Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data

•Transcriptome-based genome annotation enhancement.•Prediction of 32 additional CDS.•Identification of 176 novel RNA genes.•First X. campestris pv. campestris operon analysis. Bioinformatics tools and gene expression data were applied to identify new genes and to enhance the accuracy in genomic feature predictions for Xanthomonas campestris pv. campestris (Xcc) B100, a pathogen of cruciferous plants and model strain for the biosynthesis of xanthan, a polysaccharide with a multitude of commercial applications as a thickening agent. Results from 5′-enriched end RNA sequencing (RNA-seq) and total transcriptome RNA-seq experiments were used for this purpose. Functional gene annotations were updated where new evidence had emerged and start codon predictions were enhanced for 153 protein-coding genes (CDS). In total, 32 novel CDS, and 176 novel RNA genes and features were predicted, among them 77 isogenes of the small non-coding RNA sX9. Furthermore, the RNA-seq data facilitated the identification of 848 operons that included a total of 2551 CDS besides 1667 CDS that were mono-cistronically expressed.