A Hexapod nuclear SSU rRNA secondary‐structure model and catalog of taxon‐specific structural variation

Abstract

RNA molecules and in particular the nuclear SSU RNA play an important role in molecular systematics. With the advent of increasingly parameterized substitution models in systematic research, the incorporation of secondary-structure information became a realistic option compensating interdependence of character variation. As a prerequisite, consensus structures of eukaryotic SSU RNA molecules have become available through extensive comparative analyses and crystallographic studies. Despite extensive research in hexapod phylogenetics, consensus SSU RNA secondary structures focusing on hexapods have not yet been explored. In this study, we compiled a representative hexapod SSU data set of 261 sequences and inferred a specific consensus SSU secondary-structure model. Our search for conserved structural motives relied on a combined approach of thermodynamic and covariation analyses. The hexapod consensus-structure model deviates from the canonical eukaryotic model in a number of helices. Additionally, in several helices the hexapod sequences did not support a single consensus structure. We provide consensus structures of these sections of single less-inclusive taxa, thus facilitating the adaptation of the consensus hexapod model to less-inclusive phylogenetic questions. The secondary-structure catalog will foster the application of RNA structure models in phylogenetic analyses using the SSU rRNA molecule, and it will improve the realism of substitution models and the reliability of reconstructions based on rRNA sequences.

A Unique Box in 28S rRNA Is Shared by the Enigmatic Insect Order Zoraptera and Dictyoptera

“…Weblogo 3.0 was used to consent the sequences of expansion segment D3-4 [73], [74]. Reconstruction of secondary structure was realized by thermodynamic folding using RNAstructure 5.3 [75] and comparative methods [12], [45], [48], [54], [62]–[65], [76]. A more detailed description of the reconstruction of the secondary structure model was provided in the supplementary material File S1.…”

“…In fact, phylogenetic studies based on rDNAs can benefit considerably from information regarding rRNA secondary structure. First, the secondary structure of rRNA can be used to improve alignments and thus, improve the accuracy of tree construction [45]–[48]. The length variation in these sequences leads to ambiguous alignments, i.e., alternative arrangements of gaps.…”

“…A complete comparative study on the secondary structure of 18S rRNAs among insect orders was previously carried out by Gillespie et al [51], Misof et al [48], and Xie et al [12]. For 28S rRNAs, there are two numbering systems for LVRs, which were alternatively referred to as D (divergent) domains [52], [53] or expansion segments [54], [55].…”

A phylogeny of anisopterous dragonflies (Insecta, Odonata) using mtRNA genes and mixed nucleotide/doublet models

“…2002; Wang and Lee 2002; Espinosa de los Monteros 2003; Misof and Fleck 2003; Smith and Bond 2003; Carapelli et al. 2004; Misof et al. 2006), but mixed nucleotide/doublet models based on these structures have rarely been applied in phylogenetics (see e.g.…”

“…Hofacker et al. 2002), the inference of consensus secondary structure models based on aligned sequences is feasible and can be seen as part of the model fitting process in likelihood‐based phylogenetic analyses (Misof and Fleck 2003; Misof et al. 2006; Niehuis et al.…”