Interest and limitations of Spliced Leader Intergenic Region sequences for analyzing Trypanosoma cruzi I phylogenetic diversity in the Argentinean Chaco

TOMASINI, N; LAUTHIER, JJ; MONJE RUMI, MM; RAGONE, PG; ALBERTI D´AMATO, AM; PÉREZ BRANDAN, C; CURA, CI; SCHIJMAN, AG; BARNABÉ, C; TIBAYRENC, M; BASOMBRÍO, MA; FALLA, A; HERRERA, C; GUHL, F; DIOSQUE, P

Infection, Genetics and Evolution

ELSEVIER SCIENCE BV

Año: 2010 p. 300 - 307

1567-1348

Internal and Geographical clustering in Trypanosoma cruzi lineage I (TCI) have been revealed recently and Spliced-Leader Intergenic Region (SL-IR) sequencing has been the most used tool in determining this internal variability. This region is a multi-copy sequence repeated in tandem and a number of molecular genetic processes may impact this kind of sequences in ways that may mislead phylogenetic inference. Incomplete concerted evolution, duplication, gen conversion, past events of hybridization and/or recombination are candidate process in determining the evolution of the SL repeats. None of these processes has been previously considered and discussed for phylogenetic analysis of SL-IR in TCI. Here, we analyzed 25 strains originated in Chaco Province of Argentina by SL-IR PCR and sequencing. We detected variability between copies and included this information using a coding method to obtain better resolution into the phylogenetic analysis. In addition, we did not find evidence of recombination and gen conversion using different statistical methods and we discuss possible effects of incomplete concerted evolution. We determined 8 different genotypes clustered in 4 groups. Two of them, statistically well supported. In addition, we include representative sequences of haplogroups described into the bibliography and detected multiple ambiguous alignments into the microsatellite region of SL-IR affecting the tree topology and relation between groups due to the repetitive nature of this region. Interestingly, this region has been the most used tool to clustering. Finally, we identify Haplogroups A and E circulating in our Study area. Surprisingly, none of the strains from Chaco province were grouped with haplogroup D despite of sharing a similar microsatellite motif with it.