptome with its full features, including transcription start sites (TSSs), transcription termination sites, and operon maps. A total of 4012 TSSs were identified. Our approach provided a more in-depth view of TSS classification, showing that most internal and antisense TSSs were actually a result of gene overlapping. Sequencing transcriptome of V. parahaemolyticus grown with bile allowed us to study the landscape of pathogenicity island. Some genes in this region were re-annotated providing more accurate annotation to ensure studying these genes correctly. Some operons showed high complexity, shedding light on a higher level of regulation within the same operon. Thus, our study using direct RNA sequencing provides a quantitative and high-resolution landscaped of V. parahaemolyticus transcriptome.