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Background  Few, if any, protozoan parasites are reported to exhibit extreme organ tropism like the flagellate  Tritrichomonas foetus.  In cattle,  T. foetus  infects the reproductive system causing abortion, whereas the infection in cats results in chronic large bowel diarrhoea. In the absence of a  T. foetus  genome, we utilized a  de novo  approach to assemble the transcriptome of the bovine and feline genotype to identify host-specific adaptations and virulence factors specific to each genotype .  Furthermore, a subset of orthologs was used to characterize putative druggable targets and expose complications of  in silico  drug target mining in species with indefinite host-ranges.    Results  Illumina RNA-seq reads were assembled into two representative bovine and feline transcriptomes containing 42,363 and 36,559 contigs, respectively. Coding and non-coding regions of the genome libraries revealed striking similarities, with 24,620 shared homolog pairs reduced down to 7,547 coding orthologs between the two genotypes. The transcriptomes were near identical in functional category distribution; with no indication of selective pressure acting on orthologs despite differences in parasite origins/host. Orthologs formed a large proportion of highly expressed transcripts in both genotypes (bovine genotype: 76%, feline genotype: 56%). Mining the libraries for protease virulence factors revealed the cysteine proteases (CP) to be the most common. In total, 483 and 445 bovine and feline  T. foetus  transcripts were identified as putative proteases based on MEROPS database, with 9 hits to putative protease inhibitors. In bovine  T. foetus,  CP8 is the preferentially transcribed CP while in the feline genotype, transcription of CP7 showed higher abundance.  In silico  druggability analysis of the two genotypes revealed that when host sequences are taken into account, drug targets are genotype-specific.    Conclusion  Gene discovery analysis based on RNA-seq data analysis revealed prominent similarities between the bovine and feline  T. foetus,  suggesting recent adaptation to their respective host/niche.  T. foetus  represents a unique case of a mammalian protozoan expanding its parasitic grasp across distantly related host lineages. Consequences of the host-range for  in silico  drug targeting are exposed here, demonstrating that targets of the parasite in one host are not necessarily ideal for the same parasite in another host.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-955) contains supplementary material, which is available to authorized users.

bmc genomics

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification