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The swine respiratory ciliary epithelium is mainly colonized by  Mycoplasma hyopneumoniae ,  Mycoplasma flocculare  and  Mycoplasma hyorhinis . While colonization by  M. flocculare  is virtually asymptomatic,  M. hyopneumoniae  and  M. hyorhinis  infections may cause respiratory disease. Information regarding transcript structure and gene abundance provides valuable insight into gene function and regulation, which has not yet been analyzed on a genome-wide scale in these  Mycoplasma  species. In this study, we report the construction of transcriptome maps for  M. hyopneumoniae ,  M. flocculare  and  M. hyorhinis , which represent data for conducting comparative studies on the transcriptional repertory. For each species, three cDNA libraries were generated, yielding averages of 415,265, 695,313 and 93,578 reads for  M. hyopneumoniae, M. flocculare  and  M. hyorhinis , respectively, with an average read length of 274 bp. The reads mapping showed that 92%, 98% and 96% of the predicted genes were transcribed in the  M. hyopneumoniae, M. flocculare  and  M. hyorhinis  genomes, respectively. Moreover, we showed that the majority of the genes are co-expressed, confirming the previously predicted transcription units. Finally, our data defined the RNA populations in detail, with the map transcript boundaries and transcription unit structures on a genome-wide scale.

Unravelling the Transcriptome Profile of the Swine Respiratory Tract Mycoplasmas