Complex evolutionary pathways of the intergenic region of the mini-exon gene in Trypanosoma cruzi TcI: A possible ancient origin in the Gran Chaco and lack of strict genetic structuration

The TcI discrete typing unit (DTU) of Trypanosoma cruzi is the most abundant and widely spread in the Americas. It is found in a wide range of triatomine and mammal species, which are distributed throughout the Americas in sylvatic and domestic environments. Previous studies based on intergenic sequences of the mini-exon gene (SL-IR) have identified five genotype groups within TcI. Based in the large number of sequences available in GenBank, the present study conducted an exhaustive revision of the sequence variability of the SL-IR within TcI using 244 sequences from isolates, cellular or molecular clones, from 11 Latin American countries. First, the evolutionary branching between strains was examined by analyzing only the single nucleotide polymorphism (SNP) deleting the microsatellite region and the gaps from the total alignment. Then the variability of the microsatellite region was re-analyzed alone using principal component analysis (PCA). After haplotype reconstruction using the PHASE algorithm, because of the presence of several ambiguous nucleotides in the SNP region, a total of 131 different haplotypes were obtained. The topology reveals how difficult it is to identify an obvious structure in TcI for most of the parameters examined. Somewhat genetic and geographical structures exist, but no structure was depicted with cycle and host origins. Indeed, the long-lasting evolution with possible recombination events, the occurrence of several waves of geographical dispersions (old and recent), and the high flow of strains between sylvatic and domestic cycles partially hide the major evolutionary trends within TcI. Moreover, we identified several problems in previous analyses, and concluded that in absence of supplementary studies of TcI phylogeny with other genetic markers, it is hazardous to use only the mini-exon intergenic region as a relevant marker of the substructure within TcI.

► We reanalyzed the intergenic region of the TcI mini-exon gene using a modified strategy tracking the ancestral gene. ► We analyzed the SNPs of the intergenic region of the mini-exon without considering the microsatellite region and gaps. ► We analyzed the numbers of motif repeats that fit with a different pattern than previously proposed. ► We propose this region as an initial guide to establish a possible substructure in TcI, together with other molecular markers.