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Background   Trypanosoma cruzi marinkellei  is a bat-associated parasite of the subgenus  Schizotrypanum  and it is regarded as a  T .  cruzi  subspecies. Here we report a draft genome sequence of  T .  c .  marinkellei  and comparison with  T .  c .  cruzi . Our aims were to identify unique sequences and genomic features, which may relate to their distinct niches.    Results  The  T .  c .  marinkellei  genome was found to be ~11% smaller than that of the human-derived parasite  T .  c .  cruzi  Sylvio X10. The genome size difference was attributed to copy number variation of coding and non-coding sequences. The sequence divergence in coding regions was ~7.5% between  T .  c .  marinkellei  and  T .  c .  cruzi  Sylvio X10. A unique acetyltransferase gene was identified in  T .  c .  marinkellei , representing an example of a horizontal gene transfer from eukaryote to eukaryote. Six of eight examined gene families were expanded in  T .  c .  cruzi  Sylvio X10. The DGF gene family was expanded in  T .  c .  marinkellei .  T .  c .  cruzi  Sylvio X10 contained ~1.5 fold more sequences related to VIPER and L1Tc elements. Experimental infections of mammalian cell lines indicated that  T .  c .  marinkellei  has the capacity to invade non-bat cells and undergo intracellular replication.    Conclusions  Several unique sequences were identified in the comparison, including a potential subspecies-specific gene acquisition in  T .  c .  marinkellei . The identified differences reflect the distinct evolutionary trajectories of these parasites and represent targets for functional investigation.

Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei