18S rDNA sequence-structure phylogeny of the eukaryotes simultaneously inferred from sequences and their individual secondary structures

TL;DR

This study improves understanding of eukaryotic evolution by combining DNA sequences and their structures to build better phylogenetic trees.

Contribution

A novel method combining 18S rDNA sequences and secondary structures enhances phylogenetic analysis accuracy.

Findings

Sequence-structure approaches provided higher bootstrap support compared to sequence-only methods.

More subgroups of eukaryotic supergroups were identified as monophyletic.

Sister group relations matched multi-marker analysis results more closely.

Abstract

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.

The online version contains supplementary material available at 10.1186/s13104-024-06786-9.

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