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