In 2008 the complete genome sequence of the H. somni strain 2336 became available (GenBank CP000947). The 2,263,857 bp circular genome has a GC content of 37.4%, and 87% of the sequence is annotated to coding regions. The genome has 2065 computationally predicted genes, of which 1980 are protein coding. We sequenced the transcriptome of H. somni using Illumina RNA-Seq methodology, and obtained 9,015,318 reads, with an average read length of approximately 76 bp. We mapped approximately 9.4% reads onto the reference DNA sequence of H. somni strain 2336 using the alignment program Bowtie [20] . To determine expressed regions in the genome, we estimated the average coverage depth of reads mapped per nucleotide/base. We used pileup format, which represents the signal map file for the whole genome in which alignment results (coverage depth) are represented in per-base format. Regions where coverage depth was greater than the lower tenth percentile of expressed genes were considered significantly expressed [21] ; in the current study, this corresponded to a coverage depth of 7 reads/bp in pileup format.