Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
BMC Res Notes. 2024 May 1;17(1):124. doi: 10.1186/s13104-024-06786-9.
The eukaryotic tree of life has been subject of numerous studies ever since the nineteenth century, with more supergroups and their sister relations being decoded in the last years. In this study, we reconstructed the phylogeny of eukaryotes using complete 18S rDNA sequences and their individual secondary structures simultaneously. After the sequence-structure data was encoded, it was automatically aligned and analyzed using sequence-only as well as sequence-structure approaches. We present overall neighbor-joining trees of 211 eukaryotes as well as the respective profile neighbor-joining trees, which helped to resolve the basal branching pattern. A manually chosen subset was further inspected using neighbor-joining, maximum parsimony, and maximum likelihood analyses. Additionally, the 75 and 100 percent consensus structures of the subset were predicted.
All sequence-structure approaches show improvements compared to the respective sequence-only approaches: the average bootstrap support per node of the sequence-structure profile neighbor-joining analyses with 90.3, was higher than the average bootstrap support of the sequence-only profile neighbor-joining analysis with 73.9. Also, the subset analyses using sequence-structure data were better supported. Furthermore, more subgroups of the supergroups were recovered as monophyletic and sister group relations were much more comparable to results as obtained by multi-marker analyses.
自 19 世纪以来，人们对真核生物的系统发育树进行了大量研究，近年来又有更多的超级群及其姐妹关系被解码。在这项研究中，我们使用完整的 18S rDNA 序列及其各自的二级结构同时重建了真核生物的系统发育。在对序列-结构数据进行编码后，我们使用仅序列和序列-结构方法自动对齐和分析了该数据。我们展示了 211 种真核生物的整体邻接树以及各自的轮廓邻接树，这有助于解决基本分支模式。手动选择的子集进一步使用邻接法、最大简约法和最大似然法进行了检查。此外，还预测了子集的 75%和 100%一致结构。
与各自的仅序列方法相比，所有的序列-结构方法都有所改进：90.3%的序列-结构轮廓邻接树分析的平均引导支持率高于 73.9%的仅序列轮廓邻接树分析的平均引导支持率。此外，使用序列-结构数据的子集分析得到了更好的支持。此外，更多的超级群亚群被恢复为单系，姐妹群关系与通过多标记分析获得的结果更加可比。
