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Álvarez OE. Structural, phylogenetic and polymorphism analysis of Spliced Leader (SL) genes of Trypanosoma spp. isolated from vertebrate hosts. [Thesis Ph. D. (Parasitology)]. São Paulo: Instituto de Ciências Biomédicas da Universidade de São Paulo; 2017. Trypanosomes are obligate parasites of a great variety of vertebrate and invertebrate hosts with large number of species, lineages and genotypes. Molecular analyses have been essential to understand the complexity of trypanosomes and the evolutionary history of pathogenic in human and livestock, and non-pathogenic species of all classes of vertebrates. In addition to traditional phylogenetic markers (SSU rRNA and gGAPDH genes), Spliced Leader (SL) genes (involved in mRNA processing via trassplicing) and intergenic regions between SL repeats have been employed for identification and genotyping of trypanosomatids. However, data about SL sequences are mostly restricted to pathogenic species. Our main goal in this study was to characterize SL sequences from a large sampling of trypanosomes of all vertebrate classes representative of the major clades of Trypanosoma. Primary and secondary structures of SL-RNA (exon and intron), and intergenic region (SL-IR) polymorphism and association with 5S rRNA, were compared within an evolutionary framework, and then evaluated to define species, lineages and genotypes. Two new species of trypanosomes from bats, phylogenetically validated as new species, were herein characterized and supported by SL-RNA sequences: Trypanosoma livingstonei from bats captured in Mozambique (East Africa) and T. wauwau of Neotropical bats from Central and South America. These trypanosomes nested in the clade T. cruzi, and their phylogenetic relationships as basal species was strongly supported by SL data. The positioning of these Old and New World trypanosomes support the hypothesis that the ancestors of T. cruzi clade were bat-restricted trypanosomes that evolved in these hosts and later jumped different times into other mammals (bat seeding hypothesis), giving origin to T. cruzi and T. rangeli, which are generalists of mammals including man. Multilocus analysis, including SLRNA genes, support T. rangeli much more closely related to Old World T. vespertilionis and T. conorhini than to T. cruzi. Here, we identified three new species of trypanosomes of bats and bat bugs (cimicid) from Guinea Bissau (West Africa), all clustering with T. vespertilionis and T. conorhini. These trypanosomes share with T. rangeli highly similar SL secondary structures and intron sequences, but largely differed in their SL-IR sequences. Although T. cruzi and T. rangeli share mammalian hosts and vectors in the Neotropics, phylogenetic results support the hypothesis that these human-infective parasites have long independent evolutionary histories. T. cruzi Tcbat is a genotype originally described in Brazilian bats that does not cluster into any of the six recognized DTUs (TcI-VI). Here, Brazilian and Colombian Tcbat isolates were submitted to multilocus analysis. Results strongly supported Tcbat as a monophyletic lineage sister to TcI, and clearly separated from all DTUs, then supporting Tcbat as an independent DTU. Highly polymorphic markers including SL sequences revealed genetic groups within Tcbat, likely associated with geographical origin of the isolates. We further explored SL-RNA sequences to assess inter and intraDTUs genetic diversity, with emphasis in sylvatic cycles of TcI, TcIII and TcIV DTUs. Whole SL sequences were determined for more than 100 Brazilian isolates and compared with those from different origins. Sequences of SL-IR revealed a larger number of intra-TcI genotypes distributed in three genetic groups: TcI A, B and C. For the first time, SL-IR sequences were employed to assess intra-TcIII and TcIVSA genetic diversity, revealing greater diversity within these two DTUs compared with TcI, and supporting phylogenetic lineages that could be associated to geography, but not with domestic or sylvatic transmission cycles. Molecular markers defined by this study can be used to developed DTU and intra-DTU specific PCR assays. Comparative analyses of different regions of SL repeats revealed sequences useful for diagnostic and taxonomic purposes, allowing the identification of clades/subgenera, species, lineages and genotypes. In addition, we mapped secondary structures, length of SL repeats, and absence/presence of 5S rRNA inserted into intergenic regions onto current phylogenetic tree to evaluate evolutionary scenarios within and across all major lineages of Trypanosoma. Altogether, our findings revealed an evolutionary gradient of SL-RNA repeats in Trypanosoma spp. of all major phylogenetic lineages largely contributing to the understanding of both plasticity and conservation trends of SL-RNA one of the most intriguingly feature of these fascinating group of parasites.

Spliced Leader (SL) RNA: análises de genes e regiões intergênicas com aportes na filogenia, taxonomia e genotipagem de &lt;i&gt;Trypanosoma&lt;/i&gt; spp. de todas as classes de vertebrados.