Paramecium: RNA sequence–structure phylogenetics

Abstract

Organisms classified as members of the genus Paramecium belong to the best-known group of single-celled eukaryotes. Nevertheless, the phylogeny within the genus Paramecium has been discussed and revisited in recent decades and remains partly unresolved. By applying an RNA sequence–structure approach, we attempt to increase accuracy and robustness of phylogenetic trees. For each individual 18S and internal transcribed spacer 2 (ITS2) sequence, a putative secondary structure was predicted through homology modelling. While searching for a structural template, we found, in contrast to the available literature, that the ITS2 molecule consists of three helices in members of the genus Paramecium and four helices in members of the genus Tetrahymena. Two sequencestructure neighbor-joining overall trees were reconstructed with (1) more than 400 taxa (ITS2) and (2) more than 200 taxa (18S). For smaller subsets, neighbor-joining, maximum-parsimony, and maximum-likelihood analyses were executed using sequence–structure information simultaneously. Based on a combined data set (ITS2+18S rDNA) a well-supported tree was reconstructed with bootstrap values over 50 in at least one of the applied analyses. Our results are in general agreement with those published in the available literature based on multi-gene analyses. Our study supports the simultaneous use of sequence–structure data to reconstruct accurate and robust phylogenetic trees.

2D approach to reconstruct the evolutionary history of clevelandellids (Ciliophora, Armophorea) inhabiting the hindgut of the Panesthiinae cockroaches

“…Besides aligning, the secondary structure can be directly implemented in phylogenetic analyses with the aid of a 12‐letter code (pseudo‐protein data). This strategy is considered to have a favourable impact on the accuracy and robustness of phylogenies (Keller et al, 2010; Weimer et al, 2023). Keller et al (2010) assessed the influence of the extension of the data set and direct incorporation of the secondary structure into phylogenetic analyses on the robustness and accuracy of trees.…”

“…The involvement of the secondary structure of ITS2 sequences improved both the accuracy and the robustness of the generated trees. The 12‐letter code approach was recently utilized by Weimer et al (2023) to reconstruct the phylogeny of the ciliate model genus Paramecium Müller, 1773, simultaneously using the primary and secondary structures of the ITS2 and 18S rRNA molecules. The authors concluded that the incorporation of secondary structures directly in phylogenetic analyses can produce accurate and robust trees, whereas the accuracy and robustness were assumed to be the highest in case of concatenated data.…”

“…In the present study, maximum parsimony, neighbour‐joining, and likelihood methods (as in Weimer et al, 2023) were used to analyse a 12‐letter encoded concatenated alignment in which both the primary and secondary structure information of RNA sequences was incorporated simultaneously. Along with this strategy, we employed two likelihood‐based methods using a 4‐letter encoded 2D‐based concatenated alignment.…”

“…Keller et al (2010) and Weimer et al (2023) consider the use of secondary structures directly in reconstructing trees to be beneficial for the generated trees. On the other hand, the present results suggest that analyses using 2D‐based alignments encoded by a 4‐letter code can produce more robust trees for clevelandellid ciliates.…”

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

“…According to Keller et al [6] the simultaneous usage of RNA sequences and their individual secondary structure increases robustness and accuracy of phylogenetic analyses. Sequence-structure data (encoded in a new alphabet) have already been used in several case studies [7][8][9][10][11][12][13][14][15][16]. In this study we only use complete 18S ribosomal ribonucleic acid (rRNA) gene sequences and their individual secondary structures, as obtained from RNAcentral [17], and additionally curated manually by the Comparative RNA Web Site (CRW) [18].…”