A unique box in 28S rRNA is shared by the enigmatic insect order Zoraptera and Dictyoptera

Abstract

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.

Figure 1. Currently recognized phylogeny of the Insecta.

a) Summary cladogram, b) list of morphological and molecular studies.

Figure 2. Phylogenetic tree inferred from the regions of the complete 18S and 28S rDNA sequences with conserved lengths.

The numbers associated with the nodes are posterior probability values (first number) and bootstrap values (second number) obtained by Bayesian/ML analysis respectively. The lengths of the branches follow the phylogram of the Bayesian tree.

Figure 3. Consensus of the sequences of expansion segment D3-4 based on the homologues in GenBank.

The left column is the secondary structure of the D3-4 ‘marker-box’ of each polyneopteran order. The accession number in the bottom of each regional secondary structure stands for the corresponding sequence which is the same to the consensus sequence of each polyneopteran order or superorder. The middle column is the consensus result of the homologues in each polyneopteran order or superorder. The abscissa stand for the number of the bases, while the ordinate stand for the proportion of information content provided by each base in the same position. The right column is the number of sequences based on.

Figure 4. Secondary structure model of the 28S rRNA 5′-half of Zoraptera.

This sequence is from Zorotypus huxleyi [Genbank:JN192451]. The length-variable regions are indicated in red. And the unique indels are marked with green color. The D3-4 box was highlighted with thick red lines. The Da–Dj numbering system for LVRs, which has not been taken into account previously, is a supplementary system to the D1–D12 coding system. Base pairing is indicated as follows: standard canonical pairs by lines (C-G, G-C, A-U, U-A); wobble G·U pairs by dots (G·U); A·G and A·C pairs by open circles (A G, A C); other non-canonical pairs by filled circles (e.g., U•U).

Figure 5. Secondary structure model of the 28S rRNA 3′-half of Zoraptera.

This sequence is from Zorotypus huxleyi [Genbank:JN192451]. The length-variable regions are indicated in red. And the unique indels are marked with green color. The Da–Dj numbering system for LVRs, which has not been taken into account previously, is a supplementary system to the D1–D12 coding system. Base pairing is indicated as follows: standard canonical pairs by lines (C-G, G-C, A-U, U-A); wobble G·U pairs by dots (G·U); A·G and A·C pairs by open circles (A G, A C); other non-canonical pairs by filled circles (e.g., U•U).