18S rDNA Sequence-Structure Phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with Special Reference on Trypanosoma

Abstract

BackgroundParasites of the order Trypanosomatida are known due to their medical relevance. Trypanosomes cause African sleeping sickness and Chagas disease in South America, and Leishmania RO_SCPLOWOSSC_SCPLOW, 1903 species mutilate and kill hundreds of thousands of people each year. However, human pathogens are very few when compared to the great diversity of trypanosomatids. Despite the progresses made in the past decades on understanding the evolution of this group of organisms, there are still many open questions which require robust phylogenetic markers to increase the resolution of trees. MethodsUsing two known 18S rDNA template structures (from Trypanosoma cruzi CO_SCPLOWHAGASC_SCPLOW, 1909 and Trypanosoma brucei PO_SCPLOWLIMMERC_SCPLOW & BO_SCPLOWRADFORDC_SCPLOW, 1899), individual 18S rDNA secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood. ResultsWith a few exceptions, all nodes within a sequence-structure maximum likelihood tree of 43 representative 18S rDNA sequence-structure pairs are robustly supported (bootstrap support >75). Even a quick and easy sequence-structure neighbor-joining analysis yields accurate results and enables reconstruction and discussion of the big picture for all 240 18S rDNA sequence-structure pairs of trypanosomatids that are currently available. ConclusionsWe reconstructed the phylogeny of a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity, demonstrating that the simultaneous use of 18S rDNA sequence and secondary structure data can reconstruct robust phylogenetic trees.