Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions that require robust phylogenetic markers to increase the resolution of trees. Using two known 18S rRNA gene template structures (from Trypanosoma cruzi Chagas, 1909 and Trypanosoma brucei Plimmer and Bradford, 1899), individual 18S rRNA gene 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. The reconstructed trees allowed us to discuss not only the big picture of trypanosomatid phylogeny but also a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity. The robust support (bootstrap > 75) for well-known clades and critical branches suggests that the simultaneous use of 18S rRNA sequence and secondary structure data can reconstruct robust phylogenetic trees and can be used by the trypanosomatid research community for future analysis.

锥虫目寄生虫因其医学相关性而闻名。尽管过去几十年在理解这组生物的进化方面取得了进展，但仍有许多悬而未决的问题需要强大的系统发育标记来提高树木的分辨率。使用两个已知的 18S rRNA 基因模板结构（来自Trypanosoma cruzi Chagas, 1909 和Trypanosoma bruceiPlimmer and Bradford, 1899)，通过同源性建模预测单个 18S rRNA 基因二级结构。序列及其二级结构由 12 个字母的字母表自动编码（每个核苷酸具有三个结构状态，左配对、右配对、未配对），同时比对。序列结构树是通过邻居连接和/或最大似然生成的。重建的树使我们不仅可以讨论锥虫系统发育的大局，还可以讨论在锥虫多样性背景下评估的锥虫综合采样。强大的支持（引导>