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

• Published in: Infection, genetics and evolution Vol. 11; no. 2; pp. 300 - 307
• Main Authors: Tomasini, Nicolás, Lauthier, Juan J., Rumi, María M. Monje, Ragone, Paula G., D’Amato, Anahí A. Alberti, Brandan, Cecilia Pérez, Cura, Carolina I., Schijman, Alejandro G., Barnabé, Christian, Tibayrenc, Michel, Basombrío, Miguel A., Falla, Alejandra, Herrera, Claudia, Guhl, Felipe, Diosque, Patricio
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 01.03.2011; Elsevier
• Subjects: Argentina; Bayes Theorem; Biological and medical sciences; Chagas disease; Chagas Disease - parasitology; Chagas Disease - transmission; DNA, Intergenic - genetics; DNA, Protozoan - genetics; Epidemiology. Vaccinations; Evolution; gene conversion; General aspects; Genetic Variation; Genotype; Geography; Haplotypes; Human protozoal diseases; Humans; Infectious diseases; intergenic DNA; Medical sciences; Microsatellite Repeats; Miniexon; Molecular Sequence Data; Multilocus Sequence Typing - methods; Multiple ambiguous alignments; Parasitic diseases; Parasitology; Phylogeny; Polymerase Chain Reaction; Protozoal diseases; RNA, Spliced Leader; Sequence Analysis, DNA; topology; Trypanosoma cruzi; Trypanosoma cruzi - classification; Trypanosoma cruzi - genetics; Trypanosomiasis; Argentina; Chagas disease; Evolution; Parasitology; Multiple ambiguous alignments; Miniexon; Kinetoplastida; Protozoa; Protozoal disease; Multiple; Parasitosis; Trypanosoma cruzi; Infection; Interest; Limitation; Molecular epidemiology; Trypanosomiasis
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2010.10.020

▶ We analyzed the SL-IR sequence of 25 stocks of Trypanosoma cruzi from Chaco Province, Argentina. ▶ Eight genotypes clustered into 4 groups, two did not cluster with any of previously described. ▶ Ambiguous alignments in the microsatellite region produce contradictory phylogenetic signals. ▶ We discuss possible bias in phylogenetic inference of this region. Internal and geographical clustering within Trypanosoma cruzi I (TcI) has been recently revealed by using Multilocus Microsatellite Typing and sequencing of the Spliced-Leader Intergenic Region (SL-IR). In the present work, 14 isolates and 11 laboratory-cloned stocks obtained from a geographically restricted area in Chaco Province, Argentina, were analyzed by PCR and sequencing of SL-IR. We were able to differentiate 8 different genotypes that clustered into 4 groups. One of these groups was classified within the formerly described haplotype A and another one within the recently described SL-IR group E. Both were phylogenetically well-supported. In contrast, none of the stocks from the Chaco province were grouped within the cluster previously named haplotype D despite the fact that they shared a similar microsatellite motif in the SL-IR. No evidence of recombination or gene conversion within these stocks was found. On the other hand, multiple ambiguous alignments in the microsatellite region of SL-IR, affecting the tree topology and relationships among groups were detected. Finally, since there are multiple copies of the SL-IR, and they are arranged in tandem, we discuss how molecular processes affecting this kind of sequences could mislead phylogenetic inference.