Phylogenetic evidence based on Trypanosoma cruzi nuclear gene sequences and information entropy suggest that inter-strain intragenic recombination is a basic mechanism underlying the allele diversity of hybrid strains

Abstract

The diversity of Trypanosoma cruzi is categorized into six discrete typing units (DTUs) T. cruzi I to VI. Several studies indicate that T. cruzi I and II are ancestors of T. cruzi which are considered products of independent hybridization events. the individual haplotypes or alleles of these hybrids cluster in three groups, either closer to T. cruzi I or T. cruzi II or forming a midpoint clade between T. cruzi I and II in network phylogenies. To understand the origins of these different sets of haplotypes and test the hypothesis of a direct correlation between high entropy and positive selection, we analyzed four nuclear protein coding genes. We show that hybrid strains contain haplotypes that are mosaics probably originated by intragenic recombination. Accordingly, in phylogenies, the hybrid haplotypes are closer to one or both parentals (T. cruzi I and II) depending on the proportion of parental sequences composing the mosaics. in addition, Shannon entropy, used to measure sequence diversity, is highly correlated with positive selection in the four genes here analyzed. Our data on recombination patterns also support the hypothesis of two hybridization events in the hybrid structures of T. cruzi Data presented and discussed here are consistent with a scenario where TcI and TcII are phylogenetically divergent forming a hybrid zone in between (T. cruzi III-VI). We predict that because of the quasi-random nature of T. cruzi I and II hybridization more DTUs, with different haplotype combinations, will be discovered in the hybrid zone. (C) 2012 Elsevier B.V. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Howard Hughes Medical InstituteUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Med, Disciplina Infectol, BR-04023900 São Paulo, BrazilUniversidade Federal de São Paulo, Lab Genom Evolut & Biocomplexidade, BR-04039032 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Med, Disciplina Infectol, BR-04023900 São Paulo, BrazilUniversidade Federal de São Paulo, Lab Genom Evolut & Biocomplexidade, BR-04039032 São Paulo, BrazilWeb of Scienc