Frequent intra-family recombination in the largest repository of antigen variants in the protozoan pathogen Trypanosoma cruzi

The genome of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease, encodes a family of genes consisting of 3209 trans-sialidase (TcTS) and TcTS-like genes. Simultaneous expression of many members of the TcTS/TcTS-like family (henceforth TcTS gene family) presents variant peptide antigens to the host immune system. Recombination is a major force in generating and spreading genetic variation in gene families and such a process has been documented in Trypanosoma brucei and Plasmodium to contribute to antigenic variation. To investigate the extent to which recombination creates genetic variation in TcTS gene family, we have developed a computational pipeline capable of analyzing recombination events in the entire TcTS gene family. Using this computational pipeline, we demonstrate that TcTS gene family members are undergoing frequent recombination, generating new variants from the thousands of functional and non-functional gene segments.