We identified a total of 95 sRNAs in the H. somni genome. Twelve of these were predicted by Rfam [23] and are similar to conserved sRNA (e.g., 6S, tmRNA, FMN) in other bacterial species, which helps validate our approach. The 83 novel H. somni sRNAs may have housekeeping function, regulatory activity, or participate in virulence as described in other pathogenic bacteria [19, 35, 36] . The identified sRNAs did not show any location specific bias across the genome. Similarly, genes known to be associated with virulence are known to be scattered across bacterial genomes [37, 38] . However, the tendency to form clusters was observed with sRNAs, which could indicate that functionally related sRNAs tend to be located in close proximity. The RNA-Seq based transcriptome map of H. somni identified 38 novel protein coding genes that were missed by the initial annotation. The average length of the proteins coded by these genes exceeds 60 amino acids, suggesting that length based cutoff was not the main reason that these genes were missed by computational gene prediction programs. The novel protein coding genes identified in the current study could serve as a training set to improve gene prediction algorithms.