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Background  Recent whole genome sequencing (WGS) analysis identified a viable triploid strain of  Trypanosoma congolense . This triploid strain BANANCL2 was a clone of the field isolate BANAN/83/CRTRA/64 that was collected from cattle in Burkina Faso in 1983.    Results  We demonstrated the viability and stability of triploidy throughout the complete life-cycle of the parasite by infecting tsetse flies with the triploid clone BANANCL2. Proboscis-positive tsetse flies efficiently transmitted the parasites to mice resulting in systemic infections. WGS of the parasites was performed at all life-cycle stages, and a method based on a block alternative allele frequency spectrum was developed to efficiently detect the ploidy profiles of samples with low read depth. This approach confirmed the triploid profile of parasites throughout their life-cycle in the tsetse fly and the mammalian host, demonstrating that triploidy is present at all stages and is stable over time.    Conclusion  The presence of viable field-isolated triploid parasites indicates another possible layer of genetic diversity in natural  T. congolense  populations. The comparison between triploid and diploid parasites provides a unique model system to study the impact of chromosome copy number variations in African trypanosomes. In addition, the consequences of triploidy can be further investigated using this stable triploid model.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2406-z) contains supplementary material, which is available to authorized users.

Evidence for viable and stable triploid Trypanosoma congolense parasites