The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence–structure data are encoded and automatically aligned. Here, we present a sequence–structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence–structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.

中文翻译：

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Euglenophyceae (Euglenozoa, Euglenida) 的 18S rDNA 序列-结构系统发育

Euglenophyceae ( Euglenozoa , Euglenida )的系统发育已经讨论了几十年，在过去几年中描述了新的属。在这项研究中，我们同时使用 18S rDNA 序列和结构数据重建系统发育。使用同源建模，预测了单个二级结构。序列结构数据被编码并自动对齐。在这里，我们展示了一个包含 300 多个分类单元的序列结构邻接树，这些分类单元被归类为裸藻纲. 配置文件邻接用于解决基础分支模式。使用手动选择的子集的序列结构信息执行邻接、最大简约和最大似然分析。所有分析都支持Eutreptiella、Discoplasti、Lepocinclis、Strombomonas、Cryptoglena、Monomorphina、Euglenaria和Colacium的单系. 得到良好支持的拓扑结构通常与之前使用遗传标记组合数据集的研究一致。我们的研究支持同时使用序列和结构数据来重建更准确和稳健的树。平均 bootstrap 值明显高于从仅序列分析获得的平均 bootstrap 值，这有望解决更密切相关的分类群之间的关系。